3A18 | pdb_00003a18

Crystal Structure of Aldoxime Dehydratase (OxdRE) in Complex with Butyraldoxime (soaked crystal)

PDB DOI: https://doi.org/10.2210/pdb3A18/pdb

Classification: LYASE
Organism(s): Rhodococcus erythropolis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-03-26 Released: 2009-09-08
Deposition Author(s): Sawai, H., Sugimoto, H., Kato, Y., Asano, Y., Shiro, Y., Aono, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.280 (Depositor), 0.279 (DCC)
R-Value Work:
0.247 (Depositor), 0.247 (DCC)
R-Value Observed:
0.249 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

X-ray crystal structure of michaelis complex of aldoxime dehydratase

Sawai, H., Sugimoto, H., Kato, Y., Asano, Y., Shiro, Y., Aono, S.

(2009) J Biological Chem 284: 32089-32096

PubMed: 19740758 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M109.018762
Primary Citation Related Structures:
3A15, 3A16, 3A17, 3A18

PubMed Abstract:
Aldoxime dehydratase (Oxd) catalyzes the dehydration of aldoximes (R-CH=N-OH) to their corresponding nitrile (R-C triple bond N). Oxd is a heme-containing enzyme that catalyzes the dehydration reaction as its physiological function. We have determined the first two structures of Oxd: the substrate-free OxdRE at 1.8 A resolution and the n-butyraldoxime- and propionaldoxime-bound OxdREs at 1.8 and 1.6 A resolutions, respectively. Unlike other heme enzymes, the organic substrate is directly bound to the heme iron in OxdRE. We determined the structure of the Michaelis complex of OxdRE by using the unique substrate binding and activity regulation properties of Oxd. The Michaelis complex was prepared by x-ray cryoradiolytic reduction of the ferric dead-end complex in which Oxd contains a Fe(3+) heme form. The crystal structures reveal the mechanism of substrate recognition and the catalysis of OxdRE.

Organizational Affiliation

From the Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.

Macromolecule Content

Total Structure Weight: 171.14 kDa
Atom Count: 12,589
Modeled Residue Count: 1,411
Deposited Residue Count: 1,492
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldoxime dehydratase	A, B, C, D	373	Rhodococcus erythropolis	Mutation(s): 0 Gene Names: oxd EC: 4.99.1.5 (PDB Primary Data), 4.8.1.2 (UniProt)
UniProt
Find proteins for Q76K71 (Rhodococcus erythropolis) Explore Q76K71 Go to UniProtKB: Q76K71
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q76K71
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		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]
BXO Query on BXO Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	(1Z)-butanal oxime C₄ H₉ N O KGGVGTQEGGOZRN-PLNGDYQASA-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: 1.80 Å
R-Value Free: 0.280 (Depositor), 0.279 (DCC)
R-Value Work: 0.247 (Depositor), 0.247 (DCC)
R-Value Observed: 0.249 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.118	α = 90
b = 148.569	β = 90.3
c = 79.113	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SPACE	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-09-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-09-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2017-10-11
Changes: Refinement description
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description