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(-) Description

Title :  NMR SOLUTION STRUCTURE OF THE SINGLE-STRAND BREAK REPAIR PROTEIN XRCC1-N-TERMINAL DOMAIN
 
Authors :  A. Marintchev, G. P. Mullen
Date :  27 Feb 99  (Deposition) - 01 Sep 99  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
Keywords :  Xrcc1, 3D Nmr, Dna Repair, Single-Strand Break Dna Binding, Dna Polymerase-Beta Binding, Beta Sandwich, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Marintchev, M. A. Mullen, M. W. Maciejewski, B. Pan, M. R. Gryk, G. P. Mullen
Solution Structure Of The Single-Strand Break Repair Protein Xrcc1 N-Terminal Domain.
Nat. Struct. Biol. V. 6 884 1999
PubMed-ID: 10467102  |  Reference-DOI: 10.1038/12347
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (DNA-REPAIR PROTEIN XRCC1)
    Cellular Location: NUCLEUS
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET23A
    Expression System Strain: BL21[DE3]PLYSS
    Expression System Taxid: 562
    Fragment: N-TERMINAL DOMAIN, RESIDUES 1-183. RESIDUES 152- 183 ARE DISORDERED AND NOT SHOWN.
    Gene: XRCC1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: XRCC1-NTD

 Structural Features

(-) Chains, Units

  
NMR Structure : 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1XNA)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

NMR Structure (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_014773R7LXRCC1_HUMANPolymorphism2307186AR7L
2UniProtVAR_014774V10MXRCC1_HUMANPolymorphism2307171AV10M
3UniProtVAR_016168V72AXRCC1_HUMANPolymorphism25496AV72A
4UniProtVAR_029228R107HXRCC1_HUMANPolymorphism2228487AR107H
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XNA)

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002628871ENSE00001213791chr19:44079730-44079560171XRCC1_HUMAN1-17171A:1-1717
1.2ENST000002628872ENSE00000897653chr19:44079154-4407906293XRCC1_HUMAN18-48311A:18-4831
1.3ENST000002628873ENSE00000710723chr19:44065172-44065062111XRCC1_HUMAN49-85371A:49-8537
1.4ENST000002628874ENSE00000710692chr19:44058956-44058798159XRCC1_HUMAN86-138531A:86-13853
1.5ENST000002628875ENSE00000710666chr19:44057835-4405776175XRCC1_HUMAN139-163251A:139-15113
1.6ENST000002628876ENSE00000847423chr19:44057664-44057553112XRCC1_HUMAN164-201380--
1.7ENST000002628877ENSE00000710635chr19:44057243-44057134110XRCC1_HUMAN201-237370--
1.8ENST000002628878ENSE00000710618chr19:44057060-44056949112XRCC1_HUMAN238-275380--
1.9ENST000002628879ENSE00000710592chr19:44056427-44056169259XRCC1_HUMAN275-361870--
1.10bENST0000026288710bENSE00000710568chr19:44055839-44055723117XRCC1_HUMAN361-400400--
1.11aENST0000026288711aENSE00000710543chr19:44051129-4405103694XRCC1_HUMAN400-431320--
1.13ENST0000026288713ENSE00001674062chr19:44050879-44050747133XRCC1_HUMAN432-476450--
1.14ENST0000026288714ENSE00001737651chr19:44050258-4405020455XRCC1_HUMAN476-494190--
1.15ENST0000026288715ENSE00001695855chr19:44050109-44049970140XRCC1_HUMAN494-541480--
1.16ENST0000026288716ENSE00001614503chr19:44048386-4404829691XRCC1_HUMAN541-571310--
1.17ENST0000026288717ENSE00001797037chr19:44047839-4404776476XRCC1_HUMAN571-596260--
1.18ENST0000026288718ENSE00001669136chr19:44047657-44047464194XRCC1_HUMAN597-633370--

(-) 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:151
 aligned with XRCC1_HUMAN | P18887 from UniProtKB/Swiss-Prot  Length:633

    Alignment length:151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 
          XRCC1_HUMAN     1 MPEIRLRHVVSCSSQDSTHCAENLLKADTYRKWRAAKAGEKTISVVLQLEKEEQIHSVDIGNDGSAFVEVLVGSSAGGAGEQDYEVLLVTSSFMSPSESRSGSNPNRVRMFGPDKLVRAAAEKRWDRVKIVCSQPYSKDSPFGLSFVRFHS 151
               SCOP domains d1xnaa_ A: N-terminal domain of xrcc1                                                                                                                   SCOP domains
               CATH domains 1xnaA00 A:1-151 Galactose-binding domain-like                                                                                                           CATH domains
               Pfam domains XRCC1_N-1xnaA01 A:1-151                                                                                                                                 Pfam domains
         Sec.struct. author .......eeeeee.......hhhhh.......eee......eeeeeeee..eeee.eeeeee....eeeeeeee.........eeeeeeeee...hhhhh......eeeeee.....hhhhh.ee.eeeeeee........eee.eeeee. Sec.struct. author
                 SAPs(SNPs) ------L--M-------------------------------------------------------------A----------------------------------H-------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1         Exon 1.2  PDB: A:18-48         Exon 1.3  PDB: A:49-85 UniProt: 49-85Exon 1.4  PDB: A:86-138 UniProt: 86-138              Exon 1.5      Transcript 1
                 1xna A   1 MPEIRLRHVVSCSSQDSTHCAENLLKADTYRKWRAAKAGEKTISVVLQLEKEEQIHSVDIGNDGSAFVEVLVGSSAGGAGEQDYEVLLVTSSFMSPSESRSGSNPNRVRMFGPDKLVRAAAEKRWDRVKIVCSQPYSKDSPFGLSFVRFHS 151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: GBD (153)

(-) Gene Ontology  (17, 17)

NMR Structure(hide GO term definitions)
Chain A   (XRCC1_HUMAN | P18887)
molecular function
    GO:0003909    DNA ligase activity    Catalysis of the formation of a phosphodiester bond between the 3'-hydroxyl group at the end of one DNA chain and the 5'-phosphate group at the end of another. This reaction requires an energy source such as ATP or NAD+.
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    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).
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:0006284    base-excision repair    In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
    GO:0006288    base-excision repair, DNA ligation    The ligation by DNA ligase of DNA strands. Ligation occurs after polymerase action to fill the gap left by the action of endonucleases during base-excision repair.
    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:0000724    double-strand break repair via homologous recombination    The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule.
    GO:0006297    nucleotide-excision repair, DNA gap filling    Repair of the gap in the DNA helix by DNA polymerase and DNA ligase after the portion of the strand containing the lesion has been removed by pyrimidine-dimer repair enzymes.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0001666    response to hypoxia    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0010033    response to organic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
    GO:0000012    single strand break repair    The repair of single strand breaks in DNA. Repair of such breaks is mediated by the same enzyme systems as are used in base excision repair.
    GO:0006283    transcription-coupled nucleotide-excision repair    The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway.
cellular component
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

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        XRCC1_HUMAN | P18887: 1cdz 1xnt 2d8m 2w3o 3k75 3k77 3lqc 5e6q

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