1U1Z | pdb_00001u1z

The Structure of (3R)-hydroxyacyl-ACP dehydratase (FabZ)

PDB DOI: https://doi.org/10.2210/pdb1U1Z/pdb

Classification: LYASE
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2004-07-16 Released: 2004-09-28
Deposition Author(s): Kimber, M.S., Martin, F., Lu, Y., Houston, S., Vedadi, M., Dharamsi, A., Fiebig, K.M., Schmid, M., Rock, C.O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.258 (Depositor), 0.254 (DCC)
R-Value Work:
0.232 (Depositor), 0.226 (DCC)
R-Value Observed:
0.234 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The Structure of (3R)-hydroxyacyl-acyl carrier protein dehydratase (FabZ) from Pseudomonas aeruginosa

Kimber, M.S., Martin, F., Lu, Y., Houston, S., Vedadi, M., Dharamsi, A., Fiebig, K.M., Schmid, M., Rock, C.O.

(2004) J Biological Chem 279: 52593-52602

PubMed: 15371447 Search on PubMed
DOI: https://doi.org/10.1074/jbc.M408105200
Primary Citation Related Structures:
1U1Z

PubMed Abstract:
Type II fatty acid biosynthesis systems are essential for membrane formation in bacteria, making the constituent proteins of this pathway attractive targets for antibacterial drug discovery. The third step in the elongation cycle of the type II fatty acid biosynthesis is catalyzed by beta-hydroxyacyl-(acyl carrier protein) (ACP) dehydratase. There are two isoforms. FabZ, which catalyzes the dehydration of (3R)-hydroxyacyl-ACP to trans-2-acyl-ACP, is a universally expressed component of the bacterial type II system. FabA, the second isoform, as has more limited distribution in nature and, in addition to dehydration, also carries out the isomerization of trans-2- to cis-3-decenoyl-ACP as an essential step in unsaturated fatty acid biosynthesis. We report the structure of FabZ from the important human pathogen Pseudomonas aeruginosa at 2.5 A of resolution. PaFabZ is a hexamer (trimer of dimers) with the His/Glu catalytic dyad located within a deep, narrow tunnel formed at the dimer interface. Site-directed mutagenesis experiments showed that the obvious differences in the active site residues that distinguish the FabA and FabZ subfamilies of dehydratases do not account for the unique ability of FabA to catalyze isomerization. Because the catalytic machinery of the two enzymes is practically indistinguishable, the structural differences observed in the shape of the substrate binding channels of FabA and FabZ lead us to hypothesize that the different shapes of the tunnels control the conformation and positioning of the bound substrate, allowing FabA, but not FabZ, to catalyze the isomerization reaction.

Organizational Affiliation

Affinium Pharmaceuticals, Toronto, Ontario M5J 1V6, Canada.

Macromolecule Content

Total Structure Weight: 116.57 kDa
Atom Count: 7,285
Modeled Residue Count: 869
Deposited Residue Count: 1,008
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase	A, B, C, D, E A, B, C, D, E, F	168	Pseudomonas aeruginosa	Mutation(s): 5 Gene Names: fabZ EC: 4.2.1 (PDB Primary Data), 4.2.1.59 (UniProt)
UniProt
Find proteins for Q9HXY7 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HXY7 Go to UniProtKB: Q9HXY7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HXY7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain J [auth D] SDF format, chain I [auth D] SDF format, chain H [auth D] SDF format, chain G [auth D] MOL2 format, chain K [auth D] MOL2 format, chain J [auth D] MOL2 format, chain I [auth D] MOL2 format, chain H [auth D] MOL2 format, chain G [auth D] mmCIF format, chain K [auth D] mmCIF format, chain J [auth D] mmCIF format, chain I [auth D] mmCIF format, chain H [auth D] mmCIF format, chain G [auth D]	G [auth D], H [auth D], I [auth D], J [auth D], K [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth D] Focus chain H [auth D] Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth D] Interactions & Density Focus chain G [auth D] Focus chain H [auth D] Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.258 (Depositor), 0.254 (DCC)
R-Value Work: 0.232 (Depositor), 0.226 (DCC)
R-Value Observed: 0.234 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.031	α = 90
b = 100.897	β = 90
c = 177.252	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2004-09-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-09-28
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary