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(-) Description

Title :  SOLUTION STRUCTURE OF THE SECOND UBA DOMAIN IN THE HUMAN UBIQUITIN SPECIFIC PROTEASE 5 (ISOPEPTIDASE 5)
 
Authors :  C. Zhao, T. Kigawa, M. Sato, S. Koshiba, M. Inoue, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  14 Dec 05  (Deposition) - 14 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Isopeptidase T, Ubiquitin Specific Protease 5, Usp 5, Uba Domain, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Zhao, T. Kigawa, M. Sato, S. Koshiba, M. Inoue, S. Yokoyama
Solution Structure Of The Second Uba Domain In The Human Ubiquitin Specific Protease 5 (Isopeptidase 5)
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 5
    ChainsA
    EC Number3.1.2.15
    EngineeredYES
    Expression SystemCELL FREE SYNTHESIS
    Expression System PlasmidP050704-16
    Expression System Vector TypePLASMID
    FragmentUBA DOMAIN
    GeneUSP5
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymUBIQUITIN THIOLESTERASE 5, UBIQUITIN-SPECIFIC PROCESSING PROTEASE 5, DEUBIQUITINATING ENZYME 5, ISOPEPTIDASE T

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2DAK)

(-) Sites  (0, 0)

(no "Site" information available for 2DAK)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBAPS50030 Ubiquitin-associated domain (UBA) profile.UBP5_HUMAN654-695
722-762
  1-
A:9-47

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002292681aENSE00001603691chr12:6961285-6961454170UBP5_HUMAN1-37370--
1.2ENST000002292682ENSE00000716138chr12:6964565-6964690126UBP5_HUMAN38-79420--
1.3ENST000002292683ENSE00000716140chr12:6964919-696498567UBP5_HUMAN80-102230--
1.4ENST000002292684ENSE00000716141chr12:6965181-6965314134UBP5_HUMAN102-146450--
1.5ENST000002292685ENSE00000716142chr12:6965469-6965614146UBP5_HUMAN147-195490--
1.6ENST000002292686ENSE00000716143chr12:6965871-6966055185UBP5_HUMAN195-257630--
1.7ENST000002292687ENSE00000716144chr12:6966793-696688795UBP5_HUMAN257-288320--
1.8ENST000002292688ENSE00000716145chr12:6967588-6967781194UBP5_HUMAN289-353650--
1.9ENST000002292689ENSE00000866969chr12:6968634-696870572UBP5_HUMAN353-377250--
1.10ENST0000022926810ENSE00000716147chr12:6969315-696940288UBP5_HUMAN377-406300--
1.11ENST0000022926811ENSE00000716148chr12:6969530-6969655126UBP5_HUMAN407-448420--
1.12ENST0000022926812ENSE00000716149chr12:6970117-6970270154UBP5_HUMAN449-500520--
1.13ENST0000022926813ENSE00000716150chr12:6970607-6970781175UBP5_HUMAN500-558590--
1.14ENST0000022926814ENSE00000716151chr12:6971634-697172289UBP5_HUMAN558-588310--
1.15bENST0000022926815bENSE00000866970chr12:6972350-6972541192UBP5_HUMAN588-652650--
1.16ENST0000022926816ENSE00000716153chr12:6972994-6973137144UBP5_HUMAN652-700491A:1-33
1.17ENST0000022926817ENSE00000716154chr12:6973214-6973359146UBP5_HUMAN700-748491A:4-33 (gaps)40
1.18ENST0000022926818ENSE00000716155chr12:6973886-6974039154UBP5_HUMAN749-800521A:34-63 (gaps)33
1.19ENST0000022926819ENSE00000716156chr12:6974328-697441285UBP5_HUMAN800-828290--
1.20ENST0000022926820ENSE00001164806chr12:6975148-6975793646UBP5_HUMAN828-858310--

(-) 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:63
 aligned with UBP5_HUMAN | P45974 from UniProtKB/Swiss-Prot  Length:858

    Alignment length:101
                                   690       700       710       720       730       740       750       760       770       780 
           UBP5_HUMAN   681 GNSGAEAAMNWVMSHMDDPDFANPLILPGSSGPGSTSAAADPPPEDCVTTIVSMGFSRDQALKALRATNNSLERAVDWIFSHIDDLDAEAAMDISEGRSAA 781
               SCOP domains d2d                         aka_           A: automated matches                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...-------------------------.....----------hhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhhh........---..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE UBA  PDB: -    --------------------------UBA  PDB: A:9-47 UniProt: 722-762        ------------------- PROSITE
           Transcript 1 (1) Exon 1.16  PDB: A:1-------------------------------------------------Exon 1.18  PDB: A:34-63 (gaps)    Transcript 1 (1)
           Transcript 1 (2) -------------------Exon 1.17  PDB: A:4-33 (gaps) UniProt: 700-748   --------------------------------- Transcript 1 (2)
                 2dak A   1 GSS-------------------------GSSGP----------PEDCVTTIVSMGFSRDQALKALRATNNSLERAVDWIFSHIDDLDAEAAMS---GPSSG  63
                              |      -         -        |5  |      -   |    15        25        35        45        55  |   | 62 
                              3                         4   8          9                                               58  59    

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (1, 1)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DAK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DAK)

(-) Gene Ontology  (16, 16)

NMR Structure(hide GO term definitions)
Chain A   (UBP5_HUMAN | P45974)
molecular function
    GO:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    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:0004843    thiol-dependent ubiquitin-specific protease activity    Catalysis of the thiol-dependent hydrolysis of a peptide bond formed by the C-terminal glycine of ubiquitin and another protein.
    GO:0036459    thiol-dependent ubiquitinyl hydrolase activity    Catalysis of the thiol-dependent hydrolysis of an ester, thioester, amide, peptide or isopeptide bond formed by the C-terminal glycine of ubiquitin.
    GO:0043130    ubiquitin binding    Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    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:0071108    protein K48-linked deubiquitination    A protein deubiquitination process in which a K48-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 48 of the ubiquitin monomers, is removed from a protein.
    GO:0016579    protein deubiquitination    The removal of one or more ubiquitin groups from a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006511    ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.
cellular component
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.

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 Related Entries

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        UBP5_HUMAN | P459742dag 2g43 2g45 3ihp

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