PDBsum entry 1s5v

Lyase

PDB id: 1s5v

Contents

Protein chains

292 a.a. *

Waters ×231

* Residue conservation analysis

PDB id:

1s5v

Name:

Lyase

Title:

Crystal structure analysis of a mutant of dihydrodipicolinate synthase--residue tyr107 to phe107

Structure:

Dihydrodipicolinate synthase. Chain: a, b. Synonym: dhdps. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: dapa. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.35Å R-factor: 0.197 R-free: 0.232

Authors:

R.C.J.Dobson,K.Valegard,J.A.Gerrard

Key ref:

R.C.Dobson et al. (2004). The crystal structure of three site-directed mutants of Escherichia coli dihydrodipicolinate synthase: further evidence for a catalytic triad. J Mol Biol, 338, 329-339. PubMed id: 15066435 DOI: 10.1016/j.jmb.2004.02.060

Date:

21-Jan-04 Release date: 27-Apr-04

Protein chains

P0A6L2  (DAPA_ECOLI) -  4-hydroxy-tetrahydrodipicolinate synthase from Escherichia coli (strain K12)

Seq: 292 a.a.

Struc: 292 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.4.3.3.7 - 4-hydroxy-tetrahydrodipicolinate synthase.
• Reaction: L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy-2,3,4,5- tetrahydrodipicolinate + H2O + H⁺

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

Added reference

DOI no: 10.1016/j.jmb.2004.02.060

J Mol Biol 338:329-339 (2004)

PubMed id: 15066435

The crystal structure of three site-directed mutants of Escherichia coli dihydrodipicolinate synthase: further evidence for a catalytic triad.

R.C.Dobson, K.Valegård, J.A.Gerrard.

ABSTRACT

Dihydrodipicolinate synthase (DHDPS, EC 4.2.1.52) catalyses the branchpoint reaction of lysine biosynthesis in plants and microbes: the condensation of (S)-aspartate-beta-semialdehyde and pyruvate. The crystal structure of wild-type DHDPS has been published to 2.5A, revealing a tetrameric molecule comprised of four identical (beta/alpha)(8)-barrels, each containing one active site. Previous workers have hypothesised that the catalytic mechanism of the enzyme involves a catalytic triad of amino acid residues, Tyr133, Thr44 and Tyr107, which provide a proton shuttle to transport protons from the active site to solvent. We have tested this hypothesis using site-directed mutagenesis to produce three mutant enzymes: DHDPS-Y133F, DHDPS-T44V and DHDPS-Y107F. Each of these mutants has substantially reduced activity, consistent with the catalytic triad hypothesis. We have determined each mutant crystal structure to at least 2.35A resolution and compared the structures to the wild-type enzyme. All mutant enzymes crystallised in the same space group as the wild-type form and only minor differences in structure are observed. These results suggest that the catalytic triad is indeed in operation in wild-type DHDPS.

Selected figure(s)

Figure 2.
Figure 2. Putative roles for the catalytic triad in the mechanism of DHDPS. This mechanism has been adapted from Hutton et al.[33.]

Figure 5.
Figure 5. Stereo-view showing overlays of the active sites of wild-type (black) and mutant DHDPS structures (gold). Electron density covers the mutated residue in each image and is contoured to 1s. Shown from top to bottom: a, DHDPS-Y133F; b, DHDPS-T44V; c, DHDPS-Y107F. The images were generated using O[31.] and Molray. [35.]

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 338, 329-339) copyright 2004.

Figures were selected by an automated process.