Macromolecule Content

• Total Structure Weight: 12.34 kDa 
• Atom Count: 811 
• Modelled Residue Count: 102 
• Deposited Residue Count: 108 
• Unique protein chains: 1

2KIF

Solution NMR structure of an O6-methylguanine DNA methyltransferase family protein from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium target VpR247.

• DOI: 10.2210/pdb2KIF/pdb
• BMRB: 16272

• Classification: TRANSFERASE
• Organism(s): Vibrio parahaemolyticus AQ3810
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-05-03 Released: 2009-06-30 
• Deposition Author(s): Aramini, J.M., Belote, R.L., Ciccosanti, C.T., Jiang, M., Rost, B., Nair, R., Swapna, G.V.T., Acton, T.B., Xiao, R., Everett, J.K., Montelione, G.T., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Structural basis of O6-alkylguanine recognition by a bacterial alkyltransferase-like DNA repair protein.

Aramini, J.M., Tubbs, J.L., Kanugula, S., Rossi, P., Ertekin, A., Maglaqui, M., Hamilton, K., Ciccosanti, C.T., Jiang, M., Xiao, R., Soong, T.T., Rost, B., Acton, T.B., Everett, J.K., Pegg, A.E., Tainer, J.A., Montelione, G.T.

(2010) J Biol Chem 285: 13736-13741

• PubMed: 20212037 
• DOI: 10.1074/jbc.M109.093591
• Primary Citation of Related Structures:  
  2KIF


• PubMed Abstract: 
  

Alkyltransferase-like proteins (ATLs) are a novel class of DNA repair proteins related to O(6)-alkylguanine-DNA alkyltransferases (AGTs) that tightly bind alkylated DNA and shunt the damaged DNA into the nucleotide excision repair pathway. Here, we present the first structure of a bacterial ATL, from Vibrio parahaemolyticus (vpAtl). We demonstrate that vpAtl adopts an AGT-like fold and that the protein is capable of tightly binding to O(6)-methylguanine-containing DNA and disrupting its repair by human AGT, a hallmark of ATLs. Mutation of highly conserved residues Tyr(23) and Arg(37) demonstrate their critical roles in a conserved mechanism of ATL binding to alkylated DNA. NMR relaxation data reveal a role for conformational plasticity in the guanine-lesion recognition cavity. Our results provide further evidence for the conserved role of ATLs in this primordial mechanism of DNA repair.

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Organizational Affiliation: 

Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O6-methylguanine-DNA methyltransferase	A	108	Vibrio parahaemolyticus AQ3810	Mutation(s): 0  Gene Names: A79_1377, VP0951, D030_1023
UniProt
Find proteins for A6B4U8 (Vibrio parahaemolyticus serotype O3:K6 (strain AQ3810)) Explore A6B4U8  Go to UniProtKB:  A6B4U8

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2KIF Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-05-03 
• Released Date: 2009-06-30 
Deposition Author(s): Aramini, J.M., Belote, R.L., Ciccosanti, C.T., Jiang, M., Rost, B., Nair, R., Swapna, G.V.T., Acton, T.B., Xiao, R., Everett, J.K., Montelione, G.T., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2009-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance