spacer
spacer

PDBsum entry 2ldb

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Oxidoreductase(choh(d)-NAD(a)) PDB id
2ldb
Jmol PyMol
Contents
Protein chains
301 a.a. *
Ligands
SO4 ×8
NAD ×4
FBP ×2
Waters ×50
* Residue conservation analysis
PDB id:
2ldb
Name: Oxidoreductase(choh(d)-NAD(a))
Title: Structure determination and refinement of bacillus stearothermophilus lactate dehydrogenase
Structure: L-lactate dehydrogenase. Chain: a, b, c, d. Engineered: yes
Source: Geobacillus stearothermophilus. Organism_taxid: 1422
Biol. unit: Tetramer (from PQS)
Resolution:
3.00Å     R-factor:   0.260    
Authors: K.Piontek,M.G.Rossmann
Key ref: K.Piontek et al. (1990). Structure determination and refinement of Bacillus stearothermophilus lactate dehydrogenase. Proteins, 7, 74-92. PubMed id: 2330370
Date:
27-Mar-89     Release date:   12-Jul-89    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00344  (LDH_GEOSE) -  L-lactate dehydrogenase
Seq:
Struc:
317 a.a.
301 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.1.1.27  - L-lactate dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (S)-lactate + NAD+ = pyruvate + NADH
(S)-lactate
+
NAD(+)
Bound ligand (Het Group name = NAD)
corresponds exactly
= pyruvate
+ NADH
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
    reference    
 
 
Proteins 7:74-92 (1990)
PubMed id: 2330370  
 
 
Structure determination and refinement of Bacillus stearothermophilus lactate dehydrogenase.
K.Piontek, P.Chakrabarti, H.P.Schär, M.G.Rossmann, H.Zuber.
 
  ABSTRACT  
 
Structures have been determined of Bacillus stearothermophilus "apo" and holo lactate dehydrogenase. The holo-enzyme had been co-crystallized with the activator fructose 1,6-bisphosphate. The "apo" lactate dehydrogenase structure was solved by use of the known apo-M4 dogfish lactate dehydrogenase molecule as a starting model. Phases were refined and extended from 4 A to 3 A resolution by means of the noncrystallographic molecular 222 symmetry. The R-factor was reduced to 28.7%, using 2.8 A resolution data, in a restrained least-squares refinement in which the molecular symmetry was imposed as a constraint. A low occupancy of coenzyme was found in each of the four subunits of the "apo"-enzyme. Further refinement proceeded with the isomorphous holo-enzyme from Bacillus stearothermophilus. After removing the noncrystallographic constraints, the R-factor dropped from 30.3% to a final value of 26.0% with a 0.019 A and 1.7 degrees r.m.s. deviation from idealized bond lengths and angles, respectively. Two sulfate ions per subunit were included in the final model of the "apo"-form--one at the substrate binding site and one close to the molecular P-axis near the location of the fructose 1,6-bisphosphate activator. The final model of the holo-enzyme incorporated two sulfate ions per subunit, one at the substrate binding site and another close to the R-axis. One nicotinamide adenine dinucleotide coenzyme molecule per subunit and two fructose 1,6-bisphosphate molecules per tetramer were also included. The phosphate positions of fructose 1,6-bisphosphate are close to the sulfate ion near the P-axis in the "apo" model. This structure represents the first reported refined model of an allosteric activated lactate dehydrogenase. The structure of the activated holo-enzyme showed far greater similarity to the ternary complex of dogfish M4 lactate dehydrogenase with nicotinamide adenine dinucleotide and oxamate than to apo-M4 dogfish lactate dehydrogenase. The conformations of nicotinamide adenine dinucleotide and fructose 1,6-bisphosphate were also analyzed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
11807949 H.Uchikoba, S.Fushinobu, T.Wakagi, M.Konno, H.Taguchi, and H.Matsuzawa (2002).
Crystal structure of non-allosteric L-lactate dehydrogenase from Lactobacillus pentosus at 2.3 A resolution: specific interactions at subunit interfaces.
  Proteins, 46, 206-214.
PDB code: 1ez4
11276087 J.A.Read, V.J.Winter, C.M.Eszes, R.B.Sessions, and R.L.Brady (2001).
Structural basis for altered activity of M- and H-isozyme forms of human lactate dehydrogenase.
  Proteins, 43, 175-185.
PDB codes: 1i0z 1i10
11483495 S.Fieulaine, S.Morera, S.Poncet, V.Monedero, V.Gueguen-Chaignon, A.Galinier, J.Janin, J.Deutscher, and S.Nessler (2001).
X-ray structure of HPr kinase: a bacterial protein kinase with a P-loop nucleotide-binding domain.
  EMBO J, 20, 3917-3927.
PDB code: 1jb1
10666635 B.I.Lee, C.Chang, S.J.Cho, G.W.Han, Y.G.Yu, S.H.Eom, and S.W.Suh (2000).
Lactate dehydrogenase from the hyperthermophilic archaeon Methanococcus jannaschii: overexpression, crystallization and preliminary X-ray analysis.
  Acta Crystallogr D Biol Crystallogr, 56, 81-83.  
10712593 S.Kochhar, V.S.Lamzin, A.Razeto, M.Delley, H.Hottinger, and J.E.Germond (2000).
Roles of his205, his296, his303 and Asp259 in catalysis by NAD+-specific D-lactate dehydrogenase.
  Eur J Biochem, 267, 1633-1639.  
10187806 J.A.Read, K.W.Wilkinson, R.Tranter, R.B.Sessions, and R.L.Brady (1999).
Chloroquine binds in the cofactor binding site of Plasmodium falciparum lactate dehydrogenase.
  J Biol Chem, 274, 10213-10218.
PDB codes: 1ceq 1cet
10089509 D.Rabinovich, H.Rozenberg, and Z.Shakked (1998).
Molecular replacement: the revival of the molecular Fourier transform method.
  Acta Crystallogr D Biol Crystallogr, 54, 1336-1342.  
  9212432 K.Savijoki, and A.Palva (1997).
Molecular genetic characterization of the L-lactate dehydrogenase gene (ldhL) of Lactobacillus helveticus and biochemical characterization of the enzyme.
  Appl Environ Microbiol, 63, 2850-2856.  
7858977 M.Xie, J.Seravalli, W.P.Huskey, K.B.Schowen, and R.L.Schowen (1994).
Solvent isotope effects and the nature of electrophilic catalysis in the action of the lactate dehydrogenase of Bacillus stearothermophilus.
  Bioorg Med Chem, 2, 691-695.  
7656036 S.Iwata, K.Kamata, S.Yoshida, T.Minowa, and T.Ohta (1994).
T and R states in the crystals of bacterial L-lactate dehydrogenase reveal the mechanism for allosteric control.
  Nat Struct Biol, 1, 176-185.
PDB code: 1lth
8506353 O.Livnah, E.A.Bayer, M.Wilchek, and J.L.Sussman (1993).
Three-dimensional structures of avidin and the avidin-biotin complex.
  Proc Natl Acad Sci U S A, 90, 5076-5080.
PDB code: 2avi
8404889 R.Ostendorp, W.Liebl, H.Schurig, and R.Jaenicke (1993).
The L-lactate dehydrogenase gene of the hyperthermophilic bacterium Thermotoga maritima cloned by complementation in Escherichia coli.
  Eur J Biochem, 216, 709-715.  
1620698 K.Huang, R.Kodandapani, H.Kallwass, J.K.Hogan, W.Parris, J.D.Friesen, M.Gold, J.B.Jones, and M.N.James (1992).
Crystallization and preliminary X-ray diffraction studies of two mutants of lactate dehydrogenase from Bacillus stearothermophilus.
  Proteins, 13, 158-161.  
1396685 S.Kochhar, H.Hottinger, N.Chuard, P.G.Taylor, T.Atkinson, M.D.Scawen, and D.J.Nicholls (1992).
Cloning and overexpression of Lactobacillus helveticus D-lactate dehydrogenase gene in Escherichia coli.
  Eur J Biochem, 208, 799-805.  
1946424 D.Ghosh, C.M.Weeks, P.Grochulski, W.L.Duax, M.Erman, R.L.Rimsay, and J.C.Orr (1991).
Three-dimensional structure of holo 3 alpha,20 beta-hydroxysteroid dehydrogenase: a member of a short-chain dehydrogenase family.
  Proc Natl Acad Sci U S A, 88, 10064-10068.
PDB code: 1hsd
1784712 M.C.Lawrence (1991).
The application of the molecular replacement method to the de novo determination of protein structure.
  Q Rev Biophys, 24, 399-424.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

spacer

spacer