2BYW

Structure of Escherichia coli beta-ketoacyl (acyl carrier protein) synthase I LYS328ALA mutant

PDB DOI: 10.2210/pdb2BYW/pdb
Entry: 2BYW supersedes: 1OEQ

Classification: TRANSFERASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-08-09 Released: 2005-09-09
Deposition Author(s): Olsen, J.G., von Wettstein-Knowles, P., Henriksen, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.209
R-Value Work: 0.181
R-Value Observed: 0.181

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Fatty acid synthesis. Role of active site histidines and lysine in Cys-His-His-type beta-ketoacyl-acyl carrier protein synthases.

von Wettstein-Knowles, P., Olsen, J.G., McGuire, K.A., Henriksen, A.

(2006) FEBS J 273: 695-710

PubMed: 16441657 Search on PubMed
DOI: 10.1111/j.1742-4658.2005.05101.x
Primary Citation of Related Structures:
1H4F, 2BUH, 2BUI, 2BYW, 2BYX, 2BYY, 2BYZ, 2BZ3, 2BZ4

PubMed Abstract:

Beta-ketoacyl-acyl carrier protein (ACP) synthase enzymes join short carbon units to construct fatty acyl chains by a three-step Claisen condensation reaction. The reaction starts with a trans thioesterification of the acyl primer substrate from ACP to the enzyme. Subsequently, the donor substrate malonyl-ACP is decarboxylated to form a carbanion intermediate, which in the third step attacks C1 of the primer substrate giving rise to an elongated acyl chain. A subgroup of beta-ketoacyl-ACP synthases, including mitochondrial beta-ketoacyl-ACP synthase, bacterial plus plastid beta-ketoacyl-ACP synthases I and II, and a domain of human fatty acid synthase, have a Cys-His-His triad and also a completely conserved Lys in the active site. To examine the role of these residues in catalysis, H298Q, H298E and six K328 mutants of Escherichia colibeta-ketoacyl-ACP synthase I were constructed and their ability to carry out the trans thioesterification, decarboxylation and/or condensation steps of the reaction was ascertained. The crystal structures of wild-type and eight mutant enzymes with and/or without bound substrate were determined. The H298E enzyme shows residual decarboxylase activity in the pH range 6-8, whereas the H298Q enzyme appears to be completely decarboxylation deficient, showing that H298 serves as a catalytic base in the decarboxylation step. Lys328 has a dual role in catalysis: its charge influences acyl transfer to the active site Cys, and the steric restraint imposed on H333 is of critical importance for decarboxylation activity. This restraint makes H333 an obligate hydrogen bond donor at Nepsilon, directed only towards the active site and malonyl-ACP binding area in the fatty acid complex.

Related Citations:

Structure of B-Ketoacyl-Acyl Carrier Protein Synthase I Complexed with Fatty Acids Elucidate its Catalytic Machinery
Olsen, J.G., Kadziola, A., von Wettstein-Knowles, P., Siggaard-Andersen, M., Larsen, S.
(2001) Structure 9: 233

Organizational Affiliation:

Genetics Department, Molecular Biology and Physiology Institute, Copenhagen University, Denmark. knowles@biobase.dk

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I	A, B, C, D	418	Escherichia coli	Mutation(s): 2 EC: 2.3.1.41
UniProt
Find proteins for P0A953 (Escherichia coli (strain K12)) Explore P0A953 Go to UniProtKB: P0A953
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A953
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NH4 Query on NH4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain K [auth D] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D]	E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], K [auth D], L [auth D]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.209
R-Value Work: 0.181
R-Value Observed: 0.181
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.68	α = 90
b = 138.011	β = 90
c = 210.19	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2005-08-09
Released Date: 2005-09-09

Deposition Author(s):

Olsen, J.G.

von Wettstein-Knowles, P.

Henriksen, A.

This entry supersedes: 1OEQ

Revision History (Full details and data files)

Version 1.0: 2005-09-09
Type: Initial release
Version 1.1: 2014-02-19
Changes: Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
Version 1.2: 2018-01-17
Changes: Database references, Structure summary