3A6U

Crystal structure of MutT-8-OXO-dGMP-MN(II) complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and dynamic features of the MutT protein in the recognition of nucleotides with the mutagenic 8-oxoguanine base

Nakamura, T.Meshitsuka, S.Kitagawa, S.Abe, N.Yamada, J.Ishino, T.Nakano, H.Tsuzuki, T.Doi, T.Kobayashi, Y.Fujii, S.Sekiguchi, M.Yamagata, Y.

(2010) J Biol Chem 285: 444-452

  • DOI: 10.1074/jbc.M109.066373
  • Primary Citation of Related Structures:  
    3A6S, 3A6T, 3A6U, 3A6V

  • PubMed Abstract: 
  • Escherichia coli MutT hydrolyzes 8-oxo-dGTP to 8-oxo-dGMP, an event that can prevent the misincorporation of 8-oxoguanine opposite adenine in DNA. Of the several enzymes that recognize 8-oxoguanine, MutT exhibits high substrate specificity for 8-oxog ...

    Escherichia coli MutT hydrolyzes 8-oxo-dGTP to 8-oxo-dGMP, an event that can prevent the misincorporation of 8-oxoguanine opposite adenine in DNA. Of the several enzymes that recognize 8-oxoguanine, MutT exhibits high substrate specificity for 8-oxoguanine nucleotides; however, the structural basis for this specificity is unknown. The crystal structures of MutT in the apo and holo forms and in the binary and ternary forms complexed with the product 8-oxo-dGMP and 8-oxo-dGMP plus Mn(2+), respectively, were determined. MutT strictly recognizes the overall conformation of 8-oxo-dGMP through a number of hydrogen bonds. This recognition mode revealed that 8-oxoguanine nucleotides are discriminated from guanine nucleotides by not only the hydrogen bond between the N7-H and Odelta (N119) atoms but also by the syn glycosidic conformation that 8-oxoguanine nucleotides prefer. Nevertheless, these discrimination factors cannot by themselves explain the roughly 34,000-fold difference between the affinity of MutT for 8-oxo-dGMP and dGMP. When the binary complex of MutT with 8-oxo-dGMP is compared with the ligand-free form, ordering and considerable movement of the flexible loops surrounding 8-oxo-dGMP in the binary complex are observed. These results indicate that MutT specifically recognizes 8-oxoguanine nucleotides by the ligand-induced conformational change.


    Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mutator mutT proteinA129Escherichia coli K-12Mutation(s): 0 
Gene Names: mutTb0099JW0097
EC: 3.6.1 (PDB Primary Data), 3.6.1.55 (UniProt)
Find proteins for P08337 (Escherichia coli (strain K12))
Explore P08337 
Go to UniProtKB:  P08337
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8OG
Query on 8OG

Download CCD File 
A
8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
AQIVLFLYHYFRKU-VPENINKCSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MN
Query on MN

Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.234α = 90
b = 56.003β = 90
c = 59.339γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance