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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF S. POMBE ATL IN COMPLEX WITH DAMAGED DNA CONTAINING POB
 
Authors :  J. L. Tubbs, A. S. Arvai, J. A. Tainer, D. S. Shin
Date :  03 Apr 09  (Deposition) - 16 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  X,Y,Z
Keywords :  Dna Damage, Dna Repair, Dna-Binding, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. Tubbs, V. Latypov, S. Kanugula, A. Butt, M. Melikishvili, R. Kraehenbuehl, O. Fleck, A. Marriott, A. J. Watson, B. Verbeek, G. Mcgown, M. Thorncroft, M. F. Santibanez-Koref, C. Millington, A. S. Arvai, M. D. Kroeger, L. A. Peterson, D. M. Williams, M. G. Fried, G. P. Margison, A. E. Pegg, J. A. Tainer
Flipping Of Alkylated Dna Damage Bridges Base And Nucleotid Excision Repair.
Nature V. 459 808 2009
PubMed-ID: 19516334  |  Reference-DOI: 10.1038/NATURE08076

(-) Compounds

Molecule 1 - ALKYLTRANSFERASE-LIKE PROTEIN 1
    Chains: X
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ATL1, SPAC1250.04C
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 4896
 
Molecule 2 - DNA (5'-D(*GP*CP*CP*AP*TP*GP*GP*CP*TP*AP*GP*TP*A)-3')
    Chains: Y
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*CP*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*G)-3')
    Chains: Z
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : XYZ

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PBO1Ligand/Ion1-PYRIDIN-3-YLBUTAN-1-ONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET X:45 , LEU X:48 , PRO X:50 , TRP X:56 , ARG X:77 , ARG X:81 , DG Y:207 , DG Y:211BINDING SITE FOR RESIDUE PBO Y 200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GYH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3GYH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GYH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GYH)

(-) Exons   (0, 0)

(no "Exon" information available for 3GYH)

(-) 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 X from PDB  Type:PROTEIN  Length:108
 aligned with ATL1_SCHPO | Q9UTN9 from UniProtKB/Swiss-Prot  Length:108

    Alignment length:108
                                    10        20        30        40        50        60        70        80        90       100        
           ATL1_SCHPO     1 MRMDEFYTKVYDAVCEIPYGKVSTYGEIARYVGMPSYARQVGQAMKHLHPETHVPWHRVINSRGTISKRDISAGEQRQKDRLEEEGVEIYQTSLGEYKLNLPEYMWKP 108
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.......eehhhhhhhh....hhhhhhhhhhh.......hhh.ee...........hhhhhhhhhhhhhhh...................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 3gyh X   1 MRMDEFYTKVYDAVCEIPYGKVSTYGEIARYVGMPSYARQVGQAMKHLHPETHVPWHRVINSRGTISKRDISAGEQRQKDRLEEEGVEIYQTSLGEYKLNLPEYMWKP 108
                                    10        20        30        40        50        60        70        80        90       100        


Chain Y from PDB  Type:DNA  Length:13
                                             
                 3gyh Y 201 GCCATGGCTAGTA 213
                                   210   


Chain Z from PDB  Type:DNA  Length:13
                                             
                 3gyh Z 214 CTACTAGCCATGG 226
                                   223
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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  (0, 0)

(no "SCOP Domain" information available for 3GYH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3GYH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GYH)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (ATL1_SCHPO | Q9UTN9)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0032132    O6-alkylguanine-DNA binding    Interacting selectively and non-covalently with O6-alkylguanine adducts in DNA.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0003908    methylated-DNA-[protein]-cysteine S-methyltransferase activity    Catalysis of the reaction: DNA (containing 6-O-methylguanine) + (protein)-L-cysteine = DNA (without 6-O-methylguanine) + protein S-methyl-L-cysteine.
biological process
    GO:0006307    DNA dealkylation involved in DNA repair    The repair of alkylation damage, e.g. the removal of the alkyl group at the O6-position of guanine by O6-alkylguanine-DNA alkyltransferase (AGT).
    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.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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)

UniProtKB/Swiss-Prot
        ATL1_SCHPO | Q9UTN9: 3gva 3gx4 4enj 4enk 4enm 4enn 4hdu 4hdv

(-) Related Entries Specified in the PDB File

3gva SAME PROTEIN WITHOUT DNA
3gx4 SAME PROTEIN WITH DNA