1GEG

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.193 

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

  • DOI: https://doi.org/10.1093/oxfordjournals.jbchem.a002845
  • Primary Citation of 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.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ACETOIN REDUCTASE
A, B, C, D, E
A, B, C, D, E, F, G, H
256Klebsiella pneumoniaeMutation(s): 0 
EC: 1.1.1.5
UniProt
Find proteins for Q48436 (Klebsiella pneumoniae)
Explore Q48436 
Go to UniProtKB:  Q48436
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ48436
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD
Download Ideal Coordinates CCD File 
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
GLC
Query on GLC
Download Ideal Coordinates CCD File 
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
BME
Query on BME
Download Ideal Coordinates CCD File 
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
MG
Query on MG
Download Ideal Coordinates CCD File 
DA [auth G],
HA [auth H],
J [auth A],
N [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.16α = 90
b = 109.78β = 102.29
c = 127.28γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

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