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(-) Description

Title :  BACILLUS CEREUS ALKYLPURINE DNA GLYCOSYLASE ALKD BOUND TO DNA CONTAINING A GT MISMATCH
 
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 :  1.50
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*GP*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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3JXY)

(-) Sites  (0, 0)

(no "Site" information available for 3JXY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3JXY)

(-) 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:231
 aligned with Q816E8_BACCR | Q816E8 from UniProtKB/TrEMBL  Length:237

    Alignment length:231
                             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     - -MHPFVKALQEHFTAHQNPEKAEPMARYMKNHFLFLGIQTPERRQLLKDIIQIHTLPDQKDFQIIIRELWDLPEREFQAAALDIMQKYKKHINETHIPFLEELIVTKSWWDSVDSIVPTFLGDIFLKHPELISAYIPKWIASDNIWLQRAAILFQLKYKQKMDEELLFWIIGQLHSSKEFFIQKAIGWVLREYAKTNPDVVWEYVQNNELAPLSKREAIKHIKQNYGINNE 230
               SCOP domains d3jxya_ A: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------DNA_alkylation-3jxyA01 A:8-221                                                                                                                                                                                        --------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhh..hhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jxy A   0 PMHPFVKALQEHFTAHQNPEKAEPMARYMKNHFLFLGIQTPERRQLLKDIIQIHTLPDQKDFQIIIRELWDLPEREFQAAALDIMQKYKKHINETHIPFLEELIVTKSWWDSVDSIVPTFLGDIFLKHPELISAYIPKWIASDNIWLQRAAILFQLKYKQKMDEELLFWIIGQLHSSKEFFIQKAIGWVLREYAKTNPDVVWEYVQNNELAPLSKREAIKHIKQNYGINNE 230
                                     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
                                            
                 3jxy B   1 CGGACTGACGGG  12
                                    10  


Chain C from PDB  Type:DNA  Length:12
                                            
                 3jxy C   1 CCCGTTAGTCCG  12
                                    10
   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)

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

(-) CATH Domains  (0, 0)

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

(-) 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 3JXY)

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  3jxy
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 Related Entries

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

UniProtKB/TrEMBL
        Q816E8_BACCR | Q816E8: 3bvs 3jx7 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 ALKYLPURING DNA GLYCOSYLASE ALKD
3jx7 BACILLUS CEREUS ALKYLPURINE DNA GLYCOSYLASE ALKD BOUND TO DNA CONTAINING A 3MA ANALOG
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)