spacer
spacer

PDBsum entry 2v7p

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
2v7p
Jmol
Contents
Protein chains
310 a.a. *
Ligands
OXM ×4
NAD ×4
Waters ×535
* Residue conservation analysis
PDB id:
2v7p
Name: Oxidoreductase
Title: Crystal structure of lactate dehydrogenase from thermus thermophilus hb8 (holo form)
Structure: L-lactate dehydrogenase. Chain: a, b, c, d. Synonym: lactate dehydrogenase, l-ldh. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.10Å     R-factor:   0.192     R-free:   0.204
Authors: N.Coquelle,E.Fioravanti,M.Weik,F.Vellieux
Key ref:
N.Coquelle et al. (2007). Activity, stability and structural studies of lactate dehydrogenases adapted to extreme thermal environments. J Mol Biol, 374, 547-562. PubMed id: 17936781 DOI: 10.1016/j.jmb.2007.09.049
Date:
31-Jul-07     Release date:   25-Sep-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q5SJA1  (LDH_THET8) -  L-lactate dehydrogenase
Seq:
Struc:
310 a.a.
310 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
Bound ligand (Het Group name = OXM)
matches with 71.00% similarity
+
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   4 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2007.09.049 J Mol Biol 374:547-562 (2007)
PubMed id: 17936781  
 
 
Activity, stability and structural studies of lactate dehydrogenases adapted to extreme thermal environments.
N.Coquelle, E.Fioravanti, M.Weik, F.Vellieux, D.Madern.
 
  ABSTRACT  
 
Lactate dehydrogenase (LDH) catalyzes the conversion of pyruvate to lactate with concomitant oxidation of NADH during the last step in anaerobic glycolysis. In the present study, we present a comparative biochemical and structural analysis of various LDHs adapted to function over a large temperature range. The enzymes were from Champsocephalus gunnari (an Antarctic fish), Deinococcus radiodurans (a mesophilic bacterium) and Thermus thermophilus (a hyperthermophilic bacterium). The thermodynamic activation parameters of these LDHs indicated that temperature adaptation from hot to cold conditions was due to a decrease in the activation enthalpy and an increase in activation entropy. The crystal structures of these LDHs have been solved. Pairwise comparisons at the structural level, between hyperthermophilic versus mesophilic LDHs and mesophilic versus psychrophilic LDHs, have revealed that temperature adaptation is due to a few amino acid substitutions that are localized in critical regions of the enzyme. These substitutions, each having accumulating effects, play a role in either the conformational stability or the local flexibility or in both. Going from hot- to cold-adapted LDHs, the various substitutions have decreased the number of ion pairs, reduced the size of ionic networks, created unfavorable interactions involving charged residues and induced strong local disorder. The analysis of the LDHs adapted to extreme temperatures shed light on how evolutionary processes shift the subtle balance between overall stability and flexibility of an enzyme.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Ribbon diagram of the apo form of tetrameric TtLDH. The four monomers are labeled A–D.
Figure 3.
Fig. 3. A 30 Å slice through a ribbon diagram of a monomer of TtLDH complexed with oxamate and NADH. The color scheme used is related to C^α deviation between the apo and ternary complex. The rainbow scale bar illustrates values of deviation in angstroms. Inset: RMSD between C^α atoms in the superimposed subunits of TtLDH (apo versus ternary complex). The mobile regions (MR) that display the largest deviations are indicated.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 374, 547-562) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21276854 M.Tiberti, and E.Papaleo (2011).
Dynamic properties of extremophilic subtilisin-like serine-proteases.
  J Struct Biol, 174, 69-83.  
18312599 C.Michaux, J.Massant, F.Kerff, J.M.Frère, J.D.Docquier, I.Vandenberghe, B.Samyn, A.Pierrard, G.Feller, P.Charlier, J.Van Beeumen, and J.Wouters (2008).
Crystal structure of a cold-adapted class C beta-lactamase.
  FEBS J, 275, 1687-1697.
PDB code: 2qz6
18203855 D.F.Rodrigues, and J.M.Tiedje (2008).
Coping with our cold planet.
  Appl Environ Microbiol, 74, 1677-1686.  
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.