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(-) Description

Title :  SOLUTION STRUCTURE OF RSGI RUH-023, A UBA DOMAIN FROM ARABIDOPSIS CDNA
 
Authors :  Y. Higuchi, T. Abe, H. Hirota, K. Izumi, M. Yoshida, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  28 May 04  (Deposition) - 28 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Ubiquitin Associated Domain, Uba Domain, Three Helix Bundle, Ubiquitin Specific Protease 14, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Higuchi, T. Abe, H. Hirota, K. Izumi, M. Yoshida, S. Yokoyama
Solution Structure Of Rsgi Ruh-023, A Uba Domain From Arabidopsis Cdna
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBIQUITIN-SPECIFIC PROTEASE 14
    ChainsA
    EngineeredYES
    Expression System PlasmidP030224-56
    Expression System Vector TypePLASMID
    FragmentUBA DOMAIN
    GeneK10D20
    Organism CommonTHALE CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    Other DetailsCELL-FREE PROTEIN SYNTHESIS SYSTEM
    SynonymUBP14

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1WIV)

(-) 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)

(no "SAP(SNP)/Variant" information available for 1WIV)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBAPS50030 Ubiquitin-associated domain (UBA) profile.UBP14_ARATH613-654
670-710
  1-
A:27-67

(-) Exons   (0, 0)

(no "Exon" information available for 1WIV)

(-) 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:73
 aligned with UBP14_ARATH | Q8L6Y1 from UniProtKB/Swiss-Prot  Length:797

    Alignment length:101
                                   647       657       667       677       687       697       707       717       727       737 
          UBP14_ARATH   638 NTSNAGVEEAMNWLLSHMDDPDIDAPISHQTSDIDQSSVDTLLSFGFAEDVARKALKASGGDIEKATDWVFNNPNASVSDMDVSSSNSAQTPAQSGLPDGG 738
               SCOP domains d1wiv      a_ A: Ubiquitin isopeptidase T                                                             SCOP domains
               CATH domains 1wivA      00 A:1-73 DNA helicase RuvA subunit, C-terminal domain                                     CATH domains
           Pfam domains (1) -------------UCH-1wivA01 A:8-67                                          ---------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------UBA-1wivA02 A:28-64                  ------------------------------- Pfam domains (2)
         Sec.struct. author .....------.......................hhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhh---------------------..-.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE UBA  PDB: -      ---------------UBA  PDB: A:27-67 UniProt: 670-710       ---------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 1wiv A   1 GSSGS------SGLLSHMDDPDIDAPISHQTSDIDQSSVDTLLSFGFAEDVARKALKASGGDIEKATDWVFNN---------------------SG-PSSG  73
                                |    - |      14        24        34        44        54        64  |      -         -    || |72 
                                5      6                                                           67                    68| |   
                                                                                                                          69 |   
                                                                                                                            70   

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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  (1, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure

(-) Pfam Domains  (2, 2)

NMR Structure
(-)
Clan: UBA (32)

(-) Gene Ontology  (13, 13)

NMR Structure(hide GO term definitions)
Chain A   (UBP14_ARATH | Q8L6Y1)
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: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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0009793    embryo development ending in seed dormancy    The process whose specific outcome is the progression of the embryo over time, from zygote formation to the end of seed dormancy. An example of this process is found in Arabidopsis thaliana.
    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:0048767    root hair elongation    The process in which the root hair grows longer.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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        UBP14_ARATH | Q8L6Y11vek

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