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PDBsum entry 1j49

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1j49
Jmol
Contents
Protein chains
332 a.a. *
Ligands
NAD ×2
SO4
Waters ×279
* Residue conservation analysis
PDB id:
1j49
Name: Oxidoreductase
Title: Insights into domain closure, substrate specificity and catalysis of d-lactate dehydrogenase from lactobacillus bulgaricus
Structure: D-lactate dehydrogenase. Chain: a, b. Synonym: d-ldh. Engineered: yes
Source: Lactobacillus delbrueckii subsp. Bulgaricus. Organism_taxid: 1585. Strain: n42. Cellular_location: cytoplasm. Gene: ldha. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: nestle culture collection. Pcr amplified
Biol. unit: Dimer (from PQS)
Resolution:
2.20Å     R-factor:   0.209     R-free:   0.271
Authors: A.Razeto,S.Kochhar,H.Hottinger,M.Dauter,K.S.Wilson, V.S.Lamzin
Key ref:
A.Razeto et al. (2002). Domain closure, substrate specificity and catalysis of D-lactate dehydrogenase from Lactobacillus bulgaricus. J Mol Biol, 318, 109-119. PubMed id: 12054772 DOI: 10.1016/S0022-2836(02)00086-4
Date:
14-Aug-01     Release date:   29-May-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P26297  (LDHD_LACDA) -  D-lactate dehydrogenase
Seq:
Struc:
333 a.a.
332 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.1.1.1.28  - D-lactate dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (R)-lactate + NAD+ = pyruvate + NADH
(R)-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!
  Biological process     metabolic process   2 terms 
  Biochemical function     oxidoreductase activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0022-2836(02)00086-4 J Mol Biol 318:109-119 (2002)
PubMed id: 12054772  
 
 
Domain closure, substrate specificity and catalysis of D-lactate dehydrogenase from Lactobacillus bulgaricus.
A.Razeto, S.Kochhar, H.Hottinger, M.Dauter, K.S.Wilson, V.S.Lamzin.
 
  ABSTRACT  
 
NAD-dependent Lactobacillus bulgaricus D-Lactate dehydrogenase (D-LDHb) catalyses the reversible conversion of pyruvate into D-lactate. Crystals of D-LDHb complexed with NADH were grown and X-ray data collected to 2.2 A. The structure of D-LDHb was solved by molecular replacement using the dimeric Lactobacillus helveticus D-LDH as a model and was refined to an R-factor of 20.7%. The two subunits of the enzyme display strong asymmetry due to different crystal environments. The opening angles of the two catalytic domains with respect to the core coenzyme binding domains differ by 16 degrees. Subunit A is in an "open" conformation typical for a dehydrogenase apo enzyme and subunit B is "closed". The NADH-binding site in subunit A is only 30% occupied, while in subunit B it is fully occupied and there is a sulphate ion in the substrate-binding pocket. A pyruvate molecule has been modelled in the active site and its orientation is in agreement with existing kinetic and structural data. On domain closure, a cluster of hydrophobic residues packs tightly around the methyl group of the modelled pyruvate molecule. At least three residues from this cluster govern the substrate specificity. Substrate binding itself contributes to the stabilisation of domain closure and activation of the enzyme. In pyruvate reduction, D-LDH can adapt another protonated residue, a lysine residue, to accomplish the role of the acid catalyst His296. Required lowering of the lysine pK(a) value is explained on the basis of the H296K mutant structure.
 
  Selected figure(s)  
 
Figure 8.
Figure 8. Effects of domain closure on the architecture of the active site. Subunit B is in the darker shade. Subunit A, superimposed on subunit B, is in the lighter shade. Residues of the active site are shown in ball-and-stick.
Figure 9.
Figure 9. Hypothetical mechanism of domain closure in the Image -2-hydroxy-acid dehydrogenases.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 318, 109-119) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21264216 P.Hao, H.Zheng, Y.Yu, G.Ding, W.Gu, S.Chen, Z.Yu, S.Ren, M.Oda, T.Konno, S.Wang, X.Li, Z.S.Ji, and G.Zhao (2011).
Complete sequencing and pan-genomic analysis of Lactobacillus delbrueckii subsp. bulgaricus reveal its genetic basis for industrial yogurt production.
  PLoS One, 6, e15964.  
19774350 J.Jia, W.Mu, T.Zhang, and B.Jiang (2010).
Bioconversion of phenylpyruvate to phenyllactate: gene cloning, expression, and enzymatic characterization of D- and L1-lactate dehydrogenases from Lactobacillus plantarum SK002.
  Appl Biochem Biotechnol, 162, 242-251.  
20445235 V.Janiak, M.Petersen, M.Zentgraf, G.Klebe, and A.Heine (2010).
Structure and substrate docking of a hydroxy(phenyl)pyruvate reductase from the higher plant Coleus blumei Benth.
  Acta Crystallogr D Biol Crystallogr, 66, 593-603.
PDB code: 3baz
19966418 I.G.Shabalin, E.V.Filippova, K.M.Polyakov, E.G.Sadykhov, T.N.Safonova, T.V.Tikhonova, V.I.Tishkov, and V.O.Popov (2009).
Structures of the apo and holo forms of formate dehydrogenase from the bacterium Moraxella sp. C-1: towards understanding the mechanism of the closure of the interdomain cleft.
  Acta Crystallogr D Biol Crystallogr, 65, 1315-1325.
PDB codes: 2gsd 3fn4
  19342795 J.Domenech, P.J.Baker, S.E.Sedelnikova, H.F.Rodgers, D.W.Rice, and J.Ferrer (2009).
Crystallization and preliminary X-ray analysis of D-2-hydroxyacid dehydrogenase from Haloferax mediterranei.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 415-418.  
17928715 I.Saichana, Y.Ano, O.Adachi, K.Matsushita, and H.Toyama (2007).
Preparation of enzymes required for enzymatic quantification of 5-keto-D-gluconate and 2-keto-D-gluconate.
  Biosci Biotechnol Biochem, 71, 2478-2486.  
16957230 J.Kim, D.Darley, T.Selmer, and W.Buckel (2006).
Characterization of (R)-2-hydroxyisocaproate dehydrogenase and a family III coenzyme A transferase involved in reduction of L-leucine to isocaproate by Clostridium difficile.
  Appl Environ Microbiol, 72, 6062-6069.  
15634349 B.M.Martins, S.Macedo-Ribeiro, J.Bresser, W.Buckel, and A.Messerschmidt (2005).
Structural basis for stereo-specific catalysis in NAD(+)-dependent (R)-2-hydroxyglutarate dehydrogenase from Acidaminococcus fermentans.
  FEBS J, 272, 269-281.
PDB code: 1xdw
15734738 T.Shinoda, K.Arai, M.Shigematsu-Iida, Y.Ishikura, S.Tanaka, T.Yamada, M.S.Kimber, E.F.Pai, S.Fushinobu, and H.Taguchi (2005).
Distinct conformation-mediated functions of an active site loop in the catalytic reactions of NAD-dependent D-lactate dehydrogenase and formate dehydrogenase.
  J Biol Chem, 280, 17068-17075.  
16037987 Y.Bai, and S.T.Yang (2005).
Biotransformation of R-2-hydroxy-4-phenylbutyric acid by D-lactate dehydrogenase and Candida boidinii cells containing formate dehydrogenase coimmobilized in a fibrous bed bioreactor.
  Biotechnol Bioeng, 92, 137-146.  
12897026 C.Tokuda, Y.Ishikura, M.Shigematsu, H.Mutoh, S.Tsuzuki, Y.Nakahira, Y.Tamura, T.Shinoda, K.Arai, O.Takahashi, and H.Taguchi (2003).
Conversion of Lactobacillus pentosus D-lactate dehydrogenase to a D-hydroxyisocaproate dehydrogenase through a single amino acid replacement.
  J Bacteriol, 185, 5023-5026.  
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.