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(-) Description

Title :  BACILLUS CEREUS ALKYLPURINE DNA GLYCOSYLASE ALKD BOUND TO DNA CONTAINING AN ABASIC SITE (ACROSS FROM C)
 
Authors :  E. H. Rubinson, B. F. Eichman
Date :  21 Sep 09  (Deposition) - 22 Sep 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Heat Repeat, Dna Binding, Dna Glycosylase, Dna Alkylation, Lyase-Dna Complex, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. H. Rubinson, A. S. Gowda, T. E. Spratt, B. Gold, B. F. Eichman
An Unprecedented Nucleic Acid Capture Mechanism For Excisio Of Dna Damage.
Nature V. 468 406 2010
PubMed-ID: 20927102  |  Reference-DOI: 10.1038/NATURE09428

(-) Compounds

Molecule 1 - ALKYLPURINE DNA GLYCOSYLASE ALKD
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBG103
    Expression System Strain: HMS174
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ALKD, BC_4913
    Organism Scientific: BACILLUS CEREUS
    Organism Taxid: 222523
    Strain: ATCC 10987
 
Molecule 2 - DNA (5'-D(*TP*GP*GP*GP*(3DR)P*GP*GP*CP*TP*T)-3')
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*AP*AP*AP*GP*CP*CP*CP*CP*CP*C)-3')
    Chains: C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
13DR1Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 3JY1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3JY1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3JY1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JY1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3JY1)

(-) Exons   (0, 0)

(no "Exon" information available for 3JY1)

(-) 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:226
 aligned with Q816E8_BACCR | Q816E8 from UniProtKB/TrEMBL  Length:237

    Alignment length:226
                             1                                                                                                                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219      
         Q816E8_BACCR     - -MHPFVKALQEHFTAHQNPEKAEPMARYMKNHFLFLGIQTPERRQLLKDIIQIHTLPDQKDFQIIIRELWDLPEREFQAAALDIMQKYKKHINETHIPFLEELIVTKSWWDSVDSIVPTFLGDIFLKHPELISAYIPKWIASDNIWLQRAAILFQLKYKQKMDEELLFWIIGQLHSSKEFFIQKAIGWVLREYAKTNPDVVWEYVQNNELAPLSKREAIKHIKQNY 225
               SCOP domains d3jy1a_ A: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------DNA_alkylation-3jy1A01 A:8-221                                                                                                                                                                                        ---- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhh.hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jy1 A   0 PMHPFVKALQEHFTAHQNPEKAEPMARYMKNHFLFLGIQTPERRQLLKDIIQIHTLPDQKDFQIIIRELWDLPEREFQAAALDIMQKYKKHINETHIPFLEELIVTKSWWDSVDSIVPTFLGDIFLKHPELISAYIPKWIASDNIWLQRAAILFQLKYKQKMDEELLFWIIGQLHSSKEFFIQKAIGWVLREYAKTNPDVVWEYVQNNELAPLSKREAIKHIKQNY 225
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219      


Chain B from PDB  Type:DNA  Length:10
                                          
                 3jy1 B   1 TGGGxGGCTT  10
                                |   10
                                5-3DR 


Chain C from PDB  Type:DNA  Length:10
                                          
                 3jy1 C  11 AAAGCCCCCC  20
                                    20
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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)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3JY1)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: TPR (230)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3JY1)

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 Related Entries

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

UniProtKB/TrEMBL
        Q816E8_BACCR | Q816E8: 3bvs 3jx7 3jxy 3jxz 5cl3 5cl4 5cl5 5cl6 5cl7 5cl8 5cl9 5cla 5clb 5clc 5cld 5cle 5kub

(-) Related Entries Specified in the PDB File

3bvs CRYSTAL STRUCTURE OF BACILLUS CEREUS ALKYLPURING DNA GLYCOSYLASE ALKD
3jx7 BACILLUS CEREUS ALKYLPURINE DNA GLYCOSYLASE ALKD BOUND TO DNA CONTAINING A 3MA ANALOG
3jxy BACILLUS CEREUS ALKYLPURINE DNA GLYCOSYLASE ALKD BOUND TO DNA CONTAINING A GT MISMATCH
3jxz BACILLUS CEREUS ALKYLPURINE DNA GLYCOSYLASE ALKD BOUND TO DNA CONTAINING AN ABASIC SITE (ACROSS FROM T)