Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Refined crystal structure of dogfish M4 apo-lactate dehydrogenase.

Abad-Zapatero, C.Griffith, J.P.Sussman, J.L.Rossmann, M.G.

(1987) J Mol Biol 198: 445-467

  • DOI: 10.1016/0022-2836(87)90293-2
  • Primary Citation of Related Structures:  
    6LDH, 1LDM, 8LDH

  • PubMed 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 ...

    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.

    Related Citations: 
    • A Comparison of the Structures of Apo Dogfish M4 Lactate Dehydrogenase and its Ternary Complexes
      White, J.L., Hackert, M.L., Buehner, M., Adams, M.J., Ford, G.C., Lentzjunior, P.J., Smiley, I.E., Steindel, S.J., Rossmann, M.G.
      (1976) J Mol Biol 102: 759
    • Structural Adaptations of Lactate Dehydrogenase Isozymes
      Eventoff, W., Rossmann, M.G., Taylor, S.S., Torff, H.-J., Meyer, H., Keil, W., Kiltz, H.-H.
      (1977) Proc Natl Acad Sci U S A 74: 2677
    • A 5 Angstroms X-Ray Diffraction Study of Coenzyme-Deficient Lactate Dehydrogenase,Nad-Pyruvate Ternary Complex
      White, J., Rossmann, M.G., Ford, G.C.
      (1975) J Mol Biol 98: 259
    • A Structural Comparison of Porcine B4 and Dogfish A4 Isozymes of Lactate Dehydrogenase
      Eventoff, W., Hackert, M.L., Steindel, S.J., Rossmann, M.G.
      (1975) Isozymes-molecular Structure 1: 137
    • Lactate Dehydrogenase
      Holbrook, J.J., Liljas, A., Steindel, S.J., Rossmann, M.G.
      (1975) The Enzymes,third Edition 11: 191
    • X-Ray Studies of Protein Interactions
      Liljas, A., Rossmann, M.G.
      (1974) Annu Rev Biochem 43: 475
    • Chemical and Biological Evolution of a Nucleotide Binding Protein
      Rossmann, M.G., Moras, D., Olsen, K.W.
      (1974) Nature 250: 194
    • Recognition of Structural Domains in Globular Proteins
      Rossmann, M.G., Liljas, A.
      (1974) J Mol Biol 85: 177
    • Atomic Co-Ordinates for Dogfish M4 Apo-Lactate Dehydrogenase
      Adams, M.J., Ford, G.C., Liljas, A., Rossmann, M.G.
      (1973) Biochem Biophys Res Commun 53: 46
    • Structure-Function Relationships in Lactate Dehydrogenase
      Adams, M.J., Buehner, M., Chandrasekhar, K., Ford, G.C., Hackert, M.L., Liljas, A., Rossmann, M.G., Smiley, I.E., Allison, W.S., Everse, J., Kaplan, N.O., Taylor, S.S.
      (1973) Proc Natl Acad Sci U S A 70: 1968
    • Amino-Acid Sequence of Dogfish M4 Lactate Dehydrogenase
      Taylor, S.S., Oxley, S.S., Allison, W.S., Kaplan, N.O.
      (1973) Proc Natl Acad Sci U S A 70: 1790
    • Molecular Symmetry Axes and Subunit Interfaces in Certain Dehydrogenases
      Rossmann, M.G., Adams, M.J., Buehner, M., Ford, G.C., Hackert, M.L., Liljas, A., Rao, S.T., Banaszak, L.J., Hill, E., Tsernoglou, D., Webb, L.
      (1973) J Mol Biol 76: 533
    • Functional Anion Binding Sites in Dogfish M4 Lactate Dehydrogenase
      Adams, M.J., Liljas, A., Rossmann, M.G.
      (1973) J Mol Biol 76: 519
    • Binding of Oxamate to the Apoenzyme of Dogfish M4 Lactate Dehydrogenase
      Mcphersonjunior, A.
      (1973) J Mol Biol 76: 528
    • Conformation of Coenzyme Fragments When Bound to Lactate Dehydrogenase
      Chandrasekhar, K., Mcphersonjunior, A., Adams, M.J., Rossmann, M.G.
      (1973) J Mol Biol 76: 503
    • The 5 Angstroms Resolution Structure of an Abortive Ternary Complex of Lactate Dehydrogenase and its Comparison with the Apo-Enzyme
      Smiley, I.E., Koekoek, R., Adams, M.J., Rossmann, M.G.
      (1971) J Mol Biol 55: 467
    • Structure of Lactate Dehydrogenase at 2.8 Angstroms Resolution
      Adams, M.J., Ford, G.C., Koekoek, R., Lentzjunior, P.J., Mcphersonjunior, A., Rossmann, M.G., Smiley, I.E., Schevitz, R.W., Wonacott, A.J.
      (1970) Nature 227: 1098
    • Low Resolution Study of Crystalline L-Lactate Dehydrogenase
      Adams, M.J., Haas, D.J., Jeffery, B.A., Mcphersonjunior, A., Mermall, H.L., Rossmann, M.G., Schevitz, R.W., Wonacott, A.J.
      (1969) J Mol Biol 41: 159
    • The Crystal Structure of Lactic Dehydrogenase
      Rossmann, M.G., Jeffery, B.A., Main, P., Warren, S.
      (1967) Proc Natl Acad Sci U S A 57: 515

    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907.

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
M4 APO-LACTATE DEHYDROGENASEA330Squalus acanthiasMutation(s): 0 
Gene Names: ldha
Find proteins for P00341 (Squalus acanthias)
Explore P00341 
Go to UniProtKB:  P00341
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on CIT

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]CITRIC ACID
C6 H8 O7
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Observed: 0.191 
  • Space Group: F 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.8α = 90
b = 146.8β = 90
c = 155.4γ = 90
Software Package:
Software NamePurpose

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1989-07-12
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-04-18
    Changes: Derived calculations, Structure summary
  • Version 1.4: 2017-11-29
    Changes: Derived calculations, Other