6B2T | pdb_00006b2t

Crystal structure of Xanthomonas campestris OleA H285D

PDB DOI: https://doi.org/10.2210/pdb6B2T/pdb

Classification: TRANSFERASE
Organism(s): Xanthomonas campestris pv. campestris str. ATCC 33913
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2017-09-20 Released: 2018-02-28
Deposition Author(s): Jensen, M.R., Goblirsch, B.R., Esler, M.A., Christenson, J.K., Mohamed, F.A., Wackett, L.P., Wilmot, C.M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), BioTechnology Institute

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.247 (Depositor), 0.248 (DCC)
R-Value Work:
0.172 (Depositor), 0.177 (DCC)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The role of OleA His285 in orchestration of long-chain acyl-coenzyme A substrates.

Jensen, M.R., Goblirsch, B.R., Esler, M.A., Christenson, J.K., Mohamed, F.A., Wackett, L.P., Wilmot, C.M.

(2018) FEBS Lett 592: 987-998

PubMed: 29430657 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/1873-3468.13004
Primary Citation Related Structures:
6B2R, 6B2S, 6B2T

PubMed Abstract:
Renewable production of hydrocarbons is being pursued as a petroleum-independent source of commodity chemicals and replacement for biofuels. The bacterial biosynthesis of long-chain olefins represents one such platform. The process is initiated by OleA catalyzing the condensation of two fatty acyl-coenzyme A substrates to form a β-keto acid. Here, the mechanistic role of the conserved His285 is investigated through mutagenesis, activity assays, and X-ray crystallography. Our data demonstrate that His285 is required for product formation, influences the thiolase nucleophile Cys143 and the acyl-enzyme intermediate before and after transesterification, and orchestrates substrate coordination as a defining component of an oxyanion hole. As a consequence, His285 plays a key role in enabling a mechanistic strategy in OleA that is distinct from other thiolases.

Organizational Affiliation

Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St Paul, MN, USA.

Macromolecule Content

Total Structure Weight: 78.41 kDa
Atom Count: 5,305
Modeled Residue Count: 684
Deposited Residue Count: 716
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[ACP] synthase III	A	358	Xanthomonas campestris pv. campestris str. ATCC 33913	Mutation(s): 1 Gene Names: fabH, XCC0212 EC: 2.3.1.41 (PDB Primary Data), 2.3.3.20 (UniProt)
UniProt
Find proteins for Q8PDX2 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)) Explore Q8PDX2 Go to UniProtKB: Q8PDX2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8PDX2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[ACP] synthase III	B	358	Xanthomonas campestris pv. campestris str. ATCC 33913	Mutation(s): 1 Gene Names: fabH, XCC0212 EC: 2.3.1.41 (PDB Primary Data), 2.3.3.20 (UniProt)
UniProt
Find proteins for Q8PDX2 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)) Explore Q8PDX2 Go to UniProtKB: Q8PDX2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8PDX2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], G [auth B], H [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	F [auth A], I [auth B], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	B	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.247 (Depositor), 0.248 (DCC)
R-Value Work: 0.172 (Depositor), 0.177 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.421	α = 90
b = 84.996	β = 90
c = 102.956	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
REFMAC	phasing
HKL-2000	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-02-28

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32GM008700
BioTechnology Institute	United States	1000014885 10866 MNT11

Revision History (Full details and data files)

Version 1.0: 2018-02-28
Type: Initial release
Version 1.1: 2018-04-04
Changes: Data collection, Database references
Version 1.2: 2020-01-01
Changes: Author supporting evidence
Version 1.3: 2024-10-23
Changes: Data collection, Database references, Structure summary