PDBsum entry 2c1h

Lyase

PDB id: 2c1h

Contents

Protein chains

319 a.a. *

Ligands

DSB ×2

Metals

_MG ×2

Waters ×254

* Residue conservation analysis

PDB id:

2c1h

Name:

Lyase

Title:

The x-ray structure of chlorobium vibrioforme 5-aminolaevulinic acid dehydratase complexed with a diacid inhibitor

Structure:

Delta-aminolevulinic acid dehydratase. Chain: a, b. Synonym: 5-aminolaevulinic acid dehydratase, porphobilinogen synthase, alad, aladh. Engineered: yes. Other_details: schiff base link between lys 200 and dsb, schiff base link between lys 253 and dsb

Source:

Chlorobium vibrioforme. Organism_taxid: 1098. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Octamer (from PDB file)

Resolution:

2.60Å R-factor: 0.263 R-free: 0.320

Authors:

L.Coates,G.Beaven,P.T.Erskine,S.Beale,S.P.Wood,P.M.Shoolingin-Jordan, J.B.Cooper

Key ref:

L.Coates et al. (2005). Structure of Chlorobium vibrioforme 5-aminolaevulinic acid dehydratase complexed with a diacid inhibitor. Acta Crystallogr D Biol Crystallogr, 61, 1594-1598. PubMed id: 16304458 DOI: 10.1107/S0907444905030350

Date:

14-Sep-05 Release date: 02-Dec-05

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 = DSB) matches with 43.75% similarity) = porphobilinogen + 2 × H2O + H(+)

• Cofactor: Zn(2+)

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

Added reference

DOI no: 10.1107/S0907444905030350

Acta Crystallogr D Biol Crystallogr 61:1594-1598 (2005)

PubMed id: 16304458

Structure of Chlorobium vibrioforme 5-aminolaevulinic acid dehydratase complexed with a diacid inhibitor.

L.Coates, G.Beaven, P.T.Erskine, S.I.Beale, S.P.Wood, P.M.Shoolingin-Jordan, J.B.Cooper.

ABSTRACT

The structure of Chlorobium vibrioforme 5-aminolaevulinic acid dehydratase (ALAD) complexed with the irreversible inhibitor 4,7-dioxosebacic acid has been solved. The inhibitor binds by forming Schiff-base linkages with lysines 200 and 253 at the active site. The structure reported here provides a definition of the interactions made by both of the substrate molecules (A-side and P-side substrates) with the C. vibrioforme ALAD and is compared and contrasted with structures of the same inhibitor bound to Escherichia coli and yeast ALAD. The structure suggests why 4,7-dioxosebacic acid is a better inhibitor of the zinc-dependent ALADs than of the zinc-independent ALADs.

Selected figure(s)

Figure 1.
Figure 1 The reaction catalysed by 5-aminolaevulinic acid dehydratase (ALAD). Two molecules of 5-aminolaevulinic acid are condensed to form the pyrrole porphobilinogen.

Figure 3.
Figure 3 (a) The 2F[o] - F[c] [168][sigma] [A]-weighted electron-density map (shown in cyan) for the inhibitor 4,7-dioxosebacic acid at 2.60 Å resolution. The covalent bonds between the inhibitor and lysines 200 and 253 are also shown. (b) The hydrogen bonds made by the carboxyl groups of the inhibitor with surrounding residues (donor-acceptor distances are shown in Å). The atoms labelled C4 and C7 are attached to the invariant lysine residues by Schiff bases. In both (a) and (b) the map is contoured at 1.25 r.m.s. and the A-site of the enzyme is on the left-hand side, with the P-site on the right.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 1594-1598) copyright 2005.

Figures were selected by an automated process.