PDBsum entry: 2ojp

Lyase

PDB id: 2ojp

Contents

Protein chains

292 a.a. *

Ligands

GOL ×2

Waters ×793

* Residue conservation analysis

PDB id:

2ojp

Name:

Lyase

Title:

The crystal structure of a dimeric mutant of dihydrodipicoli synthase from e.Coli- dhdps-l197y

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:

1.70Å R-factor: 0.186 R-free: 0.228

Authors:

M.D.W.Griffin,R.C.J.Dobson,L.Antonio,M.A.Perugini,G.B.Jameso J.A.Gerrard

Key ref:

M.D.Griffin et al. (2008). Evolution of quaternary structure in a homotetrameric enzyme. J Mol Biol, 380, 691-703. PubMed id: 18556019 DOI: 10.1016/j.jmb.2008.05.038

Date:

13-Jan-07 Release date: 01-Jan-08

Protein chains

P0A6L2  (DAPA_ECOLI) -  Dihydrodipicolinate synthase

Seq: 292 a.a.

Struc: 292 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.4.2.1.52 - Dihydrodipicolinate synthase.
• Pathway: Lysine biosynthesis (early stages)
• Reaction: L-aspartate 4-semialdehyde + pyruvate = dihydrodipicolinate + 2 H₂O

L-aspartate 4-semialdehyde + pyruvate (Bound ligand (Het Group name = GOL) matches with 71.43% similarity) = dihydrodipicolinate + 2 × H(2)O

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (2 terms)
• Biological process: metabolic process (5 terms)
• Biochemical function: catalytic activity (3 terms)

reference

DOI no: 10.1016/j.jmb.2008.05.038

J Mol Biol 380:691-703 (2008)

PubMed id: 18556019

Evolution of quaternary structure in a homotetrameric enzyme.

M.D.Griffin, R.C.Dobson, F.G.Pearce, L.Antonio, A.E.Whitten, C.K.Liew, J.P.Mackay, J.Trewhella, G.B.Jameson, M.A.Perugini, J.A.Gerrard.

ABSTRACT

Dihydrodipicolinate synthase (DHDPS) is an essential enzyme in (S)-lysine biosynthesis and an important antibiotic target. All X-ray crystal structures solved to date reveal a homotetrameric enzyme. In order to explore the role of this quaternary structure, dimeric variants of Escherichia coli DHDPS were engineered and their properties were compared to those of the wild-type tetrameric form. X-ray crystallography reveals that the active site is not disturbed when the quaternary structure is disrupted. However, the activity of the dimeric enzymes in solution is substantially reduced, and a tetrahedral adduct of a substrate analogue is observed to be trapped at the active site in the crystal form. Remarkably, heating the dimeric enzymes increases activity. We propose that the homotetrameric structure of DHDPS reduces dynamic fluctuations present in the dimeric forms and increases specificity for the first substrate, pyruvate. By restricting motion in a key catalytic motif, a competing, non-productive reaction with a substrate analogue is avoided. Small-angle X-ray scattering and mutagenesis data, together with a B-factor analysis of the crystal structures, support this hypothesis and lead to the suggestion that in at least some cases, the evolution of quaternary enzyme structures might serve to optimise the dynamic properties of the protein subunits.

Selected figure(s)

Figure 3.
Fig. 3. The active site of DHDPS-L197Y contains a trapped covalent adduct. (a) Superposition of the active sites of wild-type DHDPS (grey) and DHDPS-L197Y (yellow) indicate that no significant structural changes were present in the active site of DHDPS-L197Y in the crystalline state. (b) Stereo representation of the tetrahedral electron density present at the active-site Lys161 in DHDPS-L197Y. A cyclic, covalent adduct formed between Lys161 and α-ketoglutarate has been modelled into the active site. 2F[o] − F[c] electron density is contoured at 1 σ (blue) and F[o] − F[c] electron density is contoured at 3 σ (green) and − 3 σ (red). (For omit map see Supplementary Information.) (c) The formation of the cyclic α-ketoglutarate adduct proceeds via formation of a linear Schiff base with Lys161.

Figure 5.
Fig. 5. Details of the active site of heat-activated DHDPS-Y107F. (a) Density at the active-site residue Lys161 is consistent with the presence of α-ketoglutarate in both linear (yellow) and cyclised (grey) forms. The occupancy of the two conformers (cyclic and acyclic) was set to 0.5 during model building. (b) Stereo representation of the electron density at the active site. The 2F[o] − F[c] map (blue) is contoured at 1 σ, and the F[o] − F[c] maps are contoured at 3 σ (green) and 3 σ (red).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 380, 691-703) copyright 2008.

Figures were selected by an automated process.