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(-) Description

Title :  BACILLUS CEREUS DNA GLYCOSYLASE ALKD BOUND TO 7-METHYLGUANINE NUCLEOBASE AND DNA CONTAINING AN OXOCARBENIUM-INTERMEDIATE ANALOG
 
Authors :  E. A. Mullins, B. F. Eichman
Date :  13 Jul 16  (Deposition) - 14 Sep 16  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Dna Glycosylase, Protein-Dna Complex, Heat-Like Repeat, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. D. Parsons, J. M. Bland, E. A. Mullins, B. F. Eichman
A Catalytic Role For C-H/ Pi Interactions In Base Excision Repair By Bacillus Cereus Dna Glycosylase Alkd.
J. Am. Chem. Soc. V. 138 11485 2016
PubMed-ID: 27571247  |  Reference-DOI: 10.1021/JACS.6B07399

(-) Compounds

Molecule 1 - DNA-7-METHYLGUANINE GLYCOSYLASE
    Atcc: 14579
    Chains: A
    EC Number: 3.2.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBG103
    Expression System Strain: HMS174
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BCERE0015_46090
    Organism Scientific: BACILLUS CEREUS
    Organism Taxid: 1396
    Synonym: ALKD
 
Molecule 2 - DNA (5'-D(*CP*CP*CP*GP*AP*(NRI)P*AP*GP*TP*CP*CP*G)-3')
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*CP*GP*GP*AP*CP*TP*CP*TP*CP*GP*GP*G)-3')
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1MY61Ligand/Ion2-AMINO-7-METHYL-1,7-DIHYDRO-6H-PURIN-6-ONE
2NRI1Mod. NucleotidePHOSPHORIC ACID MONO-(4-HYDROXY-PYRROLIDIN-3-YLMETHYL)ESTER

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:27 , DA B:5 , NRI B:6 , DA B:7 , DT C:6 , DC C:7 , DT C:8binding site for residue MY6 B 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KUB)

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 Sequence-Structure Mapping

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(-) 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    
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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
                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhh.hhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kub A  -1 VPMHPFVKALQEHFTAHQNPEKAEPMARYMKNHFLFLGIQTPERRQLLKDIIQIHTLPDQKDFQIIIRELWDLPEREFQAAALDIMQKYKKHINETHIPFLEELIVTKSWWDSVDSIVPTFLGDIFLKHPELISAYIPKWIASDNIWLQRAAILFQLKYKQKMDEELLFWIIGQLHSSKEFFIQKAIGWVLREYAKTNPDVVWEYVQNNELAPLSKREAIKHIKQNYGINN 229
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228 


Chain B from PDB  Type:DNA  Length:12
                                            
                 5kub B   1 CCCGAxAGTCCG  12
                                 |  10  
                                 6-NRI  


Chain C from PDB  Type:DNA  Length:12
                                            
                 5kub C   1 CGGACTCTCGGG  12
                                    10
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 Classification and Annotation

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(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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 Related Entries

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UniProtKB/TrEMBL
        Q816E8_BACCR | Q816E8: 3bvs 3jx7 3jxy 3jxz 3jy1 5cl3 5cl4 5cl5 5cl6 5cl7 5cl8 5cl9 5cla 5clb 5clc 5cld 5cle

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