Vmax regulation through domain and subunit changes. The active form of phosphoglycerate dehydrogenase

Biochemistry. 2005 Apr 19;44(15):5763-73. doi: 10.1021/bi047944b.

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 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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Carbohydrate Dehydrogenases / chemistry*
  • Carbohydrate Dehydrogenases / genetics
  • Carbohydrate Dehydrogenases / metabolism*
  • Catalytic Domain
  • Crystallography, X-Ray
  • Enzyme Activation
  • Escherichia coli / enzymology
  • Escherichia coli / genetics
  • Kinetics
  • Models, Molecular
  • Oxidation-Reduction
  • Phosphoglycerate Dehydrogenase
  • Protein Conformation
  • Protein Structure, Quaternary
  • Protein Structure, Tertiary
  • Protein Subunits
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Serine / chemistry

Substances

  • Protein Subunits
  • Recombinant Proteins
  • Serine
  • Carbohydrate Dehydrogenases
  • Phosphoglycerate Dehydrogenase

Associated data

  • PDB/1PSD
  • PDB/1YBA