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(-) Description

Title :  SOLUTION STRUCTURE OF RSGI RUH-013, A UBA DOMAIN IN MOUSE CDNA
 
Authors :  Y. Doi-Katayama, H. Hirota, K. Saito, S. Koshiba, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  23 Mar 04  (Deposition) - 23 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Uba Domain, Mouse Cdna, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Doi-Katayama, H. Hirota, K. Saito, S. Koshiba, T. Kigawa, S. Yokoyama
Solution Structure Of Rsgi Ruh-013, A Uba Domain In Mouse Cdna
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 25
    ChainsA
    EC Number3.1.2.15
    EngineeredYES
    Expression System PlasmidP030324-44
    Expression System Vector TypePLASMID
    FragmentUBA DOMAIN
    GeneRIKEN CDNA 2610101O11
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsCELL-FREE PROTEIN SYNTHESIS (E.COLI)
    SynonymRSGI RUH-013, UBIQUITIN THIOLESTERASE 25, UBIQUITIN-SPECIFIC PROCESSING PROTEASE 25, DEUBIQUITINATING ENZYME 25, MUSP25

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

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(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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 Sequence-Structure Mapping

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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:80
 aligned with UBP25_MOUSE | P57080 from UniProtKB/Swiss-Prot  Length:1055

    Alignment length:91
                                   1                                                                                   
                                   | 3        13        23        33        43        53        63        73        83 
           UBP25_MOUSE    - -------MTVEQNVLQQSAAQKHQQTFLNQLREITGINDAQILQQALKDSNGNLELAVAFLTAKNAKTPPQEETGYYQTALPGNDRYISVG 84
               SCOP domains d1vdla_ A: Ubiquitin carboxyl-terminal hydrolase 25                                         SCOP domains
               CATH domains 1vdlA00 A:1-80 DNA helicase RuvA subunit, C-terminal domain                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................hhhhhhhhhhh.....hhhhhhhhhhh...hhhhhhhhh............-------...----... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  1vdl A  1 GSSGSSGMTVEQNVLQQSAAQKHQQTFLNQLREITGINDAQILQQALKDSNGNLELAVAFLTAKNAKTPPQEET-------SGP----SSG 80
                                    10        20        30        40        50        60        70   |     - | |    79 
                                                                                                    74      75 |   78  
                                                                                                              77       

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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  (0, 0)

(no "Pfam Domain" information available for 1VDL)

(-) Gene Ontology  (18, 18)

NMR Structure(hide GO term definitions)
Chain A   (UBP25_MOUSE | P57080)
molecular function
    GO:0051117    ATPase binding    Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
    GO:0032183    SUMO binding    Interacting selectively and non-covalently with the small ubiquitin-like protein SUMO.
    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: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.
biological process
    GO:1904293    negative regulation of ERAD pathway    Any process that stops, prevents or reduces the frequency, rate or extent of ERAD pathway.
    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: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: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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0000502    proteasome complex    A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core.

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