PDBsum entry 1ldv

Membrane protein

PDB id: 1ldv

Contents

Protein chain

264 a.a.

Theoretical model

PDB id:

1ldv

Name:

Membrane protein

Title:

Plasmodium falciparum merozoite surface antigen precusor

Structure:

Merozoite surface antigen 2. Chain: a. Synonym: msa-2

Source:

Plasmodium falciparum. Malaria parasite

Authors:

A.Dash,K.K.Kakarala

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:

09-Apr-02 Release date: 01-May-02

Protein chain

P50499  (MSA2_PLAFJ) -  Merozoite surface antigen 2

Seq: 264 a.a.

Struc: 264 a.a.

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.