1GEG | pdb_00001geg

CRYATAL STRUCTURE ANALYSIS OF MESO-2,3-BUTANEDIOL DEHYDROGENASE

PDB DOI: https://doi.org/10.2210/pdb1GEG/pdb

Classification: OXIDOREDUCTASE
Organism(s): Klebsiella pneumoniae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2000-11-10 Released: 2001-02-28
Deposition Author(s): Otagiri, M., Kurisu, G., Ui, S., Kusunoki, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.209 (Depositor), 0.190 (DCC)
R-Value Work:
0.193 (Depositor), 0.189 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of meso-2,3-butanediol dehydrogenase in a complex with NAD+ and inhibitor mercaptoethanol at 1.7 A resolution for understanding of chiral substrate recognition mechanisms.

Otagiri, M., Kurisu, G., Ui, S., Takusagawa, Y., Ohkuma, M., Kudo, T., Kusunoki, M.

(2001) J Biochem 129: 205-208

PubMed: 11173520 Search on PubMed
DOI: https://doi.org/10.1093/oxfordjournals.jbchem.a002845
Primary Citation Related Structures:
1GEG

PubMed Abstract:
The crystal structure of a ternary complex of meso-2,3-butanediol dehydrogenase with NAD+ and a competitive inhibitor, mercaptoethanol, has been determined at 1.7 A resolution by means of molecular replacement and refined to a final R-factor of 0.194. The overall structure is similar to those of the other short chain dehydrogenase/reductase enzymes. The NAD+ binding site, and the positions of catalytic residues Ser139, Tyr152, and Lys156 are also conserved. The crystal structure revealed that mercaptoethanol bound specifically to meso-2,3-butanediol dehydrogenase. Two residues around the active site, Gln140 and Gly183, forming hydrogen bonds with the inhibitor, are important but not sufficient for distinguishing stereoisomerism of a chiral substrate.

Organizational Affiliation

Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.

Macromolecule Content

Total Structure Weight: 220.42 kDa
Atom Count: 16,227
Modeled Residue Count: 2,041
Deposited Residue Count: 2,048
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACETOIN REDUCTASE	A, B, C, D, E A, B, C, D, E, F, G, H	256	Klebsiella pneumoniae	Mutation(s): 0 EC: 1.1.1.5 (PDB Primary Data), 1.1.1.304 (UniProt)
UniProt
Find proteins for Q48436 (Klebsiella pneumoniae) Explore Q48436 Go to UniProtKB: Q48436
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q48436
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain EA [auth G] SDF format, chain IA [auth H] SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain U [auth D] SDF format, chain X [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain IA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D] MOL2 format, chain X [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain IA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain U [auth D] mmCIF format, chain X [auth E]	AA [auth F] EA [auth G] IA [auth H] K [auth A] O [auth B] AA [auth F], EA [auth G], IA [auth H], K [auth A], O [auth B], R [auth C], U [auth D], X [auth E]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain AA [auth F] Focus chain EA [auth G] Focus chain IA [auth H] Focus chain K [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain EA [auth G] Focus chain IA [auth H] Focus chain K [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E]
GLC Query on GLC Download:Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain GA [auth H] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth D] SDF format, chain W [auth E] SDF format, chain Z [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain GA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain GA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D] mmCIF format, chain W [auth E] mmCIF format, chain Z [auth F]	CA [auth G] GA [auth H] I [auth A] M [auth B] Q [auth C] CA [auth G], GA [auth H], I [auth A], M [auth B], Q [auth C], T [auth D], W [auth E], Z [auth F]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain CA [auth G] Focus chain GA [auth H] Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth G] Focus chain GA [auth H] Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F]
BME Query on BME Download:Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain FA [auth G] SDF format, chain JA [auth H] SDF format, chain L [auth A] SDF format, chain P [auth B] SDF format, chain S [auth C] SDF format, chain V [auth D] SDF format, chain Y [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain JA [auth H] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain BA [auth F] mmCIF format, chain FA [auth G] mmCIF format, chain JA [auth H] mmCIF format, chain L [auth A] mmCIF format, chain P [auth B] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D] mmCIF format, chain Y [auth E]	BA [auth F] FA [auth G] JA [auth H] L [auth A] P [auth B] BA [auth F], FA [auth G], JA [auth H], L [auth A], P [auth B], S [auth C], V [auth D], Y [auth E]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain FA [auth G] Focus chain JA [auth H] Focus chain L [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain FA [auth G] Focus chain JA [auth H] Focus chain L [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth E]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain DA [auth G] SDF format, chain HA [auth H] SDF format, chain J [auth A] SDF format, chain N [auth B] MOL2 format, chain DA [auth G] MOL2 format, chain HA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] mmCIF format, chain DA [auth G] mmCIF format, chain HA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B]	DA [auth G], HA [auth H], J [auth A], N [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DA [auth G] Focus chain HA [auth H] Focus chain J [auth A] Focus chain N [auth B] Interactions & Density Focus chain DA [auth G] Focus chain HA [auth H] Focus chain J [auth A] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.209 (Depositor), 0.190 (DCC)
R-Value Work: 0.193 (Depositor), 0.189 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.16	α = 90
b = 109.78	β = 102.29
c = 127.28	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2001-02-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2001-02-28
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-10-16
Changes: Data collection, Database references
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.5: 2023-12-27
Changes: Data collection, Database references, Structure summary