PDBsum entry 1w1z

Lyase

PDB id: 1w1z

Contents

Protein chains

319 a.a. *

Ligands

SHF ×2

Metals

_MG ×2

Waters ×325

* Residue conservation analysis

PDB id:

1w1z

Name:

Lyase

Title:

Structure of the plant like 5-aminolaevulinic acid dehydratase from chlorobium vibrioforme

Structure:

Delta-aminolevulinic acid dehydratase. Chain: a, b. Synonym: 5-aminolaevulinic acid dehydratase porphobilinogen synthase, alad, aladh. Engineered: yes

Source:

Prosthecochloris vibrioformis. Organism_taxid: 1098. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Octamer (from PDB file)

Resolution:

2.60Å R-factor: 0.296 R-free: 0.382

Authors:

L.Coates,G.Beaven,P.T.Erskine,S.I.Beale,Y.J.Avissar,R.Gill, F.Mohammed,S.P.Wood,P.Shoolingin-Jordan,J.B.Cooper

Key ref:

L.Coates et al. (2004). The X-ray structure of the plant like 5-aminolaevulinic acid dehydratase from Chlorobium vibrioforme complexed with the inhibitor laevulinic acid at 2.6 A resolution. J Mol Biol, 342, 563-570. PubMed id: 15327955 DOI: 10.1016/j.jmb.2004.07.007

Date:

24-Jun-04 Release date: 02-Sep-04

Protein chains

Q59334  (HEM2_CHLP8) -  Delta-aminolevulinic acid dehydratase from Chlorobaculum parvum (strain DSM 263 / NCIMB 8327)

Seq: 328 a.a.

Struc: 319 a.a.

Enzyme reactions

• Enzyme class: E.C.4.2.1.24 - porphobilinogen synthase.
• Pathway: Porphyrin Biosynthesis (early stages)
• Reaction: 2 5-aminolevulinate = porphobilinogen + 2 H2O + H⁺

2 × 5-aminolevulinate (Bound ligand (Het Group name = SHF) matches with 77.78% similarity) = porphobilinogen + 2 × H2O + H(+)

• Cofactor: Zn(2+)

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

Added reference

DOI no: 10.1016/j.jmb.2004.07.007

J Mol Biol 342:563-570 (2004)

PubMed id: 15327955

The X-ray structure of the plant like 5-aminolaevulinic acid dehydratase from Chlorobium vibrioforme complexed with the inhibitor laevulinic acid at 2.6 A resolution.

L.Coates, G.Beaven, P.T.Erskine, S.I.Beale, Y.J.Avissar, R.Gill, F.Mohammed, S.P.Wood, P.Shoolingin-Jordan, J.B.Cooper.

ABSTRACT

5-Aminolaevulinic acid dehydratase (ALAD), an early enzyme of the tetrapyrrole biosynthesis pathway, catalyses the dimerisation of 5-aminolaevulinic acid to form the pyrrole, porphobilinogen. ALAD from Chlorobium vibrioforme is shown to form a homo-octameric structure with 422 symmetry in which each subunit adopts a TIM-barrel fold with a 30 residue N-terminal arm extension. Pairs of monomers associate with their arms wrapped around each other. Four of these dimers interact principally via their arm regions to form octamers in which each active site is located on the surface. The active site contains two invariant lysine residues (200 and 253), one of which (Lys253) forms a Schiff base link with the bound substrate analogue, laevulinic acid. The carboxyl group of the laevulinic acid forms hydrogen bonds with the side-chains of Ser279 and Tyr318. The structure was examined to determine the location of the putative active-site magnesium ion, however, no evidence for the metal ion was found in the electron density map. This is in agreement with previous kinetic studies that have shown that magnesium stimulates but is not required for activity. A different site close to the active site flap, in which a putative magnesium ion is coordinated by a glutamate carboxyl and five solvent molecules may account for the stimulatory properties of magnesium ions on the enzyme.

Selected figure(s)

Figure 1.
Figure 1. The Knorr-type condensation reaction catalysed by 5-aminolaevulinic acid dehydratase (ALAD), indicating the A and P-sites of the product porphobilinogen.

Figure 5.
Figure 5. The communication pathway that links the allosteric magnesium-binding site to the active site which involves two water molecules coordinated to the allosteric magnesium ion shown as a green sphere. These water molecules form hydrogen bonds with the Nz atoms of Arg176. The Nc atom of Arg176 forms a hydrogen bond with the side-chain of Asp171 the carbonyl oxygen of which binds to a water molecule hydrogen bonded to Lys200. For clarity, only the interatomic distances of atoms involved in the communication pathway are shown and water molecules are shown as red spheres.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 342, 563-570) copyright 2004.

Figures were selected by an automated process.