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(-) Description

Title :  SOLUTION STRUCTURE OF THE HUMAN PIRH2 RING-H2 DOMAIN. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET HT2B
 
Authors :  Y. Sheng, A. Lemak, R. C. Laister, B. Wu, C. H. Arrowsmith, Northeast Structural Genomics Consortium (Nesg)
Date :  27 Jun 07  (Deposition) - 10 Jul 07  (Release) - 28 Apr 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Ubiquitin E3 Ligase, Ring Domain, Structural Genomics, Protein Structure Initiative, Psi-2, Northeast Structural Genomics Consortium, Nesg (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Sheng, R. C. Laister, A. Lemak, B. Wu, E. Tai, S. Duan, J. Lukin, M. Sunnerhagen, S. Srisailam, M. Karra, S. Benchimol, C. H. Arrowsmith
Molecular Basis Of Pirh2-Mediated P53 Ubiquitylation.
Nat. Struct. Mol. Biol. V. 15 1334 2008
PubMed-ID: 19043414  |  Reference-DOI: 10.1038/NSMB.1521
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RING FINGER AND CHY ZINC FINGER DOMAIN CONTAINING PROTEIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneRCHY1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:17 , CYS A:20 , HIS A:41 , CYS A:44BINDING SITE FOR RESIDUE ZN A 62
2AC2SOFTWARECYS A:36 , HIS A:38 , CYS A:55 , CYS A:58BINDING SITE FOR RESIDUE ZN A 63

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JRJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2JRJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2JRJ)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_RING_2PS50089 Zinc finger RING-type profile.ZN363_HUMAN145-186  1A:17-58

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003244391bENSE00002044590chr4:76439895-76439407489ZN363_HUMAN1-30300--
1.2bENST000003244392bENSE00001720950chr4:76434506-76434387120ZN363_HUMAN31-70400--
1.3bENST000003244393bENSE00001615955chr4:76434145-76434030116ZN363_HUMAN71-109390--
1.4bENST000003244394bENSE00001706744chr4:76419389-7641931179ZN363_HUMAN109-135270--
1.5bENST000003244395bENSE00001285948chr4:76417143-7641709945ZN363_HUMAN136-150151A:10-2213
1.6aENST000003244396aENSE00001077848chr4:76416992-7641693459ZN363_HUMAN151-170201A:23-4220
1.6cENST000003244396cENSE00001077852chr4:76416847-7641682127ZN363_HUMAN170-179101A:42-5110
1.6gENST000003244396gENSE00001077845chr4:76415911-76415791121ZN363_HUMAN179-219411A:51-6111
1.7jENST000003244397jENSE00001946767chr4:76407876-764042473630ZN363_HUMAN220-261420--

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:52
 aligned with ZN363_HUMAN | Q96PM5 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:52
                                   147       157       167       177       187  
          ZN363_HUMAN   138 ENVSRQNCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCMHS 189
               SCOP domains ---------------------------------------------------- SCOP domains
               CATH domains 2jrjA00 A:10-61                                      CATH domains
               Pfam domains -----zf-RING_2-2jrjA01 A:15-61                       Pfam domains
         Sec.struct. author ......ee....ee.......eee.....eeehhhhhhhhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE -------ZF_RING_2  PDB: A:17-58 UniProt: 145-186  --- PROSITE
           Transcript 1 (1) Exon 1.5b    Exon 1.6a           --------Exon 1.6g   Transcript 1 (1)
           Transcript 1 (2) --------------------------------Exon 1.6c ---------- Transcript 1 (2)
                 2jrj A  10 ENVSQQNCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCMHS  61
                                    19        29        39        49        59  

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2JRJ)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: RING (39)

(-) Gene Ontology  (19, 19)

NMR Structure(hide GO term definitions)
Chain A   (ZN363_HUMAN | Q96PM5)
molecular function
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0002039    p53 binding    Interacting selectively and non-covalently with one of the p53 family of proteins.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0070987    error-free translesion synthesis    The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions but does not causes an increase in the endogenous mutation level. For S. cerevisiae, RAD30 encodes DNA polymerase eta, which incorporates two adenines. When incorporated across a thymine-thymine dimer, it does not increase the endogenous mutation level.
    GO:0032436    positive regulation of proteasomal ubiquitin-dependent protein catabolic process    Any process that activates or increases the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    GO:0031398    positive regulation of protein ubiquitination    Any process that activates or increases the frequency, rate or extent of the addition of ubiquitin groups to a protein.
    GO:0051865    protein autoubiquitination    The ubiquitination by a protein of one or more of its own amino acid residues, or residues on an identical protein. Ubiquitination occurs on the lysine residue by formation of an isopeptide crosslink.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0042787    protein ubiquitination involved in ubiquitin-dependent protein catabolic process    The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016607    nuclear speck    A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0000151    ubiquitin ligase complex    A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ZN363_HUMAN | Q96PM52k2c 2k2d

(-) Related Entries Specified in the PDB File

ht2b