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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN DNA CROSS-LINK REPAIR 1A
 
Authors :  C. K. Allerston, G. Berridge, E. P. Carpenter, G. Kochan, T. Krojer, P. M M. Vollmar, W. W. Yue, C. H. Arrowsmith, A. Edwards, C. Bountra, F. Von O. Gileadi
Date :  24 Aug 12  (Deposition) - 28 Nov 12  (Release) - 05 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.16
Chains :  Asym./Biol. Unit :  A
Keywords :  Dclre1A, Dclre, Interstrand Crosslink Repair, Hydrolase, Nitrogen Mustard, Cancer, Chemotherapy, Pso2 Homolog, (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. K. Allerston, G. Berridge, E. P. Carpenter, G. Kochan, T. Krojer, P. Mahajan, M. Vollmar, W. W. Yue, C. H. Arrowsmith, A. Edwards, C. Bountra, F. Von Delft, O. Gileadi
Crystal Structure Of Human Dna Cross-Link Repair 1A
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DNA CROSS-LINK REPAIR 1A PROTEIN
    ChainsA
    FragmentRESIDUES 676-1040
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSNM1 HOMOLOG A, HSNM1, HSNM1A
    SyntheticYES

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2ZN1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:696 , HIS A:732 , HIS A:734 , HIS A:793 , ASP A:815BINDING SITE FOR RESIDUE ZN A2041
2AC2SOFTWAREVAL A:886 , ARG A:960 , PRO A:961 , ILE A:989 , HOH A:3108BINDING SITE FOR RESIDUE EDO A2042
3AC3SOFTWAREGLN A:955BINDING SITE FOR RESIDUE EDO A2043
4AC4SOFTWAREHIS A:744 , THR A:878 , PRO A:933 , MET A:934 , MET A:935 , EDO A:2045 , HOH A:3103BINDING SITE FOR RESIDUE EDO A2044
5AC5SOFTWAREMET A:934 , EDO A:2044BINDING SITE FOR RESIDUE EDO A2045

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:925 -A:949

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4B87)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_023291I859FDCR1A_HUMANPolymorphism11196530AI859F

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4B87)

(-) Exons   (0, 0)

(no "Exon" information available for 4B87)

(-) Sequences/Alignments

Asymmetric/Biological 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:335
 aligned with DCR1A_HUMAN | Q6PJP8 from UniProtKB/Swiss-Prot  Length:1040

    Alignment length:345
                                   705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035     
         DCR1A_HUMAN    696 SRKKTCPFYKKIPGTGFTVDAFQYGVVEGCTAYFLTHFHSDHYAGLSKHFTFPVYCSEITGNLLKNKLHVQEQYIHPLPLDTECIVNGVKVVLLDANHCPGAVMILFYLPNGTVILHTGDFRADPSMERSLLADQKVHMLYLDTTYCSPEYTFPSQQEVIRFAINTAFEAVTLNPHALVVCGTYSIGKEKVFLAIADVLGSKVGMSQEKYKTLQCLNIPEINSLITTDMCSSLVHLLPMMQINFKGLQSHLKKCGGKYNQILAFRPTGWTHSNKFTRIADVIPQTKGNISIYGIPYSEHSSYLEMKRFVQWLKPQKIIPTVNVGTWKSRSTMEKYFREWKLEAGY 1040
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhh......eee............eee....hhhhhh.........eeehhhhhhhhhhhh..hhh.eee......eee..eeeeeee.......eeeeee.....eeee......hhhhhhhhhhh....eeee............hhhhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhh...ee.hhhhhhhhhh....hhhhhee.hhhhh.eeeee.hhhhhhhhhhhhhhhhhh..eeeeeee..----------.....eee..eeeeee......hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4b87 A  696 SRKKTCPFYKKIPGTGFTVDAFQYGVVEGCTAYFLTHFHSDHYAGLSKHFTFPVYCSEITGNLLKNKLHVQEQYIHPLPLDTECIVNGVKVVLLDANHCPGAVMILFYLPNGTVILHTGDFRADPSMERSLLADQKVHMLYLDTTYCSPEYTFPSQQEVIRFAINTAFEAVTLNPHALVVCGTYSIGKEKVFLAIADVLGSKVGMSQEKYKTLQCLNIPEINSLITTDMCSSLVHLLPMMQINFKGLQSHLKKCGGKYNQILAFRPTG----------ADVIPQTKGNISIYGIPYSEHSSYLEMKRFVQWLKPQKIIPTVNVGTWKSRSTMEKYFREWKLEAGY 1040
                                   705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       | -       975       985       995      1005      1015      1025      1035     
                                                                                                                                                                                                                                                                                                     963        974                                                                  

   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  (0, 0)

(no "SCOP Domain" information available for 4B87)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B87)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B87)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DCR1A_HUMAN | Q6PJP8)
molecular function
    GO:0035312    5'-3' exodeoxyribonuclease activity    Catalysis of the sequential cleavage of mononucleotides from a free 5' terminus of a DNA molecule.
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
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:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    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:0006303    double-strand break repair via nonhomologous end joining    The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
    GO:0036297    interstrand cross-link repair    Removal of a DNA interstrand crosslink (a covalent attachment of DNA bases on opposite strands of the DNA) and restoration of the DNA. DNA interstrand crosslinks occur when both strands of duplex DNA are covalently tethered together (e.g. by an exogenous or endogenous agent), thus preventing the strand unwinding necessary for essential DNA functions such as transcription and replication.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0031848    protection from non-homologous end joining at telomere    A process that prevents non-homologous end joining at telomere, thereby ensuring that telomeres do not fuse.
cellular component
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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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 Related Entries

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

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        DCR1A_HUMAN | Q6PJP85ahr 5nzw 5nzx 5nzy

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