PDBsum entry 3i7s

Lyase

PDB id: 3i7s

Contents

Protein chains

292 a.a. *

Ligands

GOL ×8

PYR ×2

PO4 ×3

Metals

__K ×6

Waters ×170

* Residue conservation analysis

PDB id:

3i7s

Name:

Lyase

Title:

Dihydrodipicolinate synthase mutant - k161a - with the substrate pyruvate bound in the active site.

Structure:

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

Source:

Escherichia coli k-12. Organism_taxid: 83333. Gene: b2478, dapa, jw2463. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.30Å R-factor: 0.198 R-free: 0.236

Authors:

R.C.J.Dobson,G.B.Jameson,J.A.Gerrard,T.P.Soares Da Costa

Key ref:

T.P.Soares da Costa et al. (2010). How essential is the 'essential' active-site lysine in dihydrodipicolinate synthase? Biochimie, 92, 837-845. PubMed id: 20353808

Date:

08-Jul-09 Release date: 14-Apr-10

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⁺

L-aspartate 4-semialdehyde + pyruvate (Bound ligand (Het Group name = PYR) corresponds exactly) = (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

Biochimie 92:837-845 (2010)

PubMed id: 20353808

How essential is the 'essential' active-site lysine in dihydrodipicolinate synthase?

T.P.Soares da Costa, A.C.Muscroft-Taylor, R.C.Dobson, S.R.Devenish, G.B.Jameson, J.A.Gerrard.

ABSTRACT

Dihydrodipicolinate synthase (DHDPS, E.C. 4.2.1.52), a validated antibiotic target, catalyses the first committed step in the lysine biosynthetic pathway: the condensation reaction between (S)-aspartate beta-semialdehyde [(S)-ASA] and pyruvate via the formation of a Schiff base intermediate between pyruvate and the absolutely conserved active-site lysine. Escherichia coli DHDPS mutants K161A and K161R of the active-site lysine were characterised for the first time. Unexpectedly, the mutant enzymes were still catalytically active, albeit with a significant decrease in activity. The k(cat) values for DHDPS-K161A and DHDPS-K161R were 0.06 +/- 0.02 s(-1) and 0.16 +/- 0.06 s(-1) respectively, compared to 45 +/- 3 s(-1) for the wild-type enzyme. Remarkably, the K(M) values for pyruvate increased by only 3-fold for DHDPS-K161A and DHDPS-K161R (0.45 +/- 0.04 mM and 0.57 +/- 0.06 mM, compared to 0.15 +/- 0.01 mM for the wild-type DHDPS), while the K(M) values for (S)-ASA remained the same for DHDPS-K161R (0.12 +/- 0.01 mM) and increased by only 2-fold for DHDPS-K161A (0.23 +/- 0.02 mM) and the K(i) for lysine was unchanged. The X-ray crystal structures of DHDPS-K161A and DHDPS-K161R were solved at resolutions of 2.0 and 2.1 A respectively and showed no changes in their secondary or tertiary structures when compared to the wild-type structure. The crystal structure of DHDPS-K161A with pyruvate bound at the active site was solved at a resolution of 2.3 A and revealed a defined binding pocket for pyruvate that is thus not dependent upon lysine 161. Taken together with ITC and NMR data, it is concluded that although lysine 161 is important in the wild-type DHDPS-catalysed reaction, it is not absolutely essential for catalysis.