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(-) Description

Title :  SOLUTION STRUCTURE OF RSGI RUH-011, A UBA DOMAIN FROM ARABIDOPSIS CDNA
 
Authors :  Y. Higuchi, T. Abe, H. Hirota, K. Saito, S. Koshiba, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  31 Mar 04  (Deposition) - 30 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Uba Domain, Three Helix Bundle, Ubiquitin Associated Domain, 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. Saito, S. Koshiba, T. Kigawa, S. Yokoyama
Solution Structure Of Rsgi Ruh-011, 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, PUTATIVE
    Chains: A
    Clone: K10D20
    Engineered: YES
    Expression System Plasmid: P030224-52
    Expression System Vector Type: PLASMID
    Fragment: UBA DOMAIN
    Gene: ARABIDOPSIS THALIANA GENOMIC DNA, CHROMOSOME 3, TAC
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Other Details: CELL-FREE PROTEIN SYNTHESIS SYSTEM
    Synonym: UBP14

 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 1VEK)

(-) Sites  (0, 0)

(no "Site" information available for 1VEK)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VEK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VEK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBAPS50030 Ubiquitin-associated domain (UBA) profile.UBP14_ARATH613-654
670-710		  1A:27-68
-

(-) Exons   (0, 0)

(no "Exon" information available for 1VEK)

(-) 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:84
 aligned with UBP14_ARATH | Q8L6Y1 from UniProtKB/Swiss-Prot  Length:797

    Alignment length:84
                                   596       606       616       626       636       646       656       666    
          UBP14_ARATH   587 RSKGLQPGEELLPDGVPEEVMESAQPVANEEIVAQLVSMGFSQLHCQKAAINTSNAGVEEAMNWLLSHMDDPDIDAPISHQTSD 670
               SCOP domains d1veka_ A: Ubiquitin isopeptidase T                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -------UCH-1vekA01 A:8-78                                                     ------ Pfam domains (1)
           Pfam domains (2) ---------------------------UBA-1vekA02 A:28-65                   ------------------- Pfam domains (2)
         Sec.struct. author ............................hhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------UBA  PDB: A:27-68 UniProt: 613-654        ---------------U PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 1vek A   1 GSSGSSGGEELLPDGVPEEVMESAQPVANEEIVAQLVSMGFSQLHCQKAAINTSNAGVEEAMNWLLSHMDDPDIDAPISGPSSG  84
                                    10        20        30        40        50        60        70        80
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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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1VEK)

(-) Pfam Domains  (2, 2)

NMR Structure
(-)
Clan: Peptidase_CA (169)
(-)
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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