1pkn A proteindomain is a part of protein sequence and tertiary structure structure that can biological ... domain forms a compact three dimensional structure and often can be independently stable and protein ... protein chimeric proteins . Background The concept of the domain was first proposed in 1973 by Wetlaufer ... 871 9 year 2002 author George RA, Heringa J. title An analysis of proteindomain linkers their classification ..., right . Each domain in this protein occurs in diverse sets of protein families. The central barrel ... CATH a hierarchic classification of proteindomain structures pmid 9309224 doi 10.1016 S0969 2126 ... of the insertion of one domain into another during the protein s evolution. It has been shown ... M, Michie A, Swindells MB, Orengo C, Thornton JM. title Domain assignment for protein structures ... function by domain swapping pmid 11050932 doi ref Domains are units of protein structure Main Protein ... pmc 2143041 ref In domain swapping, a secondary or tertiary element of a monomeric protein is replaced by the same element of another protein. Domain swapping can range from secondary structure ... CA, Jones DT, Thornton JM. title Protein superfamilies and domain superfolds pmid 7990952 doi 10.1038 ... of an animal proteindomain by bacteria2 pmid 1409594 doi 10.1073 pnas.89.19.8990 issue 19 pmc 50050 ... journal Protein Eng volume 7 pages 1407 1410 year 1994 author Russell, R. B title Domain insertion pmid 7716150 doi 10.1093 protein 7.12.1407 issue 12 ref Since a domain can be inserted into another, there should always be at least one continuous domain in a multidomain protein. This is the main difference ... ref domain formation appears to be the optimal solution for a large protein to bury its hydrophobic ... However, the role of inter domain interactions in protein folding and in energetics of stabilisation of the native structure, probably differs for each protein. In T4 lysozyme, the influence of one domain ... of water from the domain interface. Domains and protein flexibility The presence of multiple domains ... more details
possesses a domain homologous to its activator proteins saposins B and D journal Protein Sci. volume .... volume 4 issue 3 pages 91 94 year 1996 pmid 8868085 doi 10.1016 0966 842X 96 81522 8 ref Domain organization Below is a schematic diagram of the 1D structure of the prosaposin protein depicting .... Proteolysis Proteolytic cleavage of the protein precursor proprotein occurs in the grey regions. Adjacent ... 600px Human proteins containing this domain AOAH GNLY Prosaposin PSAPL1 SFTPB References reflist Further ... links http www.expasy.org cgi bin nicedoc.pl?PDOC50015 Saposin B type domain in PROSITE Category Protein domains Category Protein families Category Peripheral membrane proteins membrane protein ... more details
Pfam box Symbol Pkinase Name Protein kinase domain image PDB 1apm EBI.jpg width caption Structure of the catalytic subunit of cAMP dependent protein kinase. ref name pmid15299526 Cite journal author Knighton ... PDB3 1cki B 9 247 PDB3 1ckj B 9 247 PDB3 1lhx A 9 276 The protein kinase domain is a structurally conserved proteindomain containing the catalytic function of protein kinase s. ref name pmid1956325 Cite journal author Hanks SK, Quinn AM title Protein kinase catalytic domain sequence database identification ... url ref ref name pmid7768349 Cite journal author Hanks SK, Hunter T title Protein kinases 6. The eukaryotic protein kinase superfamily kinase catalytic domain structure and classification journal FASEB ... Protein kinases 6. The eukaryotic protein kinase superfamily kinase catalytic domain structure and classification ... domain of protein kinases. In the N terminal extremity of the catalytic domain there is a glycine ... cells. Use dmy dates date September 2010 DEFAULTSORT Protein Kinase Domain Category Protein ... dependent protein kinase complexed with a peptide inhibitor and detergent journal Acta Crystallogr ... 1apm TCDB OPM family OPM protein 2bcj PDB PDB3 1ctp E 44 298 PDB3 2erz E 44 298 PDB3 1fot A 87 341 ... Structural evolution of the protein kinase like superfamily journal PLoS Comput. Biol. volume 1 ... url ref Protein kinases are a group of enzyme s that move a phosphate group onto proteins, in a process ..., The Protein Kinase Complement of the Human Genome , Science 6 December 2002, 298 1912 1934 DOI 10.1126 science.1075762 ref Protein kinases possess a catalytic subunit which transfers the gamma phosphate ... in a protein substrate side chain, resulting in a conformational change affecting protein function ... threonine specific protein kinase serine threonine specific and tyrosine kinase tyrosine specific . ref name PUB00005115 Cite journal author Hunter T, Hanks SK, Quinn AM title The protein kinase ... issue 4861 pages 42 51 year 1988 pmid 3291115 doi 10.1126 science.3291115 ref Function Protein kinase ... more details
protein Name LEM domain containing protein 3 caption image width HGNCid 28887 Symbol LEMD3 AltSymbols MAN1 EntrezGene 23592 OMIM 607844 RefSeq NM 014319 UniProt Q9Y2U8 PDB ECnumber Chromosome 12 Arm q Band 14 LocusSupplementaryData LEM domain containing protein 3 is a membrane protein associated with laminopathies . It is also associated with osteopoikilosis . ref name pmid17087626 cite journal author Mumm S, Wenkert D, Zhang X, McAlister WH, Mier RJ, Whyte MP title Deactivating germline mutations in LEMD3 cause osteopoikilosis and Buschke Ollendorff syndrome, but not sporadic melorheostosis journal J. Bone Miner. Res. volume 22 issue 2 pages 243 50 year 2007 pmid 17087626 doi 10.1359 jbmr.061102 ref LEMD3 protein, also known as MAN1, is an inner nuclear membrane INM protein that was isolated from the serum of a patient with an autoimmune disease Paulin Levasseur et al., 1996 . It was first named MAN1, however, the scientific community also knows it as the LEMD3 protein LEM domain containing protein 3 . MAN1 is an integral protein of the nuclear envelope. It has a LEM domain in its amino terminal region and a recognition RNA motif RRM in its carboxylic end. MAN1 seems to play an important role in regulating the expression of several fundamental genes. The LEM region is a 40 amino acid domain that is common to two other integral proteins of the INM LAP2 and EMERIN. This LEM segment enables MAN1 to attach to BAF barrier autointegration factor , and therefore, indirectly interact with the chromatin. MAN1 also has several implications in regulating the cytokine family such as TGF transforming growth factor beta and BMP bone morphogenic protein . The RRM domain in its carboxylic region attaches to the Smads proteins, the mediators of the cytokine family cellular signalling, and consequently, regulates the downstream genes. LEMD3 gene mutations are responsible for several genetic ... reflist External links MeshName LEMD3 protein, human biochemistry stub ... more details
orphan date May 2010 PBB geneid 84229 Coiled coil domain containing protein 135 , also known as CCDC135 , is a protein that in humans is encoded by the CCDC135 gene . ref name pmid11230166 cite journal ... protein 84000035?report genpept NP 001033120.1 86 93 872 coiled coil domain containing protein 135 Canis familiaris Dog http www.ncbi.nlm.nih.gov protein 73950345?report genpept XP 544386.2 85 ... protein 194208644 XP 001915581 81 87 831 Predicted similar to Coiled coil domain containing ... protein 149640764 XP 001508368.1 71 85 860 Predicted similar to Coiled coil domain containing ... domain containing 135 Danio rerio Zebrafish http www.ncbi.nlm.nih.gov protein 292628136 XP 683491 46 66 721 Predicted similar to Coiled coil domain containing protein 135 Tetraodon nigroviridis Tetraodon ... protein 198431234 XP 002123665 49 69 837 Predicted similar to coiled coil domain containing 135 ... genes and proteins sequencing and analysis of 500 novel complete protein coding human cDNAs journal ... gr.GR1547R url issn ref ref name entrez cite web title Entrez Gene coiled coil domain containing ...&hgtgroup encodeChrom close 1&hgtgroup encodeCompAndVar close 1 ref GPR97 , G protein coupled receptor 97. GPR56 , encodes a member of the G protein coupled receptor family G protein coupled receptor 56 . The gene is implicated in the regulation of brain cortical patterning. The protein binds specifically ... protein that helps targets the enzyme to the centrosome. KIFC3 , kinesin family member C3 isoform ... hydrolysis to translocate cargoes along microtubules. Protein Structure This protein is characterized ... The protein has 17 predicted alpha helices sites, a characteristic of coiled ... align center style background f0f0f0 Gene common name Homo sapiens Human http www.ncbi.nlm.nih.gov protein 223941912?report genpept NP 115645.4 100 100 874 Homo sapiens coiled coil domain containing 135 CCDC135 Macaca mulatta Rhesus Monkey http www.ncbi.nlm.nih.gov protein 109128753 XP 001100628.1 96 ... more details
PBB geneid 8932 Methyl CpG binding domainprotein 2 is a protein that in humans is encoded by the MBD2 ... Entrez Gene MBD2 methyl CpG binding domainprotein 2 url http www.ncbi.nlm.nih.gov sites entrez?Db gene&Cmd ShowDetailView&TermToSearch 8932 accessdate ref Interactions Methyl CpG binding domainprotein 2 has been shown to Proteinprotein interaction interact with HDAC1 , ref name pmid12183469 cite ... Summary template is automatically maintained by Protein Box Bot. See Template PBB Controls to Stop ... CpG binding domain MBD . Each of these proteins, with the exception of MBD3, is capable of binding ... gene promoters. The protein encoded by this gene may function as a mediator of the biological consequences of the methylation signal. It is also reported that this protein functions as a demethylase ... Ammerpohl O, Kegel S, Moehren U, Renkawitz R year 2000 month Nov. title The minimal repression domain of MBD2b overlaps with the methyl CpG binding domain and binds directly to Sin3A journal J. Biol. Chem ... protein, MIZF, in transcriptional repression by interacting with a methyl CpG binding protein, MBD2 ... MBD3L1 is a transcriptional repressor that interacts with methyl CpG binding protein 2 MBD2 and components ... protein with specific demethylase activity for mCpG DNA. journal Nature volume 397 issue 6720 ... author Boeke J, Ammerpohl O, Kegel S, et al. title The minimal repression domain of MBD2b overlaps with the methyl CpG binding domain and binds directly to Sin3A. journal J. Biol. Chem. volume 275 ... of SANT domain proteins CoREST kiaa0071 and Mta L1. journal J. Biol. Chem. volume 276 issue ... A, Homma Y title Involvement of a novel zinc finger protein, MIZF, in transcriptional repression by interacting with a methyl CpG binding protein, MBD2. journal J. Biol. Chem. volume 276 issue ... C, K gler K, Diederichs S, et al. title Loss of expression of HDAC recruiting methyl CpG binding domain ... 546.2002 pmc 139742 cite journal author Bakker J, Lin X, Nelson WG title Methyl CpG binding domain ... more details
PBB geneid 8295 Transformation transcription domain associated protein , also known as TRRAP , is a protein which in humans is encoded by the TRRAP gene . ref name pmid9708738 cite journal author McMahon SB, Van Buskirk HA, Dugan KA, Copeland TD, Cole MD title The novel ATM related protein TRRAP is an essential cofactor for the c Myc and E2F oncoproteins journal Cell volume 94 issue 3 pages 363 74 date August 1998 pmid 9708738 doi 10.1016 S0092 8674 00 81479 8 url issn ref ref name pmid9885574 cite journal author Vassilev A, Yamauchi J, Kotani T, Prives C, Avantaggiati ML, Qin J, Nakatani Y title ... domain associated protein has been shown to Proteinprotein interaction interact with ACTL6A ... 9 url issn ref TRRAP belongs to the phosphatidylinositol 3 kinase related kinase protein family. Function TRRAP is an adapter protein , which is found in various multiprotein chromatin complexes with histone ... transformation domain recruits the human STAGA complex and requires TRRAP and GCN5 acetylase activity ... ATM related protein TRRAP is an essential cofactor for the c Myc and E2F oncoproteins journal Cell ... ref Transcription initiation protein SPT3 homolog , ref name pmid11564863 MAX gene MAX ref name pmid9708738 ... The novel ATM related protein TRRAP is an essential cofactor for the c Myc and E2F oncoproteins ... K, Staub A, Tora L title Identification of TATA binding protein free TAFII containing complex subunits ... journal author Brand M, Moggs JG, Oulad Abdelghani M, et al. title UV damaged DNA binding protein in the TFTC ... Park J, Kunjibettu S, McMahon SB, Cole MD title The ATM related domain of TRRAP is required for histone ... of the TATA binding protein free TAFII containing transcription complex identified by matrix assisted ... cite journal author Liu X, Tesfai J, Evrard YA, et al. title c Myc transformation domain ... for Protein Box Bot, please see Template PBB Controls for details. PBB Controls update page yes require manual inspection no update protein box yes update summary no update citations yes gene 7 stub ... more details
PBB geneid 9372 Zinc finger FYVE domain containing protein 9 or SARA u S u MAD u a u nchor for u r u eceptor u a u ctivation is a protein that in humans is encoded by the ZFYVE9 gene . ref name pmid9865696 cite journal author Tsukazaki T, Chiang TA, Davison AF, Attisano L, Wrana JL title SARA, a FYVE domainprotein that recruits Smad2 to the TGFbeta receptor journal Cell volume 95 issue 6 pages 779 91 year 1998 month December pmid 9865696 doi url issn ref SARA contains a double zinc finger FYVE domain . SARA is an anchoring protein involved in TGF beta signaling pathway SMAD phosphorylation TGF beta signaling . It binds to the MH2 domain of the R SMAD s SMAD2 and SMAD3 as well as the type I TGF beta receptors. ref name pmid15356634 cite journal author Lin HK, Bergmann S, Pandolfi PP title Cytoplasmic PML function in TGF beta signalling journal Nature volume 431 issue 7005 pages 205 11 year 2004 month September pmid 15356634 doi 10.1038 nature02783 url issn ref It facilitates the phosphorylation of the R SMAD, which subsequently dissociates form SARA and the receptor and binds a coSMAD where they enter the nucleus as transcription factor s. References reflist TGF beta signaling gene 1 stub Category Developmental genes and proteins Category FYVE domain ... more details
PBB geneid 7704 Zinc finger and BTB domain containing protein 16 is a protein that in humans is encoded by the ZBTB16 gene . Function This gene is a member of the Krueppel C2H2 type zinc finger protein ... Zinc finger and BTB domain containing protein 16 has been shown to Proteinprotein interaction ... last9 Waxman first9 S title Amino terminal proteinprotein interaction motif POZ domain is responsible ... yes update citations yes DEFAULTSORT Zinc Finger And Btb Domain Containing Protein 16 Category Transcription ... at the carboxyl terminus. This protein is located in the nucleus, is involved in cell cycle progression ... zinc finger and BTB domain containing 16 url http www.ncbi.nlm.nih.gov sites entrez?Db gene&Cmd ... last9 Owen title A novel BTB POZ transcriptional repressor protein interacts with the Fanconi anemia group C protein and PLZF volume 94 issue 11 pages 3737 47 journal Blood url http bloodjournal.hematologylibrary.org ... domain of proHB EGF volume 320 issue 2 pages 376 82 journal Biochemical and biophysical research communications ... leukaemia associated protein PLZF volume 23 issue 54 pages 8777 84 journal Oncogene ref ref name ... Licht first4 JD last5 Sch fer first5 BW title The LIM only protein DRAL FHL2 interacts with and is a corepressor for the promyelocytic leukemia zinc finger protein volume 277 issue 40 pages 37045 53 journal ... with mSin3A mediates repression by the acute promyelocytic leukemia associated PLZF protein volume ... interactions with the POZ domain oncoproteins PLZF, PLZF RARalpha, and BCL 6 volume 273 issue 42 pages ... promyelocytic leukemia associated protein, promyelocytic leukemia zinc finger, regulates 1,25 ... first7 B last8 Hiebert first8 SW last9 Licht first9 JD title The ETO protein disrupted in t 8 21 associated acute myeloid leukemia is a corepressor for the promyelocytic leukemia zinc finger protein ... SW last6 Licht first6 JD title AML 1 ETO fusion protein is a dominant negative inhibitor of transcriptional repression by the promyelocytic leukemia zinc finger protein volume 96 issue 12 pages 3939 47 ... more details
devices Domain wall , a term used in physics which can have one of two distinct but similar meanings in either magnetism or string theory Magnetic domain , a region within a magnetic material which has uniform magnetization Proteindomain , a part of a protein that can exist independently of the rest of the protein chain Information technology Administrative domain , a service provider holding ...NOTOC Wiktionary domainDomain may refer to General Territory administrative division , a non sovereign geographic area which has come under the authority of another government Public domain , a body of works and knowledge without proprietary interest Eminent domain , the power of government to confiscate private property for public use Domain board game Domain , a game published by Parker Brothers in 1983 Sciences Domain biology , a subdivision even larger than a kingdom Domain knowledge , a specific expert knowledge valid for a pre selected area of activity, such as surgery Domain specificity ... domain , the kinds of purposes for which users use a software system Broadcast domain , in computer networking, a group of special purpose addresses to receive network announcements Clock domain crossing , when a signal crosses from one clock domain into another CLR application domain , a mechanism for separating executed applications similar to a process Collision domain , a physical network segment that is a shared medium where data packets can collide with one another Data domain , in database theory, a set of all permitted values Domain software engineering , a field of study that defines ... to solve a problem in that field Domain analysis , the process of analyzing related software systems in a domain to find their common and variable parts Domain driven design , an approach to the design of software Domain engineering , the reusing of domain knowledge in the production of new software Domain model , a conceptual model of a system that describes the various entities involved and their relationships ... more details
url ref Protein S can bind to negatively charged phospholipids via the carboxylated Gla domain GLA domain . This property allows Protein S to function in the removal of cells which are undergoing ...PBB geneid 5627 Protein S is a vitamin K dependent plasma glycoprotein synthesized in the endothelium. In the circulation, Protein S exists in two forms a free form and a complex form bound to complement system complement protein C4b. In humans, protein S is encoded by the PROS1 gene . ref name pmid2944113 ... J, Wydro R title Isolation and sequence of the cDNA for human protein S, a regulator of blood coagulation ... in Seattle, Wash, first discovered protein S and arbitrarily named it after the city of its ... title A comparison of human prothrombin, factor IX Christmas factor , factor X Stuart factor , and protein ... of protein S, a gamma carboxyglutamic acid containing protein from bovine and human plasma ... bi00572a026 ref Function The best characterized function of Protein S is its role in the anti coagulation pathway, where it functions as a cofactor to Protein C in the inactivation of factor V Factors ... journal author Castoldi E, Hackeng TM title Regulation of coagulation by protein S journal Curr. Opin ... membrane. These negatively charged phospholipids are recognized by phagocytes such as macrophages . Protein ... the apoptotic cell and the phagocyte. The bridging property of Protein S enhances the phagocytosis ... occurring. Pathology Mutations in the PROS1 gene can lead to Protein S deficiency ... of, and molecular defects underlying, inherited protein S deficiency in the general population ... Prior P, Hurtado B, Sala N title Molecular basis of protein S deficiency journal Thromb. Haemost ... Protein S has been shown to Proteinprotein interaction interact with Factor V . ref name pmid10593904 ... J, Tans G, Griffin J H year 1999 month Dec. title C terminal residues 621 635 of protein S are essential ... coauthors Mesters R M, Tans G, Rosing J, Griffin J H year 1993 month Feb. title Binding of protein ... more details
structure prediction of small protein structural domain domains ref name Keskin2008 are two methods ...About a class of molecules protein as a nutrient Protein nutrient other uses pp semi indef pp move indef File Myoglobin.png thumb right 250px A representation of the 3D structure of the protein myoglobin showing colored alpha helix alpha helices . This protein was the first to have its structure solved ... compound compounds consisting of one or more polypeptide s typically folded into a globular protein globular or fibrous protein fibrous form in a biologically functional way. A polypeptide is a single ... acids in a protein is defined by the DNA sequence sequence of a gene , which is encoded in the genetic ... or even during synthesis, the residues in a protein are often chemically modified by post translational ... together to achieve a particular function, and they often associate to form stable protein complex complex ... to be single structure. Other proteins undergo large rearrangements from one protein conformation ... signaling event . Thus, the structure of a protein serves as a medium through which to regulate either the function of a protein or activity of an enzyme. Not all proteins requiring a folding process ... ingested protein into free amino acids that are then used in metabolism. Proteins were first described ... Jakob Berzelius in 1838. Early nutritional scientists such as the German Carl von Voit believed that protein ... urease was in fact a protein. ref name Sumner1926 The first protein to be protein sequencing .... The first protein structure s to be solved were hemoglobin and myoglobin , by Max Perutz and John ... may be protein purification purified from other cellular components using a variety of techniques such as ultracentrifugation .... Methods commonly used to study protein structure and function include immunohistochemistry , site ... protein folding the statistical analysis techniques employed to calculate a protein s probable ... bond that links individual amino acids to form a protein polymer Most proteins consist of linear polymer ... more details
Protein A is a 40 60 Atomic mass unit kDa MSCRAMM surface protein originally found in the cell wall of the bacteria Staphylococcus aureus . It is encoded by the spa gene and its regulation is controlled by DNA topology, cellular osmolarity, and a two component regulatory system two component system called ArlS ArlR. It has found use in biochemical research because of its ability to bind immunoglobulins . It binds proteins from many of mammalian species, most notably IgG s. It binds with the Fc region ... antibody function on their surface which disrupts opsonization and phagocytosis . Protein A antibody .... Protein A binds with moderate affinity to human IgM , IgA and IgE as well as to mouse IgG3 and IgG1 .... Other antibody binding proteins In addition to Protein A, other immunoglobulin binding bacterial proteins such as Protein G , Protein A G and Protein L are all commonly used to purify, immobilize or detect immunoglobulins. Role in pathogenesis As a pathogen Staphylococcus aureus utilizes Protein .... Protein A helps inhibit phagocytic engulfment and acts as an immunological disguise. Mutants of S. aureus lacking protein A are more efficiently phagocytosed in vitro, and mutants in infection models ... 197 1125 1139. ref Research Recombinant Staphylococcal Protein A is often produced in E. coli for use in immunology and other biological research. One recombinant form of Protein A is called MabSelect ... 18114994AE.pdf ref . Protein A is often coupled to other molecules such as a fluorescent dye , enzyme ... widely utilized coupled to magnetic, latex and agarose beads. Protein A is often immobilized onto a solid support and used as reliable method for purifying total IgG from crude protein mixtures ... of antibodies. Immunoprecipitation studies with protein A conjugated to beads are also commonly used to purify proteins or protein complexes indirectly through antibodies against the protein or protein complex of interest. References reflist Category Proteins Category Staphylococcaceae de Protein ... more details
Unreferenced date October 2010 A binding domain is a proteindomain which binding molecular binds to a specific atom or molecule, such as calcium or DNA . Upon binding, proteins may undergo a conformational change . Binding domains are essential for the function of many proteins. Examples of binding domains include Zinc finger , which binds to DNA, and EF hand , which binds to calcium. See also DNA binding domainprotein stub Protein topics Category Protein structure Category Protein domains ... more details
Infobox protein family Symbol PAAD DAPIN Name PAAD DAPIN Pyrin domain image PDB 1pn5 EBI.jpg width caption Pfam PF02758 Pfam clan CL0041 InterPro IPR004020 SMART PROSITE PS50824 MEROPS SCOP 1pn5 TCDB OPM family OPM protein PDB PDB2 1pn5 , PDB2 1ucp , PDB2 2hm2 A pyrin domain is a proteindomain it allows a pyrin domain containing protein to interact with other protein s that contain a pyrin domain. It is also known as a PYD or PAAD DAPIN domain, and is distantly evolutionarily related to the Death domain family of proteindomain s. ref name pmid11514682 cite journal author Fairbrother WJ, Gordon NC, Humke EW, et al. title The PYRIN domain a member of the death domain fold superfamily journal Protein Sci. volume 10 issue 9 pages 1911 8 year 2001 month September pmid 11514682 pmc 2253208 doi 10.1110 ps.13801 url ref ref name pmid11166557 cite journal author Staub E, Dahl E, Rosenthal A title The DAPIN family a novel domain links apoptotic and interferon response proteins journal Trends Biochem. Sci. volume 26 issue 2 pages 83 5 year 2001 month February pmid 11166557 doi url ref ref name pmid11166558 cite journal author Paw owski K, Pio F, Chu Z, Reed JC, Godzik A title PAAD a new proteindomain associated with apoptosis, cancer and autoimmune diseases journal Trends Biochem. Sci. volume 26 issue 2 pages 85 7 year 2001 month February pmid 11166558 doi url ref Proteins containing a pyrin domain are frequently involved in biological processes called inflammation and apoptosis . ref name pmid11270363 cite journal author Bertin J, DiStefano PS title The PYRIN domain a novel motif found ..., such as PYCARD and certain fish caspase s. References references protein stub Protein domains Category Protein domains commons cat Pyrin domain, PYD ... journal author Gumucio DL, Diaz A, Schaner P, et al. title Fire and ICE the role of pyrin domain ... 26 pages S45 53 year 2002 pmid 12371636 doi url ref Proteins that possess a pyrin domain include ... more details
as found in the breast cancer DNA repair protein BRCA1 . The domain is an approximately 100 amino acid tandem repeat, which appears to act as a phospho protein binding domain ref name PUB00014805 ... domain is a phospho protein binding domain journal Science volume 302 issue 5645 pages 639 642 year 2003 pmid 14576433 ref . Examples Human proteins containing this domain include BARD1 BRCA1 CTDP1 DNTT ... References Reflist InterPro content IPR001357 DEFAULTSORT Brct Domain Category Protein domains Category Human protein families protein stub ...Pfam box Symbol BRCT Name BRCA1 C Terminus BRCT domain image PDB 1cdz EBI.jpg width caption Structure of an XRCC1 BRCT domain. ref name pmid9799248 cite journal author Zhang X, Mor ra S, Bates PA, et al. title Structure of an XRCC1 BRCT domain a new proteinprotein interaction module journal EMBO J. volume 17 issue 21 pages 6404 11 year 1998 month November pmid 9799248 pmc 1170965 doi 10.1093 emboj 17.21.6404 url ref Pfam PF00533 InterPro IPR001357 SMART Prosite SCOP 1cdz TCDB OPM family OPM protein PDB PDB3 2azm B 1906 1957 PDB3 2ado B 1906 1957 PDB3 2etx A 1906 1957 PDB3 1kzy C 1795 1835 PDB3 1l0b A 1589 1669 PDB3 1t2v C 1646 1723 PDB3 1n5o X 1646 1723 PDB3 1t2u A 1646 1723 PDB3 1jnx X 1646 1723 PDB3 1t15 A 1646 1723 PDB3 1t29 A 1646 1723 PDB3 1y98 A 1646 1723 PDB3 2cou A 91 166 PDB3 1l7b A 589 664 PDB3 2cok A 385 463 PDB3 1wf6 A 354 431 PDB3 1ik9 C 681 717 PDB3 1cdz A 538 616 PDB3 1oqa A 1756 1842 PDB3 2coe A 27 111 BRCA1 C Terminus BRCT domain is a Protein family family of evolutionarily related proteins . The BRCT domain after the C terminal domain of a breast cancer susceptibility protein is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage ref name PUB00001533 cite journal author Bork P, Hofmann K, Koonin EV, Bucher P, Neuwald AF, Altschul SF title A superfamily of conserved domains in DNA damage responsive cell cycle checkpoint ... more details
Pfam box Symbol MENTAL Name MENTAL domain image width caption Pfam PF10457 InterPro IPR019498 SMART Prosite PS51439 SCOP TCDB OPM family OPM protein PDB The MENTAL or MLN64 NH sub 2 sub terminal domain is a membrane spanning domain that is conserved in two endosome late endosomal proteins in vertebrates, MLN64 and STARD3NL MENTHO . ref name pmid12393907 cite journal author Alpy F, Wendling C, Rio MC, Tomasetto C title MENTHO, a MLN64 Homologue Devoid of the START Domain. journal J. Biol. Chem. volume 277 issue 18 pages 50780 7 year 2002 pmid 12393907 doi 10.1074 jbc.M208290200 ref The domain is 170 amino acids long. Current data indicates that this domain allows for protein dimer dimerization between MLN64 and MENTHO molecules and with themselves. ref name pmid15718238 cite journal author Alpy F, Latchumanan VK, Kedinger V, Janoshazi A, Thiele C, Wendling C, Rio MC, Tomasetto C title Functional characterization of the MENTAL domain. journal J. Biol. Chem. volume 280 issue 18 pages 17945 52 year 2005 pmid 15718238 doi 10.1074 jbc.M500723200 ref The domain may also direct cholesterol transport. References reflist Category Protein domains ... more details
Pfam box Symbol LIM Name LIM domain image Lims.png width 200 caption Structure of the 4th LIM domain of Pinch protein. Zinc atoms are shown in grey Pfam PF00412 InterPro IPR001781 SMART PROSITE PDOC50178 SCOP 1ctl TCDB OPM family OPM protein PDB PDB3 1ctl A 11 67 LIM domains are protein structural domain s, composed of two contiguous zinc finger domains, separated by a two amino acid residue hydrophobic linker. ref name pmid15520811 cite journal author Kadrmas JL, Beckerle MC title The LIM domain from the cytoskeleton to the nucleus journal Nat. Rev. Mol. Cell Biol. volume 5 issue 11 pages 920 31 year 2004 pmid 15520811 doi 10.1038 nrm1499 issn ref They are named after their initial discovery in the proteins L in11, I sl 1 & M ec 3. ref name pmid10704826 cite journal author Bach I title The LIM domain regulation by association journal Mech. Dev. volume 91 issue 1 2 pages 5 17 year 2000 pmid 10704826 doi 10.1016 S0925 4773 99 00314 7 issn ref LIM domain containing proteins have been shown to play roles in cytoskeleton cytoskeletal organisation, organ development and oncogenesis . LIM domains mediate proteinprotein interactions proteinprotein interactions that are critical to cellular processes. LIM domains have highly divergent sequences, apart from certain key residues. The sequence divergence allow a great many different binding sites to be grafted onto the same basic domain. The conserved residues are those involved in zinc binding or the hydrophobic core of the protein. The sequence signature of LIM domains is as follows C X sub 2 4 sub C X sub 13 19 sub W H X sub 2 4 sub C F LVI C X sub 2 4 sub C X sub 13 20 sub C X sub 2 4 sub C Image Lim diag.png thumb 200px Lim domain organsiation LIM domains frequently occur in multiples, as seen in proteins such as TES protein TES , LMO4, and can also be attached to other domains in order to confer a binding or targeting function ... column count 2 references div molecular cell biology stub Protein domains Category Protein domains Category ... more details
PUB00004459 The region of shared similarity, known as the Runt domain, is responsible for DNA binding and proteinprotein interaction. In addition to the highly conserved Runt domain, the AML 1 gene product ...Pfam box Symbol Runt Name Runt domain image width caption Pfam PF00853 InterPro IPR013524 SMART Prosite SCOP 1cmo TCDB OPM family OPM protein PDB PDB3 1eaq A 48 182 PDB3 1hjb C 60 182 PDB3 1hjc D 60 182 PDB3 1io4 C 60 182 PDB3 1eao A 48 182 PDB3 1ean A 48 182 PDB3 1e50 E 50 182 PDB3 1co1 A 61 175 PDB3 1h9d C 50 182 PDB3 1ljm B 51 181 PDB3 1cmo A 52 178 The Runt domain is an evolutionary conserved proteindomain . ref name pmid8273148 cite journal author Kagoshima H, Shigesada K, Satake M, Ito Y, Miyoshi H, Ohki M, Pepling M, Gergen P title The Runt domain identifies a new family of heteromeric transcriptional regulators journal Trends Genet. volume 9 issue 10 pages 338 41 year 1993 month October pmid 8273148 doi url issn ref The RUNX1 AML1 RUNX1 gene is rearranged by the t 8 21 translocation in acute myeloid leukemia. ref name PUB00004459 cite journal author Hirai H, Shimizu K, Miyoshi H, Ohira M, Mitani K, Imai T, Yokoyama K, Soeda E, Ohki M title Alternative splicing and genomic structure of the AML1 gene involved in acute myeloid leukemia journal Nucleic Acids Res. volume 23 issue ... residues. The protein known as acute myeloid leukemia 1 protein, oncogene AML 1, core binding ... and promoters. The protein is a heterodimer of alpha and beta subunits. The alpha subunit binds DNA ... protein expressed in numerous tissue types, except brain and heart highest levels have been found to occur in thymus, bone marrow and peripheral blood. This domain occurs towards the N terminus of the proteins in this entry. Examples Human genes encoding proteins containing this domain include RUNX1 , RUNX2 , RUNX3 References reflist InterPro content IPR013524 DEFAULTSORT Runt Domain Category Protein domains protein stub ... more details
Pfam box Symbol NACHT Name NACHT domain image width caption Pfam PF05729 InterPro IPR007111 SMART Prosite PS50837 SCOP TCDB OPM family OPM protein PDB The NACHT domain is an evolutionary conserved proteindomain . This NTPase domain is found in apoptosis protein s as well as those involved in MHC Transcription genetics transcription . ref name pmid10782090 cite journal author Koonin EV, Aravind L title The NACHT family a new group of predicted NTPases implicated in apoptosis and MHC transcription activation journal Trends Biochem. Sci. volume 25 issue 5 pages 223 4 year 2000 month May pmid 10782090 doi url issn ref The NACHT domain contains 300 to 400 amino acid s. It is a predicted nucleoside triphosphatase NTPase domain, which is found in animal, fungus fungal and bacteria l proteins. The NACHT domain has been named after NAIP, CIITA, HET E and TP1. It is found in association with other domains, such as the CARD domain InterPro IPR001315 , the pyrin domain InterPro IPR004020 , the HEAT repeat domain InterPro IPR004155 , the WD40 repeat InterPro IPR001680 , the leucine rich repeat LRR or the BIR repeat InterPro IPR001370 . ref name pmid10782090 The NACHT domain consists of seven distinct conserved motifs, including the ATP GTPase specific P loop, the Mg sup 2 sup binding site Walker motifs Walker A and B motifs , respectively and five more specific motifs. The unique features of the NACHT domain include the prevalence of tiny residues glycine, alanine or serine directly C terminal of the Mg sup 2 sup coordinating aspartate in the Walker B motif, in place of a second acidic residue prevalent in other NTPases. A second acidic residue is typically found in the NACHT containing ... Examples Human proteins containing this domain include CIITA NAIP gene NAIP NLRC3 , NLRC4 ... , NLRP13 , NLRP14 , NLRX1 NOD1 , NOD2 NWD1 TEP1 References Reflist Category Protein domains Category Human protein families protein stub Protein domains InterPro content IPR007111 ... more details
Infobox protein family Symbol PASTA Name PASTA domain image PDB 1rp5 EBI.jpg width caption Structure the PASTA domain in a penicillin binding protein. Pfam PF03793 InterPro IPR005543 SMART PASTA PROSITE PDOC51178 SCOP 1rp5 TCDB OPM family OPM protein PDB PDB2 1k25 A 694 750, PDB2 1qme A 694 750, PDB2 1rp5 B 694 750, PDB2 1qmf A 694 750, PDB2 1pyy A 694 750 The PASTA domain is a small proteindomain that can bind to beta lactam rings found in antibiotics. ref name pmid12217513 cite journal author Yeats C, Finn RD, Bateman A title The PASTA domain a beta lactam binding domain journal Trends Biochem. Sci. volume 27 issue 9 pages 438 year 2002 month September pmid 12217513 doi url ref The domain was initially discovered in 2002 by Yeats and colleagues as a region of sequence similarity found in penicillin binding proteins and PknB like kinases found in some bacteria. The name is an acronym derived from P BP a nd S erine T hreonine kinase A ssociated domain. Structure The PASTA domain adopts a structure composed of an alpha helix followed by three beta strand s. Recent structural studies show that the extracellular region of PknB that is composed of four PASTA domains shows a linear arrangement of the domains. ref name pmid20462494 cite journal author Barthe P, Mukamolova GV, Roumestand C, Cohen Gonsaud M title The structure of PknB extracellular PASTA domain from mycobacterium tuberculosis suggests a ligand dependent kinase activation journal Structure volume 18 issue 5 pages 606 15 year 2010 month May pmid 20462494 doi 10.1016 j.str.2010.02.013 url ref Species distribution PASTA domains are found in a variety of bacterial species including gram positive firmicutes and actinobacteria . References reflist Category Protein domains ... more details
Pfam box Symbol MAM Name MAM domain image width caption Pfam PF00629 InterPro IPR000998 SMART Prosite PDOC00604 SCOP TCDB OPM family OPM protein PDB PDB3 2c9a A 27 184 MAM domain is an evolutionary conserved proteindomain . It is an extracellular domain found in many receptors. A 170 amino acid domain, the so called MAM domain, has been recognised in the extracellular region of functionally diverse proteins ref name PUB00005405 cite journal author Bork P, Beckmann G title An adhesive domain detected in functionally diverse receptors journal Trends Biochem. Sci. volume 18 issue 2 pages 40 41 year 1993 pmid 8387703 ref . These proteins have a modular, receptor like architecture comprising a signal peptide, an N terminal extracellular domain, a single transmembrane domain and an intracellular domain. Such proteins include meprin a cell surface glycoprotein ref name PUB00002774 cite journal author Grant GA, Jiang W, Gorbea CM, Flannery AV, Beynon RJ, Bond JS title The alpha subunit of meprin A. Molecular cloning and sequencing, differential expression in inbred mouse strains, and evidence for divergent evolution of the alpha and beta subunits journal J. Biol. Chem. volume 267 issue 13 pages 9185 9193 year 1992 pmid 1374387 ref A5 antigen a developmentally regulated cell surface protein ref name PUB00004307 cite journal author Takagi S, Hirata T, Agata K, Eguchi G, Fujisawa H, Mochii M title The A5 antigen, a candidate for the neuronal recognition molecule, has homologies to complement ... 1908252 ref and receptor like tyrosine protein phosphatase ref name PUB00001624 cite journal author ... A title Cloning, expression and chromosomal localization of a new putative receptor like protein ... 10.1016 0014 5793 91 81241 Y ref . The MAM domain is thought to have an adhesive function. It contains ... this domain Anaplastic lymphoma kinase ALK EGFL6 MAMDC2 MAMDC4 MDGA1 MDGA2 MEP1A MEP1B NPNT neuropilin ... IPR000998 Category Protein domains Category Single pass transmembrane proteins membrane protein ... more details
Infobox protein family Symbol L27 Name L27 domain image PDB 1rso EBI.jpg width caption Structure of presynaptic protein SAP97. ref name pmid15048107 cite journal author Feng W, Long JF, Fan JS, Suetake T, Zhang M title The tetrameric L27 domain complex as an organization platform for supramolecular assemblies journal Nat. Struct. Mol. Biol. volume 11 issue 5 pages 475 80 year 2004 month May pmid 15048107 doi 10.1038 nsmb751 url ref Pfam PF02828 InterPro IPR014775 SMART PROSITE SCOP TCDB OPM family OPM protein PDB PDB2 1rso , PDB2 1va8 , PDB2 1y74 , PDB2 1zl8 The L27 domain is a proteindomain that is found in receptor targeting proteins CASK Lin 2 and Lin 7 LIN7A , LIN7B , LIN7C , as well as some protein kinase s and human MPP2 protein. Notes reflist References Refbegin cite journal author Petrosky KY, Ou HD, L hr F, D tsch V, Lim WA title A general model for preferential hetero oligomerization of LIN 2 7 domains mechanism underlying directed assembly of supramolecular signaling complexes journal J. Biol. Chem. volume 280 issue 46 pages 38528 36 year 2005 month November pmid 16147993 doi 10.1074 jbc.M506536200 url issn cite journal author Doerks T, Bork P, Kamberov E, Makarova O, Muecke S, Margolis B title L27, a novel heterodimerization domain in receptor targeting proteins Lin 2 and Lin 7 journal Trends Biochem. Sci. volume 25 issue 7 pages 317 8 year 2000 month July pmid 10871881 doi url issn cite journal author Feng W, Long JF, Fan JS, Suetake T, Zhang M title The tetrameric L27 domain complex as an organization platform for supramolecular assemblies journal Nat. Struct. Mol. Biol. volume 11 issue 5 pages 475 80 year 2004 month May pmid 15048107 doi 10.1038 nsmb751 url issn cite journal author Feng W, Long JF, Zhang M title A unified assembly mode revealed by the structures of tetrameric L27 domain complexes formed by mLin 2 mLin 7 and Patj Pals1 scaffold proteins ... L27 Domain Category Protein domains Category Protein structure protein stub ... more details
SSF50044 SCOP 1shf TCDB OPM family OPM protein PDB The SRC Homology 3 Domain or SH3 domain is a small proteindomain of about 60 amino acids residues first identified as a conserved sequence in the viral adaptor protein v Crk and the non catalytic parts of enzymes such as phospholipase and several ... also been identified in several other protein families such as PI3 Kinase , Ras GAP GTPase Activating Protein GTPase activating protein , CDC24 and CDC25 . ref name pmid1639195 cite journal author Musacchio A, Gibson T, Lehto VP, Saraste M title SH3 an abundant proteindomain in search of a function ... . Proteins with SH3 domain Adaptor protein s CDC24 CDC25 Phosphoinositide 3 kinase PI3 kinase Phospholipase RasGAP Ras GTPase activating protein Vav proto oncogene GRB2 p54 S6 kinase 2 S6K2 See also Src homology 2 domain containing Structural domain References Reflist External links http nashlab.bsd.uchicago.edu ...Pfam box Symbol SH3 1 Name SH3 domain image 1shg SH3 domain.png width 200 caption Ribbon diagram of the SH3 domain, alpha spectrin, from chicken PDB accession code 1SHG , colored from blue N terminus to red ... doi url issn ref ref name pmid7531822 cite journal author Pawson T title Protein modules and signalling ... doi 10.1038 373573a0 url issn ref The SH3 domain has a characteristic beta barrel fold which consists ... DNA binding domain. Such functionally distinct SH3 like domains often have no recognizable homology on the amino acid level. The classical SH3 domain is usually found in proteins that interact with other proteins and mediate assembly of specific protein complexes, typically via binding to proline rich ... proteins, although the small human MIA family of extracellular proteins also contain a domain .... The sequence binds to the hydrophobe hydrophobic pocket of the SH3 domain. More recently, SH3 domains ... the versatility of this domain. SH3 domains are found in proteins of signaling pathways regulating the cytoskeleton , the Ras protein , and the Src kinase and many others. They also regulate the activity ... more details
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