1YGY

Crystal Structure of D-3-Phosphoglycerate dehydrogenase From Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystal Structure of Mycobacterium tuberculosis D-3-Phosphoglycerate Dehydrogenase: EXTREME ASYMMETRY IN A TETRAMER OF IDENTICAL SUBUNITS

Dey, S.Grant, G.A.Sacchettini, J.C.

(2005) J Biol Chem 280: 14892-14899

  • DOI: 10.1074/jbc.M414489200
  • Primary Citation of Related Structures:  
    1YGY

  • PubMed Abstract: 
  • Phosphoglycerate dehydrogenases exist in at least three different structural motifs. The first D-3-phosphoglycerate dehydrogenase structure to be determined was from Escherichia coli and is a tetramer composed of identical subunits that contain three discernable structural domains ...

    Phosphoglycerate dehydrogenases exist in at least three different structural motifs. The first D-3-phosphoglycerate dehydrogenase structure to be determined was from Escherichia coli and is a tetramer composed of identical subunits that contain three discernable structural domains. The crystal structure of D-3-phosphoglycerate dehydrogenase from Mycobacterium tuberculosis has been determined at 2.3 A. This enzyme represents a second structural motif of the D-3-phosphoglycerate dehydrogenase family, one that contains an extended C-terminal region. This structure is also a tetramer of identical subunits, and the extended motif of 135 amino acids exists as a fourth structural domain. This intervening domain exerts quite a surprising characteristic to the structure by introducing significant asymmetry in the tetramer. The asymmetric unit is composed of two identical subunits that exist in two different conformations characterized by rotation of approximately 180 degrees around a hinge connecting two of the four domains. This asymmetric arrangement results in the formation of two different and distinct domain interfaces between identical domains in the asymmetric unit. As a result, the surface of the intervening domain that is exposed to solvent in one subunit is turned inward in the other subunit toward the center of the structure where it makes contact with other structural elements. Significant asymmetry is also seen at the subunit level where different conformations exist at the NAD-binding site and the putative serine-binding site in the two unique subunits.


    Related Citations: 
    • D-3-Phosphoglycerate Dehydrogenase from Mycobacterium tuberculosis Is a Link between the Escherichia coli and Mammalian Enzymes
      Dey, S., Hu, Z., Xu, X.L., Sacchettini, J.C., Grant, G.A.
      (2005) J Biol Chem 280: 14884

    Organizational Affiliation

    Department of Biochemistry & Biophysics, Texas A & M University, College Station, Texas 77843, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D-3-phosphoglycerate dehydrogenaseA, B529Mycobacterium tuberculosisMutation(s): 0 
Gene Names: serA1
EC: 1.1.1.95 (PDB Primary Data), 1.1.1.399 (UniProt)
Find proteins for P9WNX3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WNX3 
Go to UniProtKB:  P9WNX3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TLA
Query on TLA

Download Ideal Coordinates CCD File 
C [auth A], D [auth B], E [auth B]L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 165.513α = 90
b = 165.513β = 90
c = 218.144γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-01-25
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Derived calculations, Version format compliance
  • Version 2.0: 2019-07-10
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary