PDBsum entry 1ebf

Oxidoreductase

PDB id: 1ebf

Contents

Protein chains

358 a.a. *

Ligands

NAD

Metals

_NA ×2

Waters ×253

* Residue conservation analysis

PDB id:

1ebf

Name:

Oxidoreductase

Title:

Homoserine dehydrogenase from s. Cerevisiae complex with NAD+

Structure:

Homoserine dehydrogenase. Chain: a, b. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: hom6p. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.30Å R-factor: 0.218 R-free: 0.269

Authors:

B.Delabarre,P.R.Thompson,G.D.Wright,A.M.Berghuis

Key ref:

B.DeLaBarre et al. (2000). Crystal structures of homoserine dehydrogenase suggest a novel catalytic mechanism for oxidoreductases. Nat Struct Biol, 7, 238-244. PubMed id: 10700284 DOI: 10.1038/73359

Date:

24-Jan-00 Release date: 08-Mar-00

Protein chains

P31116  (DHOM_YEAST) -  Homoserine dehydrogenase from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 359 a.a.

Struc: 358 a.a.

Enzyme reactions

• Enzyme class: E.C.1.1.1.3 - homoserine dehydrogenase.
• Pathway: Threonine Biosynthesis
• Reaction:
  1. L-homoserine + NAD⁺ = L-aspartate 4-semialdehyde + NADH + H⁺
  2. L-homoserine + NADP⁺ = L-aspartate 4-semialdehyde + NADPH + H⁺

L-homoserine + NAD(+) (Bound ligand (Het Group name = NAD) corresponds exactly) = L-aspartate 4-semialdehyde + NADH + H(+)

L-homoserine + NADP(+) (Bound ligand (Het Group name = NAD) matches with 91.67% similarity) = L-aspartate 4-semialdehyde + NADPH + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/73359

Nat Struct Biol 7:238-244 (2000)

PubMed id: 10700284

Crystal structures of homoserine dehydrogenase suggest a novel catalytic mechanism for oxidoreductases.

B.DeLaBarre, P.R.Thompson, G.D.Wright, A.M.Berghuis.

ABSTRACT

The structure of the antifungal drug target homoserine dehydrogenase (HSD) was determined from Saccharomyces cerevisiae in apo and holo forms, and as a ternary complex with bound products, by X-ray diffraction. The three forms show that the enzyme is a dimer, with each monomer composed of three regions, the nucleotide-binding region, the dimerization region and the catalytic region. The dimerization and catalytic regions have novel folds, whereas the fold of the nucleotide-binding region is a variation on the Rossmann fold. The novel folds impose a novel composition and arrangement of active site residues when compared to all other currently known oxidoreductases. This observation, in conjunction with site-directed mutagenesis of active site residues and steady-state kinetic measurements, suggest that HSD exhibits a new variation on dehydrogenase chemistry.

Selected figure(s)

Figure 1.
Figure 1. Electron density maps for the two crystal forms of HSD. a, Stereo view of a 2F[o]- F[c] electron density map calculated with coefficients from the final tetragonal crystal form model and contoured at 1 . The portion of the molecule shown here is the dimer interfacial region of the extended -sheet and is composed of residues 320 -335 from monomer A, and residues 332 -335 and 319 -325 from monomer B. b, Stereo view of the F[o]- F[c] simulated annealing omit map for the NAD^+ molecule in the tetragonal crystal form, contoured at 2 . c, Stereo view of the F[o]- F[c] simulated annealing omit map for the NADA and l-Hse molecules in the monoclinic crystal form, contoured at 2 .

Figure 5.
Figure 5. Proposed reaction mechanisms of hydride transfer for HSD. a, Probable reaction mechanism for the forward direction with the substrate in the aldehyde form. Asp 214, Glu 208 and Wat460 serve to bind the substrate, whereas Lys 223, oriented by Asp 219, donates a proton to the C4 oxygen of l-ASA. The cofactor NADH delivers its pro-S hydride to the C4 carbon of l-ASA. Arrows indicate electron flow. b, Alternative reaction mechanism for the forward direction with the substrate in the gem-diol form. The main difference from the reaction proposed for the aldehyde form is that Lys 223 donates a proton to the hydroxyl group, which departs as a water molecule, and Asp 219 hydrogen bonds to the hydroxyl group, which remains in the product alcohol.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2000, 7, 238-244) copyright 2000.

Figures were selected by an automated process.