4PZ9

The native structure of mycobacterial glucosyl-3-phosphoglycerate phosphatase Rv2419c


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mechanism of dephosphorylation of glucosyl-3-phosphoglycerate by a histidine phosphatase

Zheng, Q.Jiang, D.Zhang, W.Zhang, Q.Zhao, Q.Jin, J.Li, X.Yang, H.Bartlam, M.Shaw, N.Zhou, W.Rao, Z.

(2014) J.Biol.Chem. 289: 21242-21251

  • DOI: 10.1074/jbc.M114.569913
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mycobacterium tuberculosis (Mtb) synthesizes polymethylated polysaccharides that form complexes with long chain fatty acids. These complexes, referred to as methylglucose lipopolysaccharides (MGLPs), regulate fatty acid biosynthesis in vivo, includin ...

    Mycobacterium tuberculosis (Mtb) synthesizes polymethylated polysaccharides that form complexes with long chain fatty acids. These complexes, referred to as methylglucose lipopolysaccharides (MGLPs), regulate fatty acid biosynthesis in vivo, including biosynthesis of mycolic acids that are essential for building the cell wall. Glucosyl-3-phosphoglycerate phosphatase (GpgP, EC 5.4.2.1), encoded by Rv2419c gene, catalyzes the second step of the pathway for the biosynthesis of MGLPs. The molecular basis for this dephosphorylation is currently not understood. Here, we describe the crystal structures of apo-, vanadate-bound, and phosphate-bound MtbGpgP, depicting unliganded, reaction intermediate mimic, and product-bound views of MtbGpgP, respectively. The enzyme consists of a single domain made up of a central β-sheet flanked by α-helices on either side. The active site is located in a positively charged cleft situated above the central β-sheet. Unambiguous electron density for vanadate covalently bound to His(11), mimicking the phosphohistidine intermediate, was observed. The role of residues interacting with the ligands in catalysis was probed by site-directed mutagenesis. Arg(10), His(11), Asn(17), Gln(23), Arg(60), Glu(84), His(159), and Leu(209) are important for enzymatic activity. Comparison of the structures of MtbGpgP revealed conformational changes in a key loop region connecting β1 with α1. This loop regulates access to the active site. MtbGpgP functions as dimer. L209E mutation resulted in monomeric GpgP, rendering the enzyme incapable of dephosphorylation. The structures of GpgP reported here are the first crystal structures for histidine-phosphatase-type GpgPs. These structures shed light on a key step in biosynthesis of MGLPs that could be targeted for development of anti-tuberculosis therapeutics.


    Organizational Affiliation

    From the College of Life Sciences, Nankai University, Tianjin 300071, China.,From the College of Life Sciences, Nankai University, Tianjin 300071, China, zhouwh@nankai.edu.cn.,From the College of Life Sciences, Nankai University, Tianjin 300071, China, the National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China, the Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing 100084, China, and raozh@xtal.tsinghua.edu.cn.,the College of Life Sciences, Tianjin University, Tianjin 300073, China.,the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114.,From the College of Life Sciences, Nankai University, Tianjin 300071, China, the National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucosyl-3-phosphoglycerate phosphatase
A, B
223Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)Mutation(s): 0 
Gene Names: gpgP
EC: 3.1.3.85
Find proteins for P9WIC6 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Go to UniProtKB:  P9WIC6
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.309α = 90.00
b = 77.091β = 90.00
c = 126.484γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASESphasing
HKL-2000data collection
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-11
    Type: Initial release
  • Version 1.1: 2014-10-29
    Type: Database references