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PDBsum entry 8ldh

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Oxidoreductase PDB id
8ldh
Jmol
Contents
Protein chain
330 a.a. *
Ligands
CIT ×2
Waters ×281
* Residue conservation analysis
PDB id:
8ldh
Name: Oxidoreductase
Title: Refined crystal structure of dogfish m4 apo-lactate dehydrog
Structure: M4 apo-lactate dehydrogenase. Chain: a. Engineered: yes
Source: Squalus acanthias. Spiny dogfish. Organism_taxid: 7797
Biol. unit: Tetramer (from PQS)
Resolution:
2.80Å     R-factor:   0.191    
Authors: C.Abad-Zapatero,M.G.Rossmann
Key ref:
C.Abad-Zapatero et al. (1987). Refined crystal structure of dogfish M4 apo-lactate dehydrogenase. J Mol Biol, 198, 445-467. PubMed id: 3430615 DOI: 10.1016/0022-2836(87)90293-2
Date:
04-Jan-88     Release date:   12-Jul-89    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00341  (LDHA_SQUAC) -  L-lactate dehydrogenase A chain
Seq:
Struc:
333 a.a.
329 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 18 residue positions (black crosses)

 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 = CIT)
matches with 46.15% similarity
+ NAD(+)
= 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: 10.1016/0022-2836(87)90293-2 J Mol Biol 198:445-467 (1987)
PubMed id: 3430615  
 
 
Refined crystal structure of dogfish M4 apo-lactate dehydrogenase.
C.Abad-Zapatero, J.P.Griffith, J.L.Sussman, M.G.Rossmann.
 
  ABSTRACT  
 
The crystal structure of M4 apo-lactate dehydrogenase from the spiny dogfish (Squalus acanthius) was initially refined by a constrained-restrained, and subsequently restrained, least-squares technique. The final structure contained 286 water molecules and two sulfate ions per subunit and gave an R-factor of 0.202 for difraction data between 8.0 and 2.0 A resolution. The upper limit for the co-ordinate accuracy of the atoms was estimated to be 0.25 A. The elements of secondary structure of the refined protein have not changed from those described previously, except for the appearance of a one-and-a-half turn 3(10) helix immediately after beta J. There is also a short segment of 3(10) helix between beta C and beta D in the part of the chain that connects the two beta alpha beta alpha beta units of the six-stranded parallel sheet (residues Tyr83 to Ala87). Examination of the interactions among the different elements of secondary structure by means of a surface accessibility algorithm supports the four structural clusters in the subunit. The first of the two sulfate ions is in the active site and occupies a cavity near the essential His195. Its nearest protein ligands are Arg171, Asp168 and Asn140. The second sulfate ion is located near the P-axis subunit interface. It is liganded by His188 and Arg173. These two residues are conserved in bacterial lactate dehydrogenase and form part of the fructose 1,6-bisphosphate effector binding site. Two other data sets in which one (collected at pH 7.8) or both (collected at pH 6.0) sulfate ions were replaced by citrate ions were also analyzed. Five cycles of refinement with respect to the pH 6.0 data (25 to 2.8 A resolution) resulted in an R value of 0.191. Only water molecules occupy the subunit boundary anion binding site at pH 7.8. The amino acid sequence was found to be in poor agreement with (2Fobs-Fcalc) electron density maps for the peptide between residues 207 and 211. The original sequence WNALKE was replaced by NVASIK. The essential His195 is hydrogen bonded to Asp168 on one side and Asn140 on the other. The latter residue is part of a turn that contains the only cis peptide bond of the structure at Pro141. The "flexible loop" (residues 97 to 123), which folds down over the active center in ternary complexes of the enzyme with substrate and coenzyme, has a well-defined structure. Analysis of the environment of Tyr237 suggests how its chemical modification inhibits the enzyme.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Schematic diagram of the polypeptide fold of one subunit of the apo-LDHase structure. The elements of secondary structure have been labeled with the accepted nomenclature: beta-A to beta-J for the beta-strands and alpha-A to alpha-H for the alpha-helices. The view is such that the molecular R-axis is vertical and the Q-axis points towards the viewer. Inset: arrangement of the monomers in the LDHase tetramer with 222 symmetry.
 
  The above figure is reprinted by permission from Elsevier: J Mol Biol (1987, 198, 445-467) copyright 1987.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
11741996 Z.Hou, W.Wang, H.J.Fromm, and R.B.Honzatko (2002).
IMP Alone Organizes the Active Site of Adenylosuccinate Synthetase from Escherichia coli.
  J Biol Chem, 277, 5970-5976.
PDB codes: 1kjx 1kkb 1kkf
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.  
10206992 S.Y.Kim, K.Y.Hwang, S.H.Kim, H.C.Sung, Y.S.Han, and Y.Cho (1999).
Structural basis for cold adaptation. Sequence, biochemical properties, and crystal structure of malate dehydrogenase from a psychrophile Aquaspirillium arcticum.
  J Biol Chem, 274, 11761-11767.
PDB codes: 1b8p 1b8u 1b8v
9525918 C.Mazza, R.Breton, D.Housset, and J.C.Fontecilla-Camps (1998).
Unusual charge stabilization of NADP+ in 17beta-hydroxysteroid dehydrogenase.
  J Biol Chem, 273, 8145-8152.
PDB codes: 1fdu 1fdv 1fdw
8550549 F.Takusagawa, S.Kamitori, S.Misaki, and G.D.Markham (1996).
Crystal structure of S-adenosylmethionine synthetase.
  J Biol Chem, 271, 136-147.
PDB codes: 1xra 1xrb 1xrc
  178752936 , (0).
  , (), 0.  
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