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(-) Description

Title :  BACILLUS CEREUS ALKYLPURINE DNA GLYCOSYLASE ALKD BOUND TO DNA CONTAINING A 3-METHYLADENINE ANALOG
 
Authors :  E. H. Rubinson, B. F. Eichman
Date :  18 Sep 09  (Deposition) - 22 Sep 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
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(*CP*GP*GP*AP*CP*TP*(DZM)P*AP*CP*GP*GP*G)-3')
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*CP*CP*CP*GP*TP*TP*AP*GP*TP*CP*CP*G)-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
1DZM1Mod. Nucleotide3-DEAZA-3-METHYLADENINE

(-) Sites  (0, 0)

(no "Site" information available for 3JX7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3JX7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3JX7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JX7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3JX7)

(-) Exons   (0, 0)

(no "Exon" information available for 3JX7)

(-) 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:232
 aligned with Q816E8_BACCR | Q816E8 from UniProtKB/TrEMBL  Length:237

    Alignment length:232
                             1                                                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229  
         Q816E8_BACCR     - -MHPFVKALQEHFTAHQNPEKAEPMARYMKNHFLFLGIQTPERRQLLKDIIQIHTLPDQKDFQIIIRELWDLPEREFQAAALDIMQKYKKHINETHIPFLEELIVTKSWWDSVDSIVPTFLGDIFLKHPELISAYIPKWIASDNIWLQRAAILFQLKYKQKMDEELLFWIIGQLHSSKEFFIQKAIGWVLREYAKTNPDVVWEYVQNNELAPLSKREAIKHIKQNYGINNEK 231
               SCOP domains d3jx7a_ A: automated matches                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------DNA_alkylation-3jx7A01 A:8-221                                                                                                                                                                                        ---------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhh..hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jx7 A   0 PMHPFVKALQEHFTAHQNPEKAEPMARYMKNHFLFLGIQTPERRQLLKDIIQIHTLPDQKDFQIIIRELWDLPEREFQAAALDIMQKYKKHINETHIPFLEELIVTKSWWDSVDSIVPTFLGDIFLKHPELISAYIPKWIASDNIWLQRAAILFQLKYKQKMDEELLFWIIGQLHSSKEFFIQKAIGWVLREYAKTNPDVVWEYVQNNELAPLSKREAIKHIKQNYGINNEK 231
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229  


Chain B from PDB  Type:DNA  Length:12
                                            
                 3jx7 B   1 CGGACTaACGGG  12
                                  | 10  
                                  7-DZM 


Chain C from PDB  Type:DNA  Length:12
                                            
                 3jx7 C  13 CCCGTTAGTCCG  24
                                    22
   Legend:   → Mismatch (orange background)
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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 3JX7)

(-) 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 3JX7)

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 Related Entries

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

UniProtKB/TrEMBL
        Q816E8_BACCR | Q816E8: 3bvs 3jxy 3jxz 3jy1 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 ALKYLPURINE DNA GLYCOSYLASE ALKD
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)
3jy1 BACILLUS CEREUS ALKYLPURINE DNA GLYCOSYLASE ALKD BOUND TO DNA CONTAINING AN ABASIC SITE (ACROSS FROM C)