1LDN

STRUCTURE OF A TERNARY COMPLEX OF AN ALLOSTERIC LACTATE DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILUS AT 2.5 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a ternary complex of an allosteric lactate dehydrogenase from Bacillus stearothermophilus at 2.5 A resolution.

Wigley, D.B.Gamblin, S.J.Turkenburg, J.P.Dodson, E.J.Piontek, K.Muirhead, H.Holbrook, J.J.

(1992) J.Mol.Biol. 223: 317-335


  • PubMed Abstract: 
  • We report the refined structure of a ternary complex of an allosterically activated lactate dehydrogenase, including the important active site loop. Eightfold non-crystallographic symmetry averaging was utilized to improve the density maps. Interacti ...

    We report the refined structure of a ternary complex of an allosterically activated lactate dehydrogenase, including the important active site loop. Eightfold non-crystallographic symmetry averaging was utilized to improve the density maps. Interactions between the protein and bound coenzyme and oxamate are described in relation to other studies using site-specific mutagenesis. Fructose 1,6-bisphosphate (FruP2) is bound to the enzyme across one of the 2-fold axes of the tetramer, with the two phosphate moieties interacting with two anion binding sites, one on each of two subunits, across this interface. However, because FruP2 binds at this special site, yet does not possess an internal 2-fold symmetry axis, the ligand is statistically disordered and binds to each site in two different orientations. Binding of FruP2 to the tetramer is signalled to the active site principally through two interactions with His188 and Arg173. His188 is connected to His195 (which binds the carbonyl group of the substrate) and Arg173 is connected to Arg171 (the residue that binds the carboxylate group of the substrate).


    Related Citations: 
    • Cloning, Expression and Complete Nucleotide Sequence of the Bacillus Stearothermophilus L-Lactate Dehydrogenase Gene
      Barstow, D.A.,Clarke, A.R.,Chia, W.N.,Wigley, D.B.,Sharman, A.F.,Holbrook, J.J.,Atkinson, T.,Minton, N.P.
      (1986) Gene 46: 47
    • Crystallization of a Ternary Complex of Lactate Dehydrogenase from Bacillus Stearothermophilus
      Wigley, D.B.,Muirhead, H.,Gamblin, S.J.,Holbrook, J.J.
      (1988) J.Mol.Biol. 204: 1041


    Organizational Affiliation

    Department of Biochemistry, University of Leicester, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-LACTATE DEHYDROGENASE
A, B, C, D, E, F, G, H
316Geobacillus stearothermophilusGene Names: ldh (lct)
EC: 1.1.1.27
Find proteins for P00344 (Geobacillus stearothermophilus)
Go to UniProtKB:  P00344
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXM
Query on OXM

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
OXAMIC ACID
C2 H3 N O3
SOWBFZRMHSNYGE-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
FBP
Query on FBP

Download SDF File 
Download CCD File 
A, B, E, F
BETA-FRUCTOSE-1,6-DIPHOSPHATE
FRUCTOSE-1,6-BISPHOSPHATE
C6 H14 O12 P2
RNBGYGVWRKECFJ-ARQDHWQXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 84.900α = 90.00
b = 118.200β = 96.07
c = 135.500γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance