2IX5 | pdb_00002ix5

Short chain specific acyl-CoA oxidase from Arabidopsis thaliana, ACX4 in complex with acetoacetyl-CoA

PDB DOI: https://doi.org/10.2210/pdb2IX5/pdb

Classification: OXIDOREDUCTASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2006-07-07 Released: 2006-08-08
Deposition Author(s): Mackenzie, J., Pedersen, L., Arent, S., Henriksen, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.232 (Depositor), 0.199 (DCC)
R-Value Work:
0.186 (Depositor)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Controlling Electron Transfer in Acyl-Coa Oxidases and Dehydrogenases: A Structural View.

Mackenzie, J., Pedersen, L., Arent, S., Henriksen, A.

(2006) J Biological Chem 281: 31012

PubMed: 16887802 Search on PubMed
DOI: https://doi.org/10.1074/jbc.M603405200
Primary Citation Related Structures:
2IX5, 2IX6

PubMed Abstract:
Plants produce a unique peroxisomal short chain-specific acyl-CoA oxidase (ACX4) for beta-oxidation of lipids. The short chain-specific oxidase has little resemblance to other peroxisomal acyl-CoA oxidases but has an approximately 30% sequence identity to mitochondrial acyl-CoA dehydrogenases. Two biochemical features have been linked to structural properties by comparing the structures of short chain-specific Arabidopsis thaliana ACX4 with and without a substrate analogue bound in the active site to known acyl-CoA oxidases and dehydrogenase structures: (i) a solvent-accessible acyl binding pocket is not required for oxygen reactivity, and (ii) the oligomeric state plays a role in substrate pocket architecture but is not linked to oxygen reactivity. The structures indicate that the acyl-CoA oxidases may encapsulate the electrons for transfer to molecular oxygen by blocking the dehydrogenase substrate interaction site with structural extensions. A small binding pocket observed adjoining the flavin adenine dinucleotide N5 and C4a atoms could increase the number of productive encounters between flavin adenine dinucleotide and O2.

Organizational Affiliation

Biostructure Group, Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark.

Macromolecule Content

Total Structure Weight: 196.97 kDa
Atom Count: 13,234
Modeled Residue Count: 1,664
Deposited Residue Count: 1,744
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACYL-COENZYME A OXIDASE 4, PEROXISOMAL	A, B, C, D	436	Arabidopsis thaliana	Mutation(s): 0 EC: 1.3.3.6
UniProt
Find proteins for Q96329 (Arabidopsis thaliana) Explore Q96329 Go to UniProtKB: Q96329
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96329
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAA Query on CAA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	ACETOACETYL-COENZYME A C₂₅ H₄₀ N₇ O₁₈ P₃ S OJFDKHTZOUZBOS-CITAKDKDSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.232 (Depositor), 0.199 (DCC)
R-Value Work: 0.186 (Depositor)
R-Value Observed: 0.189 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.747	α = 90
b = 144.747	β = 90
c = 149.208	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-08-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-08-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2018-01-17
Changes: Data collection
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Other, Refinement description