1YBA

The active form of phosphoglycerate dehydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Vmax Regulation through Domain and Subunit Changes. The Active Form of Phosphoglycerate Dehydrogenase

Thompson, J.R.Bell, J.K.Bratt, J.Grant, G.A.Banaszak, L.J.

(2005) Biochemistry 44: 5763-5773

  • DOI: 10.1021/bi047944b
  • Primary Citation of Related Structures:  
    1YBA

  • PubMed Abstract: 
  • An active conformation of phosphoglycerate dehydrogenase (PGDH) from Escherichia coli has been obtained using X-ray crystallography. The X-ray crystal structure is used to examine the potential intermediates for V(max) regulation, for the redox react ...

    An active conformation of phosphoglycerate dehydrogenase (PGDH) from Escherichia coli has been obtained using X-ray crystallography. The X-ray crystal structure is used to examine the potential intermediates for V(max) regulation, for the redox reaction, and for cooperative effects of serine binding. The crystal structure at 2.2 A resolution contains bound NAD(+) cofactor, either sulfate or phosphate anions, and alpha-ketoglutarate, a nonphysiological substrate. A PGDH subunit is formed from three distinct domains: regulatory (RBD), substrate (SBD), and nucleotide binding (NBD). The crystal conformation of the homotetramer points to the fact that, in the absence of serine, coordinated movement of the RBD-SBD domains occurs relative to the NBD. The result is a conformational change involving the steric relationships of both the domains and the subunits. Within the active site of each subunit is a bound molecule of alpha-ketoglutarate and the coenzyme, NAD. The catalytic or active site cleft is changed slightly although it is still solvent exposed; therefore, the catalytic reaction probably involves additional conformational changes. By comparing the inhibited with the uninhibited complex, it is possible to describe changes in conformation that are involved in the inhibitory signal transduction of serine.


    Related Citations: 
    • The allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase
      Schuller, D.J., Grant, G.A., Banaszak, L.J.
      (1995) Nat Struct Mol Biol 2: 69

    Organizational Affiliation

    Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D-3-phosphoglycerate dehydrogenaseABCD410Escherichia coliMutation(s): 8 
Gene Names: serA
EC: 1.1.1.95 (PDB Primary Data), 1.1.1.399 (UniProt)
Find proteins for P0A9T0 (Escherichia coli (strain K12))
Explore P0A9T0 
Go to UniProtKB:  P0A9T0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download CCD File 
A, B, C, D
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
AKG
Query on AKG

Download CCD File 
A, B, C, D
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A, B, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
UNL
Query on UNL

Download CCD File 
A, B, C, D
Unknown ligand
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,B,C,DL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.159α = 90
b = 76.159β = 90
c = 354.144γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-04-26
    Type: Initial release
  • Version 1.1: 2008-04-02
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance