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 

wwPDB Validation 3D Report Full Report



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: 10.1107/S2059798320010992
  • Primary Citation of Related Structures:  
    6M69, 6M65, 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 d ...

    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.


    Related Citations: 
    • Biochemical and structural studies of Mycobacterium smegmatis MutT1, a sanitization enzyme with unusual modes of association.
      Arif, S.M., Patil, A.G., Varshney, U., Vijayan, M.
      (2017) Acta Crystallogr D Struct Biol 73: 349
    • Hydrolysis of diadenosine polyphosphates. Exploration of an additional role of Mycobacterium smegmatis MutT1.
      Arif, S.M., Varshney, U., Vijayan, M.
      (2017) J Struct Biol 199: 165

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hydrolase, NUDIX family proteinA342Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_2390mutT1MSMEI_2330
EC: 3.6.1.69 (UniProt), 3.6.1.58 (UniProt), 3.6.1.61 (UniProt)
Find proteins for A0QUZ2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QUZ2 
Go to UniProtKB:  A0QUZ2
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8GD
Query on 8GD

Download CCD File 
A
2'-deoxy-8-oxoguanosine 5'-(trihydrogen diphosphate)
C10 H15 N5 O11 P2
LJMLTZSNWOCYNQ-VPENINKCSA-N
 Ligand Interaction
POP
Query on POP

Download CCD File 
A
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2020-10-14
    Type: Initial release