1N5I

CRYSTAL STRUCTURE OF INACTIVE MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP) AT PH 4.6 (RESOLUTION 1.85 A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

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This is version 1.4 of the entry. See complete history


Literature

Mycobacterium tuberculosis Thymidylate Kinase: Structural Studies of Intermediates along the Reaction Pathway

Fioravanti, E.Haouz, A.Ursby, T.Munier-Lehmann, H.Delarue, M.Bourgeois, D.

(2003) J Mol Biol 327: 1077-1092

  • DOI: 10.1016/s0022-2836(03)00202-x
  • Primary Citation of Related Structures:  
    1N5I, 1N5J, 1N5K, 1N5L

  • PubMed Abstract: 
  • Mycobacterium tuberculosis TMP kinase (TMPK(Mtub)) represents a promising target for developing drugs against tuberculosis because the configuration of its active site is unique in the TMPK family. To help elucidate the phosphorylation mechanism employed by this enzyme, structural changes occurring upon binding of substrates and subsequent catalysis were investigated by protein crystallography ...

    Mycobacterium tuberculosis TMP kinase (TMPK(Mtub)) represents a promising target for developing drugs against tuberculosis because the configuration of its active site is unique in the TMPK family. To help elucidate the phosphorylation mechanism employed by this enzyme, structural changes occurring upon binding of substrates and subsequent catalysis were investigated by protein crystallography. Six new structures of TMPK(Mtub) were solved at a resolution better than 2.3A, including the first structure of an apo-TMPK, obtained by triggering catalysis in a crystal of a TMPK(Mtub)-TMP complex, which resulted in the release of the TDP product. A series of snapshots along the reaction pathway is obtained, revealing the closure of the active site in going from an empty to a fully occupied state, suggestive of an induced-fit mechanism typical of NMPKs. However, in TMPK(Mtub) the LID closure couples to the binding with an unusual location for a magnesium ion coordinating TMP in the active site. Our data suggest strongly that this ion is required for catalysis, acting as a clamp, possibly in concert with Arg95, to neutralise electrostatic repulsion between the anionic substrates, optimise their proper alignment and activate them through direct and water-mediated interactions. The 3'-hydroxyl moiety of TMP, critical to metal stabilisation, appears to be a target of choice for the design of potent inhibitors. On the other hand, the usual NTP-bound magnesium is not seen in our structures and Arg14, a P-loop residue unique to TMPK(Mtub), may take over its role. Therefore, TMPK(Mtub) seems to have swapped the use of a metal ion as compared with e.g. human TMPK. Finally, TTP was observed in crystals of TMPK(Mtub), locked by Arg14, thus providing a structural explanation for the observed inhibitory effect of TTP putatively involved in a mechanism of feedback regulation of the enzymatic activity.


    Related Citations: 
    • Cryo-Photolysis of Caged Compounds: A Technique for Trapping Intermediate States in Protein Crystals
      Ursby, T., Weik, M., Fioravanti, E., Delarue, M., Goeldner, M., Bourgeois, D.
      (2002) Acta Crystallogr D Biol Crystallogr 58: 607
    • X-Ray Structure of Tmp Kinase from Mycobacterium Tuberculosis Complexed with Tmp at 1.95 A Resolution
      Li De La Sierra, I., Munier-Lehmann, H., Gilles, A.M., Barzu, O., Delarue, M.
      (2001) J Mol Biol 311: 87
    • Crystallization and Preliminary X-Ray Analysis of the Thymidylate Kinase from Mycobacterium Tuberculosis
      Li De La Sierra, I., Munier-Lehmann, H., Gilles, A.M., Barzu, O., Delarue, M.
      (2000) Acta Crystallogr D Biol Crystallogr 56: 226

    Organizational Affiliation

    LCCP, UMR 9015, IBS, 41 avenue Jules Horowitz, 38027 1, Grenoble, Cedex, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
THYMIDYLATE KINASEA214Mycobacterium tuberculosisMutation(s): 0 
EC: 2.7.4.9
UniProt
Find proteins for P9WKE1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WKE1 
Go to UniProtKB:  P9WKE1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WKE1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
F [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
TMP
Query on TMP

Download Ideal Coordinates CCD File 
E [auth A]THYMIDINE-5'-PHOSPHATE
C10 H15 N2 O8 P
GYOZYWVXFNDGLU-XLPZGREQSA-N
 Ligand Interaction
FLC
Query on FLC

Download Ideal Coordinates CCD File 
D [auth A]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.51α = 90
b = 75.51β = 90
c = 136.02γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
CNSrefinement
CCP4data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-08
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-05-10
    Changes: Other
  • Version 1.4: 2018-01-31
    Changes: Experimental preparation