5XD5

Crystal structure of Mycobacterium smegmatis MutT1 in complex with ATP, magnesium fluoride and phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

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


Literature

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: 165-176

  • DOI: https://doi.org/10.1016/j.jsb.2017.07.002
  • Primary Citation of Related Structures:  
    5XD1, 5XD2, 5XD3, 5XD4, 5XD5

  • PubMed Abstract: 

    Diadenosine polyphosphates (Ap n A, n=2-6), particularly Ap 4 A, are involved in several important physiological processes. The substantial sequence identity of the Nudix hydrolase domain (domain 1) of Mycobacterium smegmatis MutT1 (MsMutT1) with a known Ap 4 A hydrolase suggested that MsMutT1 could also hydrolyse diadenosine polyphosphates. Biochemical experiments yielded results in conformity with this suggestion, with Ap 4 A as the best among the substrates. ATP is a product in all experiments; small amounts of ADP were also observed in the experiments involving Ap 4 A and Ap 6 A. Hydrolysis was inhibited by fluoride ions in all cases. The mechanism of action and its inhibition in relation to Ap n A were explored through the X-ray analysis of the crystals of the MsMutT1 complexes with Ap 5 A; Ap 5 A and MnCl 2 ; Ap 4 A; ATP; and ATP.NaF.MgCl 2 . The aggregation pattern of molecules in the first four crystals is similar to that found in a majority of MsMutT1-NTP crystals. Substrate molecules occupy the primary binding site and ATP occupies a site at an intermolecular interface, in the first two. ATP occupies both the sites in the third and fourth crystal. The protein-ligand interactions observed in these crystal structures lead to an explanation of the molecular mechanism of hydrolysis of Ap n A by MsMutT1. The fifth crystal exhibits a new packing arrangement. The structure of the complex provides an explanation for the fluoride inhibition of the activity of the enzyme. It would thus appear that MutT1 has a major role involving the hydrolysis of diadenosine polyphosphates, which could be elucidated at the molecular level.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hydrolase, NUDIX family proteinA [auth B],
B [auth A]
342Mycolicibacterium 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
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
C [auth B],
S [auth A]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
D [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

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E [auth B]
F [auth B]
G [auth B]
H [auth B]
T [auth A]
E [auth B],
F [auth B],
G [auth B],
H [auth B],
T [auth A],
U [auth A],
V [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

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DA [auth A]
EA [auth A]
FA [auth A]
GA [auth A]
P [auth B]
DA [auth A],
EA [auth A],
FA [auth A],
GA [auth A],
P [auth B],
Q [auth B],
R [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth B]
J [auth B]
K [auth B]
L [auth B]
W [auth A]
I [auth B],
J [auth B],
K [auth B],
L [auth B],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
F
Query on F

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
CA [auth A]
M [auth B]
N [auth B]
AA [auth A],
BA [auth A],
CA [auth A],
M [auth B],
N [auth B],
O [auth B]
FLUORIDE ION
F
KRHYYFGTRYWZRS-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.05α = 90
b = 64.44β = 102.59
c = 103.04γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata processing
SCALAdata scaling
PHASERphasing
iMOSFLMdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description