PDBsum entry: 1mkb

Fatty acid biosynthesis

PDB id: 1mkb

Contents

Protein chains

171 a.a. *

Waters ×163

* Residue conservation analysis

PDB id:

1mkb

Name:

Fatty acid biosynthesis

Title:

Escherichia coli beta-hydroxydecanoyl thiol ester dehydrase at ph 5 and 21 degrees c

Structure:

Beta-hydroxydecanoyl thiol ester dehydrase. Chain: a, b. Synonym: beta-hydroxydecanoyl acp dehydrase. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Strain: ra244. Gene: faba. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: tac promoter

Biol. unit:

Dimer (from PQS)

Resolution:

2.00Å R-factor: 0.183 R-free: 0.243

Authors:

M.Leesong

Key ref:

M.Leesong et al. (1996). Structure of a dehydratase-isomerase from the bacterial pathway for biosynthesis of unsaturated fatty acids: two catalytic activities in one active site. Structure, 4, 253-264. PubMed id: 8805534 DOI: 10.1016/S0969-2126(96)00030-5

Date:

08-Jan-96 Release date: 11-Jul-96

Protein chains

P0A6Q3  (FABA_ECOLI) -  3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

Seq: 172 a.a.

Struc: 171 a.a.

Enzyme reactions

• Enzyme class: E.C.4.2.1.60 - 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase.
• Reaction:
  1. (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] = trans-dec-2-enoyl- [acyl-carrier-protein] + H₂O
  2. (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] = cis-dec-3-enoyl- [acyl-carrier-protein] + H₂O

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: biosynthetic process (3 terms)
• Biochemical function: catalytic activity (3 terms)

reference

DOI no: 10.1016/S0969-2126(96)00030-5

Structure 4:253-264 (1996)

PubMed id: 8805534

Structure of a dehydratase-isomerase from the bacterial pathway for biosynthesis of unsaturated fatty acids: two catalytic activities in one active site.

M.Leesong, B.S.Henderson, J.R.Gillig, J.M.Schwab, J.L.Smith.

ABSTRACT

BACKGROUND. Escherichia coli beta-hydroxydecanoyl thiol ester dehydrase (dehydrase) is essential to the biosynthesis of unsaturated fatty acids, by shunting a 10-carbon intermediate from the saturated fatty acid pathway into the unsaturated fatty acid pathway. Dehydrase catalyzes reactions of dehydration and of double-bond isomerization on 10-carbon thiol esters of acyl carrier protein (ACP). The aim of this work is to elucidate mechanisms for the two enzymatic reactions, which occur in an unusual bifunctional active site, and to understand the specificity of the enzyme for substrates with 10-carbon fatty acyl chains. RESULTS. Crystal structures at 2.0 A resolution for free dehydrase and for the enzyme modified by its classic, mechanism-based inactivator, 3-decynoyl-N-acetylcysteamine, have been determined. Dehydrase is a symmetric dimer with an unusual alpha+beta 'hot dog' fold. Each of the two independent active sites is located between the two subunits of the enzyme, and is a tunnel-shaped pocket completely isolated from the general solvent. Side chains of histidine from one subunit and aspartic acid from the other are the only potentially reactive protein groups in the active site. CONCLUSION. A two-base mechanism by which the histidine and aspartic acid together catalyze dehydration and isomerization reactions is consistent with the active-site structure. The unique topology of the protein fold and the identification of the active-site components reveal features of predictive value for another enzyme, FabZ, which may be the non-specific dehydratase involved in elongation of fatty acyl chains. A positively charged area surrounding the entrance to the active site, which could interact with the negatively charged ACP, was also found.

Selected figure(s)

Figure 1.
Figure 1. Catalytic reactions of dehydrase. (a) Biological reactions of dehydration and isomerization. (b) Inactivation of dehydrase by the mechanism-based inactivator 3-decenoyl-NAC. The first product of inactivation is the 3,4-unsaturated adduct, but this slowly isomerizes to the 2,3-unsaturated form [11]. The double bond configuration has been shown by the present study. Figure 1. Catalytic reactions of dehydrase. (a) Biological reactions of dehydration and isomerization. (b) Inactivation of dehydrase by the mechanism-based inactivator 3-decenoyl-NAC. The first product of inactivation is the 3,4-unsaturated adduct, but this slowly isomerizes to the 2,3-unsaturated form [[4]11]. The double bond configuration has been shown by the present study.

Figure 4.
Figure 4. Structure of the dehydrase monomer. (a) Topology of the polypeptide fold. β strands are represented as arrows labelled β1–β7. The helices are represented as cylinders labelled α1–α3 (α2 is a 3[10]-helix). The dyad axis is adjacent to β4. (b) Stereo view of the Cα trace of the purple subunit of Figure 3, viewed along the dyad axis. The positions of the two non-proline cis peptides are shown as shaded boxes. Figure 4. Structure of the dehydrase monomer. (a) Topology of the polypeptide fold. β strands are represented as arrows labelled β1–β7. The helices are represented as cylinders labelled α1–α3 (α2 is a 3[10]-helix). The dyad axis is adjacent to β4. (b) Stereo view of the Cα trace of the purple subunit of [4]Figure 3, viewed along the dyad axis. The positions of the two non-proline cis peptides are shown as shaded boxes.

The above figures are reprinted by permission from Cell Press: Structure (1996, 4, 253-264) copyright 1996.

Figures were selected by an automated process.