1DIO

DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA

PDB DOI: https://doi.org/10.2210/pdb1DIO/pdb

Classification: LYASE
Organism(s): Klebsiella oxytoca
Expression System: Escherichia coli
Mutation(s): No

Deposited: 1999-01-27 Released: 2000-01-30
Deposition Author(s): Shibata, N., Masuda, J., Tobimatsu, T., Toraya, T., Suto, K., Morimoto, Y., Yasuoka, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.236
R-Value Work: 0.187
R-Value Observed: 0.188

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

A new mode of B12 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase.

Shibata, N., Masuda, J., Tobimatsu, T., Toraya, T., Suto, K., Morimoto, Y., Yasuoka, N.

(1999) Structure 7: 997-1008

PubMed: 10467140 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(99)80126-9
Primary Citation of Related Structures:
1DIO

PubMed Abstract:
Diol dehydratase is an enzyme that catalyzes the adenosylcobalamin (coenzyme B12) dependent conversion of 1,2-diols to the corresponding aldehydes. The reaction initiated by homolytic cleavage of the cobalt-carbon bond of the coenzyme proceeds by a radical mechanism. The enzyme is an alpha2beta2gamma2 heterooligomer and has an absolute requirement for a potassium ion for catalytic activity. The crystal structure analysis of a diol dehydratase-cyanocobalamin complex was carried out in order to help understand the mechanism of action of this enzyme.

Organizational Affiliation

Department of Life Science, Himeji Institute of Technology, Hyogo, Japan.

Macromolecule Content

Total Structure Weight: 210.39 kDa
Atom Count: 13,912
Modelled Residue Count: 1,734
Deposited Residue Count: 1,902
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (DIOL DEHYDRATASE)	A, D [auth L]	554	Klebsiella oxytoca	Mutation(s): 0 EC: 4.2.1.28
UniProt
Find proteins for Q59470 (Klebsiella oxytoca) Explore Q59470 Go to UniProtKB: Q59470
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q59470
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (DIOL DEHYDRATASE)	B, E	224	Klebsiella oxytoca	Mutation(s): 0 EC: 4.2.1.28
UniProt
Find proteins for Q59471 (Klebsiella oxytoca) Explore Q59471 Go to UniProtKB: Q59471
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q59471
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (DIOL DEHYDRATASE)	C [auth G], F [auth M]	173	Klebsiella oxytoca	Mutation(s): 0 EC: 4.2.1.28
UniProt
Find proteins for Q59472 (Klebsiella oxytoca) Explore Q59472 Go to UniProtKB: Q59472
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q59472
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B12 Query on B12 Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain L [auth E] MOL2 format, chain I [auth B] MOL2 format, chain L [auth E]	I [auth B], L [auth E]	COBALAMIN C₆₂ H₈₉ Co N₁₃ O₁₄ P LKVIQTCSMMVGFU-DWSMJLPVSA-N		Interactions Focus chain I [auth B] Focus chain L [auth E] Interactions & Density Focus chain I [auth B] Focus chain L [auth E]
PGO Query on PGO Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth L] MOL2 format, chain H [auth A] MOL2 format, chain K [auth L]	H [auth A], K [auth L]	S-1,2-PROPANEDIOL C₃ H₈ O₂ DNIAPMSPPWPWGF-VKHMYHEASA-N		Interactions Focus chain H [auth A] Focus chain K [auth L] Interactions & Density Focus chain H [auth A] Focus chain K [auth L]
K Query on K Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth L] MOL2 format, chain G [auth A] MOL2 format, chain J [auth L]	G [auth A], J [auth L]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth L] Interactions & Density Focus chain G [auth A] Focus chain J [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.236
R-Value Work: 0.187
R-Value Observed: 0.188
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.2	α = 90
b = 122.3	β = 90
c = 209.6	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2000-01-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2000-01-30
Type: Initial release
Version 1.1: 2007-10-16
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2012-10-24
Changes: Non-polymer description
Version 1.4: 2023-12-27
Changes: Data collection, Database references, Derived calculations