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(-) Description

Title :  STRUCTURE OF THE ZNF UBP DOMAIN FROM DEUBIQUITINATING ENZYME ISOPEPTIDASE T (ISOT)
 
Authors :  F. E. Reyes-Turcu, J. R. Horton, J. E. Mullally, A. Heroux, X. Cheng, K. D. Wilkinson
Date :  21 Feb 06  (Deposition) - 04 Apr 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Zinc Finger, Deubiquitinating Enzyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. E. Reyes-Turcu, J. R. Horton, J. E. Mullally, A. Heroux, X. Cheng, K. D. Wilkinson
The Ubiquitin Binding Domain Znf Ubp Recognizes The C-Terminal Diglycine Motif Of Unanchored Ubiquitin.
Cell(Cambridge, Mass. ) V. 124 1197 2006
PubMed-ID: 16564012  |  Reference-DOI: 10.1016/J.CELL.2006.02.038
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 5
    ChainsA, B
    EC Number3.1.2.15
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPRSET B (INVITROGEN)
    Expression System Vector TypePLASMID
    FragmentTHE ZN FINGER UMP DOMAIN OF ISOT (RESIDUES 163- 291)
    GeneUSP5, ISOT
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUBIQUITIN THIOLESTERASE 5, UBIQUITIN-SPECIFIC PROCESSING PROTEASE 5, DEUBIQUITINATING ENZYME 5, ISOPEPTIDASE T

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1UNX3Ligand/IonUNKNOWN ATOM OR ION
2ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1UNX-1Ligand/IonUNKNOWN ATOM OR ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1UNX3Ligand/IonUNKNOWN ATOM OR ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:38 , CYS A:41 , CYS A:58 , HIS A:71BINDING SITE FOR RESIDUE ZN A 1
2AC2SOFTWARECYS B:38 , CYS B:41 , CYS B:58 , HIS B:71BINDING SITE FOR RESIDUE ZN B 131
3AC3SOFTWAREGLY B:59 , ARG B:60 , UNX B:133 , UNX B:134BINDING SITE FOR RESIDUE UNX B 132
4AC4SOFTWARETRP B:48 , TYR B:98 , TYR B:100 , UNX B:132 , UNX B:134BINDING SITE FOR RESIDUE UNX B 133
5AC5SOFTWAREARG B:60 , ALA B:72 , TYR B:100 , UNX B:132 , UNX B:133 , HOH B:135BINDING SITE FOR RESIDUE UNX B 134

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:34 -B:34

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2G43)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2G43)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_UBPPS50271 Zinc finger UBP-type profile.UBP5_HUMAN197-269
 
  2A:36-108
B:36-108
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_UBPPS50271 Zinc finger UBP-type profile.UBP5_HUMAN197-269
 
  1A:36-108
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_UBPPS50271 Zinc finger UBP-type profile.UBP5_HUMAN197-269
 
  1-
B:36-108

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 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_HUMAN147-195492A:8-34
B:12-34
27
23
1.6ENST000002292686ENSE00000716143chr12:6965871-6966055185UBP5_HUMAN195-257632A:34-96
B:34-96
63
63
1.7ENST000002292687ENSE00000716144chr12:6966793-696688795UBP5_HUMAN257-288322A:96-124
B:96-124
29
29
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_HUMAN652-700490--
1.17ENST0000022926817ENSE00000716154chr12:6973214-6973359146UBP5_HUMAN700-748490--
1.18ENST0000022926818ENSE00000716155chr12:6973886-6974039154UBP5_HUMAN749-800520--
1.19ENST0000022926819ENSE00000716156chr12:6974328-697441285UBP5_HUMAN800-828290--
1.20ENST0000022926820ENSE00001164806chr12:6975148-6975793646UBP5_HUMAN828-858310--

(-) Sequences/Alignments

Asymmetric Unit
   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:117
 aligned with UBP5_HUMAN | P45974 from UniProtKB/Swiss-Prot  Length:858

    Alignment length:117
                                   178       188       198       208       218       228       238       248       258       268       278       
           UBP5_HUMAN   169 WDGEVRQVSKHAFSLKQLDNPARIPPCGWKCSKCDMRENLWLNLTDGSILCGRRYFDGSGGNNHAVEHYRETGYPLAVKLGTITPDGADVYSYDEDDMVLDPSLAEHLSHFGIDMLK 285
               SCOP domains d2g43a1 A:8-124 Ubiquitin carboxyl-terminal hydrolase 5, UBP5                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................................eeee.....eee...........hhhhhhhhhhh..eeee..........eee....eee...hhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------ZF_UBP  PDB: A:36-108 UniProt: 197-269                                   ---------------- PROSITE
           Transcript 1 (1) Exon 1.5  PDB: A:8-34      -------------------------------------------------------------Exon 1.7  PDB: A:96-124       Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.6  PDB: A:34-96 UniProt: 195-257                        ---------------------------- Transcript 1 (2)
                 2g43 A   8 WDGEVRQVSKHAFSLKQLDNPARIPPCGWKCSKCDMRENLWLNLTDGSILCGRRYFDGSGGNNHAVEHYRETGYPLAVKLGTITPDGADVYSYDEDDMVLDPSLAEHLSHFGIDMLK 124
                                    17        27        37        47        57        67        77        87        97       107       117       

Chain B from PDB  Type:PROTEIN  Length:113
 aligned with UBP5_HUMAN | P45974 from UniProtKB/Swiss-Prot  Length:858

    Alignment length:113
                                   182       192       202       212       222       232       242       252       262       272       282   
           UBP5_HUMAN   173 VRQVSKHAFSLKQLDNPARIPPCGWKCSKCDMRENLWLNLTDGSILCGRRYFDGSGGNNHAVEHYRETGYPLAVKLGTITPDGADVYSYDEDDMVLDPSLAEHLSHFGIDMLK 285
               SCOP domains d2g43b_ B: Ubiquitin carboxyl-terminal hydrolase 5, UBP5                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee...............................eeee.....eee...........hhhhhhhhhhh..eeee..........eee....eeee..hhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------ZF_UBP  PDB: B:36-108 UniProt: 197-269                                   ---------------- PROSITE
           Transcript 1 (1) Exon 1.5  PDB: B:12-34 -------------------------------------------------------------Exon 1.7  PDB: B:96-124       Transcript 1 (1)
           Transcript 1 (2) ----------------------Exon 1.6  PDB: B:34-96 UniProt: 195-257                        ---------------------------- Transcript 1 (2)
                 2g43 B  12 VRQVSKHAFSLKQLDNPARIPPCGWKCSKCDMRENLWLNLTDGSILCGRRYFDGSGGNNHAVEHYRETGYPLAVKLGTITPDGADVYSYDEDDMVLDPSLAEHLSHFGIDMLK 124
                                    21        31        41        51        61        71        81        91       101       111       121   

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2G43)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2G43)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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

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

UniProtKB/Swiss-Prot
        UBP5_HUMAN | P459742dag 2dak 2g45 3ihp

(-) Related Entries Specified in the PDB File

2g45