2AF6

Crystal structure of Mycobacterium tuberculosis Flavin dependent thymidylate synthase (Mtb ThyX) in the presence of co-factor FAD and substrate analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (BrdUMP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the Mycobacterium tuberculosis Flavin Dependent Thymidylate Synthase (MtbThyX) at 2.0A Resolution.

Sampathkumar, P.Turley, S.Ulmer, J.E.Rhie, H.G.Sibley, C.H.Hol, W.G.

(2005) J Mol Biol 352: 1091-1104

  • DOI: 10.1016/j.jmb.2005.07.071
  • Primary Citation of Related Structures:  
    2AF6

  • PubMed Abstract: 
  • A novel flavin-dependent thymidylate synthase was identified recently as an essential gene in many archaebacteria and some pathogenic eubacteria. This enzyme, ThyX, is a potential antibacterial drug target, since humans and most eukaryotes lack the thyX gene and depend upon the conventional thymidylate synthase (TS) for their dTMP requirements ...

    A novel flavin-dependent thymidylate synthase was identified recently as an essential gene in many archaebacteria and some pathogenic eubacteria. This enzyme, ThyX, is a potential antibacterial drug target, since humans and most eukaryotes lack the thyX gene and depend upon the conventional thymidylate synthase (TS) for their dTMP requirements. We have cloned and overexpressed the thyX gene (Rv2754c) from Mycobacterium tuberculosis in Escherichia coli. The M.tuberculosis ThyX (MtbThyX) enzyme complements the E.coli chi2913 strain that lacks its conventional TS activity. The crystal structure of the homotetrameric MtbThyX was determined in the presence of the cofactor FAD and the substrate analog, 5-bromo-2'-deoxyuridine-5'-monophosphate (BrdUMP). In the active site, which is formed by three monomers, FAD is bound in an extended conformation with the adenosine ring in a deep pocket and BrdUMP in a closed conformation near the isoalloxazine ring. Structure-based mutational studies have revealed a critical role played by residues Lys165 and Arg168 in ThyX activity, possibly by governing access to the carbon atom to be methylated of a totally buried substrate dUMP.


    Organizational Affiliation

    Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thymidylate synthase thyXA, B, C, D, E, F, G, H258Mycobacterium tuberculosisMutation(s): 5 
Gene Names: thyX
EC: 2.1.1.148
UniProt
Find proteins for P9WG57 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WG57 
Go to UniProtKB:  P9WG57
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
FA [auth E], K [auth A], LA [auth F], P [auth B], QA [auth G], TA [auth H], U [auth C], Z [auth D]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
BRU
Query on BRU

Download Ideal Coordinates CCD File 
AA [auth D], GA [auth E], L [auth A], MA [auth F], Q [auth B], RA [auth G], UA [auth H], V [auth C]5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
C9 H12 Br N2 O8 P
LHLHVDBXXZVYJT-RRKCRQDMSA-N
 Ligand Interaction
IOD
Query on IOD

Download Ideal Coordinates CCD File 
DA [auth E] , EA [auth E] , I [auth A] , J [auth A] , JA [auth F] , KA [auth F] , PA [auth G] , T [auth C] , 
DA [auth E],  EA [auth E],  I [auth A],  J [auth A],  JA [auth F],  KA [auth F],  PA [auth G],  T [auth C],  X [auth D],  Y [auth D]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth D] , CA [auth D] , HA [auth E] , IA [auth E] , M [auth A] , N [auth A] , NA [auth F] , O [auth A] , 
BA [auth D],  CA [auth D],  HA [auth E],  IA [auth E],  M [auth A],  N [auth A],  NA [auth F],  O [auth A],  OA [auth F],  R [auth B],  S [auth B],  SA [auth G],  VA [auth H],  W [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, HL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.09α = 90
b = 78.3β = 96.8
c = 168.72γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-04
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance