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(-) Description

Title :  STRUCTURE OF OTUD2 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 :  1.47
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 - UBIQUITIN THIOESTERASE OTU1
    ChainsA
    EC Number3.4.19.12
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantROSETTA PLACI
    FragmentRESIDUES 132-314
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDUBA-8, HIV-1-INDUCED PROTEASE 7, HIN-7, HSHIN7, OTU DOMAIN-CONTAINING PROTEIN 2, OTUD2

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:235 , ARG A:248 , GLY A:250 , GLU A:251 , GLY A:254 , TYR A:255 , SER A:288BINDING SITE FOR RESIDUE GOL A1310
2AC2SOFTWAREARG A:273 , LEU A:283 , PHE A:286 , SER A:287 , ASP A:290 , HOH A:2111 , HOH A:2129BINDING SITE FOR RESIDUE GOL A1311
3AC3SOFTWAREPRO A:147 , ALA A:177 , ARG A:273 , ILE A:292 , HOH A:2010 , HOH A:2111 , HOH A:2121 , HOH A:2130BINDING SITE FOR RESIDUE GOL A1312
4AC4SOFTWARELYS A:135 , TRP A:212 , GLY A:221 , ALA A:222 , ILE A:223 , GLU A:224 , HOH A:2062BINDING SITE FOR RESIDUE GOL A1313

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OTUPS50802 OTU domain profile.OTU1_HUMAN149-274  1A:149-274
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OTUPS50802 OTU domain profile.OTU1_HUMAN149-274  2A:149-274

(-) Exons   (0, 0)

(no "Exon" information available for 4BOQ)

(-) 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:175
 aligned with OTU1_HUMAN | Q5VVQ6 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:175
                                   144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304     
           OTU1_HUMAN   135 KRGASSYVRETLPVLTRTVVPADNSCLFTSVYYVVEGGVLNPACAPEMRRLIAQIVASDPDFYSEAILGKTNQEYCDWIKRDDTWGGAIEISILSKFYQCEICVVDTQTVRIDRFGEDAGYTKRVLLIYDGIHYDPLQRNFPDPDTPPLTIFSSNDDIVLVQALELADEARRRRQ 309
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh......eeee.......hhhhhhhhhhhh.......hhhhhhhhhhhhhhhh....hhhhhh.hhhhhhhhhh......hhhhhhhhhhhhh.eeeeee....eeeee.......eeeeeee....eeeeeee...........ee...hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------OTU  PDB: A:149-274 UniProt: 149-274                                                                                          ----------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4boq A 135 KRGASSYVRETLPVLTRTVVPADNSCLFTSVYYVVEGGVLNPACAPEMRRLIAQIVASDPDFYSEAILGKTNQEYCDWIKRDDTWGGAIEISILSKFYQCEICVVDTQTVRIDRFGEDAGYTKRVLLIYDGIHYDPLQRNFPDPDTPPLTIFSSNDDIVLVQALELADEARRRRQ 309
                                   144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304     

   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 4BOQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A   (OTU1_HUMAN | Q5VVQ6)
molecular function
    GO:1990380    Lys48-specific deubiquitinase activity    Hydrolysis of Lys48-linked ubiquitin unit(s) from a ubiquitinated protein.
    GO:0061578    Lys63-specific deubiquitinase activity    Hydrolysis of Lys63-Linked ubiquitin unit(s) from a ubiquitinated protein.
    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:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
    GO:1904265    ubiquitin-specific protease activity involved in negative regulation of retrograde protein transport, ER to cytosol    Any ubiquitin-specific protease activity (deubiquitinase activity) that is involved in negative regulation of retrograde protein transport, ER to cytosol.
biological process
    GO:0030968    endoplasmic reticulum unfolded protein response    The series of molecular signals generated as a consequence of the presence of unfolded proteins in the endoplasmic reticulum (ER) or other ER-related stress; results in changes in the regulation of transcription and translation.
    GO:1904153    negative regulation of retrograde protein transport, ER to cytosol    Any process that stops, prevents or reduces the frequency, rate or extent of retrograde protein transport, ER to cytosol.
    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:1990167    protein K27-linked deubiquitination    A protein deubiquitination process in which a K27-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 27 of the ubiquitin monomers, is removed from a protein.
    GO:0035523    protein K29-linked deubiquitination    A protein deubiquitination process in which a K29-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 29 of the ubiquitin monomers, is removed from a protein.
    GO:1990168    protein K33-linked deubiquitination    A protein deubiquitination process in which a K33-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 33 of the ubiquitin monomers, is removed from a protein.
    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:0070536    protein K63-linked deubiquitination    A protein deubiquitination process in which a K63-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 63 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.
    GO:0006986    response to unfolded protein    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an unfolded protein stimulus.
    GO:0030433    ubiquitin-dependent ERAD pathway    The series of steps necessary to target endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. Begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein ubiquitination necessary for correct substrate transfer, transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.

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        OTU1_HUMAN | Q5VVQ64bos 4boz

(-) Related Entries Specified in the PDB File

4bop STRUCTURE OF OTUD1 OTU DOMAIN