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(-) Description

Title :  SOLUTION NMR STRUCTURE OF UBIQUITIN THIOESTERASE OTU1 (EC 3.1.2.-) FROM MUS MUSCULUS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET MMT2A
 
Authors :  S. Chitayat, A. Gutmanas, A. Lemak, A. Yee, I. Bezsonova, B. Wu, R. S. Doh A. Semesi, G. T. Montelione, C. H. Arrowsmith, S. Dhe-Paganon, Northe Structural Genomics Consortium (Nesg)
Date :  23 Jun 10  (Deposition) - 07 Jul 10  (Release) - 04 Aug 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Structural Genomics, Northeast Structural Genomics Consortium (Nesg), Psi-2, Protein Structure Initiative, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Chitayat, A. Gutmanas, A. Lemak, A. Yee, I. Bezsonova, B. Wu, R. S. Doherty, A. Semesi, C. H. Arrowsmith, S. Dhe-Paganon
Northeast Structural Genomics Consortium Target Mmt2A
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UBIQUITIN THIOESTERASE OTU1
    ChainsA
    EC Number3.1.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)PMGK
    Expression System Taxid469008
    Expression System VectorPET28-MHL
    FragmentUBX-LIKE DOMAIN 42-127
    GeneYOD1
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) 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
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Chain A from PDB  Type:PROTEIN  Length:86
 aligned with OTU1_MOUSE | Q8CB27 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:86
                                    51        61        71        81        91       101       111       121      
           OTU1_MOUSE    42 WRVRCKAKGGTHLLQGLSSRTRLRELQGQIAAITGIAPGSQRILVGYPPECLDLSDRDITLGDLPIQSGDMLIVEEDQTRPKASPA 127
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeeee.......hhhhhhhhhhhhh.........ee.........................eee............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 2kzr A   1 WRVRCKAKGGTHLLQGLSSRTRLRELQGQIAAITGIAPGSQRILVGYPPECLDLSDRDITLGDLPIQSGDMLIVEEDQTRPKASPS  86
                                    10        20        30        40        50        60        70        80      

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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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

NMR Structure(hide GO term definitions)
Chain A   (OTU1_MOUSE | Q8CB27)
molecular function
    GO:1990380    Lys48-specific deubiquitinase activity    Hydrolysis of Lys48-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: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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