6M72

Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-dGDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Plasticity, ligand conformation and enzyme action of Mycobacterium smegmatis MutT1.

Raj, P.Karthik, S.Arif, S.M.Varshney, U.Vijayan, M.

(2020) Acta Crystallogr D Struct Biol 76: 982-992

  • DOI: https://doi.org/10.1107/S2059798320010992
  • Primary Citation of Related Structures:  
    6M65, 6M69, 6M6Y, 6M72

  • PubMed Abstract: 

    Mycobacterium smegmatis MutT1 (MsMutT1) is a sanitation enzyme made up of an N-terminal Nudix hydrolase domain and a C-terminal domain resembling a histidine phosphatase. It has been established that the action of MutT1 on 8-oxo-dGTP, 8-oxo-GTP and diadenosine polyphosphates is modulated by intermolecular interactions. In order to further explore this and to elucidate the structural basis of its differential action on 8-oxo-NTPs and unsubstituted NTPs, the crystal structures of complexes of MsMutT1 with 8-oxo-dGTP, GMPPNP and GMPPCP have been determined. Replacement soaking was used in order to ensure that the complexes were isomorphous to one another. Analysis of the structural data led to the elucidation of a relationship between the arrangements of molecules observed in the crystals, molecular plasticity and the action of the enzyme on nucleotides. The dominant mode of arrangement involving a head-to-tail sequence predominantly leads to the generation of NDPs. The other mode of packing arrangement appears to preferentially generate NMPs. This work also provides interesting insights into the dependence of enzyme action on the conformation of the ligand. The possibility of modulating the enzyme action through differences in intermolecular interactions and ligand conformations makes MsMutT1 a versatile enzyme.


  • Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560 012, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hydrolase, NUDIX family protein342Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_2390
EC: 3.6.1.61 (UniProt), 3.6.1.69 (UniProt), 3.6.1.58 (UniProt)
UniProt
Find proteins for A0QUZ2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QUZ2 
Go to UniProtKB:  A0QUZ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0QUZ2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 192.029α = 90
b = 37.09β = 90
c = 44.65γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)IndiaBT/PR20529/BRB/10/1525/2016

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-14
    Type: Initial release
  • Version 1.1: 2020-10-28
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Advisory, Data collection, Database references, Refinement description