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(-) Description

Title :  SOLUTION STRUCTURE OF THE INTERNAL UBA DOMAIN OF HHR23A
 
Authors :  T. D. Mueller, J. Feigon
Date :  13 Apr 01  (Deposition) - 03 Jul 02  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Ubiquitin Associated Domain, Uba Domain, Ubiquitin Proteosome Pathway, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. D. Mueller, J. Feigon
Solution Structures Of Uba Domains Reveal A Conserved Hydrophobic Surface For Protein-Protein Interactions.
J. Mol. Biol. V. 319 1243 2002
PubMed-ID: 12079361  |  Reference-DOI: 10.1016/S0022-2836(02)00302-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG A
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX2T
    Expression System StrainBL21(DE3) STAR
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentINTERNAL UBA DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHHR23A

 Structural Features

(-) Chains, Units

  
NMR Structure (10x)

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1IFY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

NMR Structure (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020377R179QRD23A_HUMANPolymorphism4987203AR179Q
2UniProtVAR_016252T200MRD23A_HUMANPolymorphism4987202AT200M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBAPS50030 Ubiquitin-associated domain (UBA) profile.RD23A_HUMAN161-201
318-358
  1A:161-201
-

(-) Exons   (0, 0)

(no "Exon" information available for 1IFY)

(-) 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:49
 aligned with RD23A_HUMAN | P54725 from UniProtKB/Swiss-Prot  Length:363

    Alignment length:49
                                   165       175       185       195         
          RD23A_HUMAN   156 TLVTGSEYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTGIPG 204
               SCOP domains d1ifya_ A: DNA repair protein Hhr23a              SCOP domains
               CATH domains 1ifyA00 A:156-204                                 CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh..hhhhhhhhhhh....hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -----------------------Q--------------------M---- SAPs(SNPs)
                    PROSITE -----UBA  PDB: A:161-201 UniProt: 161-201     --- PROSITE
                 Transcript ------------------------------------------------- Transcript
                 1ify A 156 TLVTGSEYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTGIPG 204
                                   165       175       185       195         

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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  (1, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

NMR Structure(hide GO term definitions)
Chain A   (RD23A_HUMAN | P54725)
molecular function
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0031593    polyubiquitin modification-dependent protein binding    Interacting selectively and non-covalently with a protein upon poly-ubiquitination of the target protein.
    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:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
    GO:1990381    ubiquitin-specific protease binding    Interacting selectively and non-covalently with a ubiquitin-specific protease.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0006289    nucleotide-excision repair    A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
    GO:0045070    positive regulation of viral genome replication    Any process that activates or increases the frequency, rate or extent of viral genome replication.
    GO:0043161    proteasome-mediated 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 ubiquitin, and mediated by the proteasome.
    GO:0032434    regulation of proteasomal ubiquitin-dependent protein catabolic process    Any process that modulates the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        RD23A_HUMAN | P547251dv0 1f4i 1oqy 1p98 1p9d 1qze 1tp4 1zo6 2wyq 5xbo

(-) Related Entries Specified in the PDB File

1dv0 1DV0 IS THE C-TERMINAL UBA DOMAIN OF HHR23A
1f4i 1F4I IS THE P333E MUTANT OF C-TERMINAL UBA DOMAIN OF HHR23A