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(-) Description

Title :  SOLUTION STRUCTURE OF THE ZINC FINGER DOMAIN OF USP13
 
Authors :  Y. Zhang, C. Zhou, Z. Zhou, A. Song, H. Hu
Date :  28 Dec 10  (Deposition) - 14 Dec 11  (Release) - 14 Dec 11  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
NMR Structure *:  A  (1x)
Keywords :  Zinc Finger, Usp13, Ubiquitin Binding, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Zhang, A. Song, C. Zhou, Z. Zhou, H. Hu
Biochemical Characterization Of The Ubiquitin Receptors In Usp13 Reveals Different Catalytic Activation Of Deubiquitination From Its Analogue Usp5
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 13
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET-M
    Expression System Vector TypeVECTOR
    FragmentZINC FINGER DOMAIN, UBP-TYPE, UNP RESIDUES 188-301
    GeneUSP13
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUSP13, DEUBIQUITINATING ENZYME 13, ISOPEPTIDASE T-3, ISOT-3, UBIQUITIN THIOLESTERASE 13, UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 13

 Structural Features

(-) Chains, Units

  1
NMR Structure (10x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION
NMR Structure * (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:24 , CYS A:27 , CYS A:44 , HIS A:57BINDING SITE FOR RESIDUE ZN A 124

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2L80)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2L80)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2L80)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_UBPPS50271 Zinc finger UBP-type profile.UBP13_HUMAN209-281  1A:22-94
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_UBPPS50271 Zinc finger UBP-type profile.UBP13_HUMAN209-281  1A:22-94

(-) Exons   (0, 0)

(no "Exon" information available for 2L80)

(-) 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:114
 aligned with UBP13_HUMAN | Q92995 from UniProtKB/Swiss-Prot  Length:863

    Alignment length:114
                                   197       207       217       227       237       247       257       267       277       287       297    
          UBP13_HUMAN   188 VSKYANNLTQLDNGVRIPPSGWKCARCDLRENLWLNLTDGSVLCGKWFFDSSGGNGHALEHYRDMGYPLAVKLGTITPDGADVYSFQEEEPVLDPHLAKHLAHFGIDMLHMHGT 301
               SCOP domains d2l80a_ A: automated matches                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ................................eeee.....eee...........hhhhhhhhhh...eeeee........eeee.....ee...hhhhhhhhh...hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------ZF_UBP  PDB: A:22-94 UniProt: 209-281                                    -------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 2l80 A   1 VSKYANNLTQLDNGVRIPPSGWKCARCDLRENLWLNLTDGSVLCGKWFFDSSGGNGHALEHYRDMGYPLAVKLGTITPDGADVYSFQEEEPVLDPHLAKHLAHFGIDMLHMHGT 114
                                    10        20        30        40        50        60        70        80        90       100       110    

   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, 1)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2L80)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2L80)

(-) Gene Ontology  (28, 28)

NMR Structure(hide GO term definitions)
Chain A   (UBP13_HUMAN | Q92995)
molecular function
    GO:1904288    BAT3 complex binding    Interacting selectively and non-covalently with a BAT3 complex.
    GO:0051087    chaperone binding    Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport.
    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:0070628    proteasome binding    Interacting selectively and non-covalently with a proteasome, a large multisubunit protein complex that catalyzes protein degradation.
    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:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
    GO:0044389    ubiquitin-like protein ligase binding    Interacting selectively and non-covalently with a ubiquitin-like protein ligase, such as ubiquitin-ligase.
    GO:1904454    ubiquitin-specific protease activity involved in positive regulation of ERAD pathway    Any ubiquitin-specific protease activity that is involved in positive regulation of ERAD pathway.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006914    autophagy    The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:1904378    maintenance of unfolded protein involved in ERAD pathway    Maintaining an endoplasmic reticulum (ER) protein in an unfolded, soluble state that contributes to its degradation by the cytoplasmic proteasome. Maintaining ER-resident proteins in an unfolded yet soluble state condition after their retro-translocation favors their turnover by the cytosolic proteasome.
    GO:0030318    melanocyte differentiation    The process in which a relatively unspecialized cell acquires specialized features of a melanocyte.
    GO:1904294    positive regulation of ERAD pathway    Any process that activates or increases the frequency, rate or extent of ERAD pathway.
    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:0016579    protein deubiquitination    The removal of one or more ubiquitin groups from a protein.
    GO:0050821    protein stabilization    Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0010506    regulation of autophagy    Any process that modulates the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        UBP13_HUMAN | Q929952lbc

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