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(-) Description

Title :  STRUCTURE OF OTUD3 OTU DOMAIN
 
Authors :  T. E. T. Mevissen, M. K. Hospenthal, P. P. Geurink, P. R. Elliott, M. Akut N. Arnaudo, R. Ekkebus, Y. Kulathu, T. Wauer, F. El Oualid, S. M. V. Fre H. Ovaa, D. Komander
Date :  22 May 13  (Deposition) - 17 Jul 13  (Release) - 17 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. E. T. Mevissen, M. K. Hospenthal, P. P. Geurink, P. R. Elliott, M. Akutsu, N. Arnaudo, R. Ekkebus, Y. Kulathu, T. Wauer, F. El Oualid, S. M. V. Freund, H. Ovaa, D. Komander
Otu Deubiquitinases Reveal Mechanisms Of Linkage Specificity And Enable Ubiquitin Chain Restriction Analysis.
Cell(Cambridge, Mass. ) V. 154 169 2013
PubMed-ID: 23827681  |  Reference-DOI: 10.1016/J.CELL.2013.05.046

(-) Compounds

Molecule 1 - OTU DOMAIN-CONTAINING PROTEIN 3
    Chains: A
    EC Number: 3.4.19.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: POPINK
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA PLACI
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 52-209
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: OTUD3

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4BOU)

(-) Sites  (0, 0)

(no "Site" information available for 4BOU)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4BOU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4BOU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BOU)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OTUPS50802 OTU domain profile.OTUD3_HUMAN65-189  1A:65-189
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OTUPS50802 OTU domain profile.OTUD3_HUMAN65-189  2A:65-189

(-) Exons   (0, 0)

(no "Exon" information available for 4BOU)

(-) Sequences/Alignments

Asymmetric Unit
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:141
 aligned with OTUD3_HUMAN | Q5T2D3 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:143
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187   
          OTUD3_HUMAN    48 GCEEEFVSFANQLQALGLKLREVPGDGNCLFRALGDQLEGHSRNHLKHRQETVDYMIKQREDFEPFVEDDIPFEKHVASLAKPGTFAGNDAIVAFARNHQLNVVIHQLNAPLWQIRGTEKSSVRELHIAYRYGEHYDSVRRIN 190
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .--....hhhhhhhhh.eeee......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh.....hhhhhhhhhhhh..eeeee......eeee........eeeeeee...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------OTU  PDB: A:65-189 UniProt: 65-189                                                                                           - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bou A  50 G--PEFVSFANQLQALGLKLREVPGDGNCLFRALGDQLEGHSRNHLKHRQETVDYMIKQREDFEPFVEDDIPFEKHVASLAKPGTFAGNDAIVAFARNHQLNVVIHQLNAPLWQIRGTEKSSVRELHIAYRYGEHYDSVRRIN 190
                            |  |    57        67        77        87        97       107       117       127       137       147       157       167       177       187   
                            | 51                                                                                                                                           
                           50
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  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 4BOU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BOU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BOU)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (OTUD3_HUMAN | Q5T2D3)
molecular function
    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: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: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.
biological process
    GO:0035871    protein K11-linked deubiquitination    A protein deubiquitination process in which a K11-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 11 of the ubiquitin monomers, is removed from a protein.
    GO:0044313    protein K6-linked deubiquitination    A protein deubiquitination process in which a K6-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 6 of the ubiquitin monomers, is removed from a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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  4bou
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 Related Entries

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(-) Related Entries Specified in the PDB File

4bop STRUCTURE OF OTUD1 OTU DOMAIN
4boq STRUCTURE OF OTUD2 OTU DOMAIN
4bos STRUCTURE OF OTUD2 OTU DOMAIN IN COMPLEX WITH UBIQUITIN K11-LINKED PEPTIDE