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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE UBIQUITIN-LIKE (UBL) DOMAIN OF HHR23A (HUMAN HOMOLOGUE A OF RAD23)
 
Authors :  Y. W. Chen
Date :  19 Nov 09  (Deposition) - 10 Nov 10  (Release) - 22 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (1x)
Keywords :  Dna Binding Protein, Dna Excision Repair, Proteasomal Degradation, Polyubiquitin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. W. Chen, T. Tajima, S. Agrawal
The Crystal Structure Of The Ubiquitin-Like (Ubl) Domain Of Human Homologue A Of Rad23 (Hhr23A) Protein
Protein Eng. Des. Sel. V. 24 131 2011
PubMed-ID: 21047872  |  Reference-DOI: 10.1093/PROTEIN/GZQ084
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG A
    ChainsA
    Expression SystemESCHERICHIA COLI
    Expression System StrainROSETTA 2 (DE3)
    Expression System Taxid562
    FragmentUBIQUITIN-LIKE DOMAIN, RESIDUES 1-82
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHHR23A

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A
Biological Unit 2 (1x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:14 , ARG A:62 , HOH A:2107 , HOH A:2108BINDING SITE FOR RESIDUE SO4 A1078
2AC2SOFTWARELYS A:53 , ASP A:63 , TYR A:64BINDING SITE FOR RESIDUE SO4 A1079

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.RD23A_HUMAN3-81  1A:3-77
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.RD23A_HUMAN3-81  2A:3-77
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.RD23A_HUMAN3-81  1A:3-77

(-) Exons   (0, 0)

(no "Exon" information available for 2WYQ)

(-) Sequences/Alignments

Asymmetric Unit
   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:77
 aligned with RD23A_HUMAN | P54725 from UniProtKB/Swiss-Prot  Length:363

    Alignment length:77
                                    10        20        30        40        50        60        70       
           RD23A_HUMAN    1 MAVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVT 77
               SCOP domains d2wyqa_ A: automated matches                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains -------ubiquitin-2wyqA01 A:8-77                                               Pfam domains
         Sec.struct. author ..eeeeeee....eeeeee....hhhhhhhhhhhhhh....hhh.eeeee..ee......hhhhh.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --UBIQUITIN_2  PDB: A:3-77 UniProt: 3-81                                      PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                  2wyq A  1 MAVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVT 77
                                    10        20        30        40        50        60        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)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Ubiquitin (279)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(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 1ify 1oqy 1p98 1p9d 1qze 1tp4 1zo6 5xbo

(-) Related Entries Specified in the PDB File

1dv0 REFINED NMR SOLUTION STRUCTURE OF THE C- TERMINAL UBA DOMAIN OF THE HUMAN HOMOLOGUE OF RAD23A (HHR23A)
1f4i SOLUTION STRUCTURE OF THE HHR23A UBA(2) MUTANT P333E,DEFICIENT IN BINDING THE HIV- 1 ACCESSORY PROTEIN VPR
1ify SOLUTION STRUCTURE OF THE INTERNAL UBA DOMAIN OF HHR23A
1oqy STRUCTURE OF THE DNA REPAIR PROTEIN HHR23A
1p98 HIGH-RESOLUTION NMR STRUCTURE OF THE UBL- DOMAIN OF HHR23A
1p9d HIGH-RESOLUTION STRUCTURE OF THE COMPLEX OF HHR23AUBIQUITIN-LIKE DOMAIN AND THE C- TERMINAL UBIQUITIN-INTERACTING MOTIF OF PROTEASOME SUBUNIT S5A
1qze HHR23A PROTEIN STRUCTURE BASED ON RESIDUAL DIPOLAR COUPLINGDATA
1tp4 SOLUTION STRUCTURE OF THE XPC BINDING DOMAIN OF HHR23APROTEIN