PDBsum entry: 1dpy

Hydrolase

PDB id: 1dpy

Contents

Protein chain

117 a.a. *

Metals

_NA

Waters ×79

* Residue conservation analysis

PDB id:

1dpy

Name:

Hydrolase

Title:

Three-dimensional structure of a novel phospholipase a2 from indian common krait at 2.45 a resolution

Structure:

Phospholipase a2. Chain: a. Synonym: pla2. Ec: 3.1.1.4

Source:

Bungarus caeruleus. Organism_taxid: 132961. Secretion: venom

Biol. unit:

Trimer (from PQS)

Resolution:

2.45Å R-factor: 0.202 R-free: 0.281

Authors:

G.Singh,S.Gourinath,S.Sharma,M.Paramasivam,A.Srinivasan, T.P.Singh

Key ref:

G.Singh et al. (2001). Sequence and crystal structure determination of a basic phospholipase A2 from common krait (Bungarus caeruleus) at 2.4 A resolution: identification and characterization of its pharmacological sites. J Mol Biol, 307, 1049-1059. PubMed id: 11286555 DOI: 10.1006/jmbi.2001.4550

Date:

28-Dec-99 Release date: 28-Jun-00

Protein chain

Q9DF52  (PA2K_BUNCE) -  Phospholipase A2 KPA2

Seq: 145 a.a.

Struc: 117 a.a.*

* PDB and UniProt seqs differ at 10 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.1.1.4 - Phospholipase A(2).
• Reaction: Phosphatidylcholine + H₂O = 1-acylglycerophosphocholine + a carboxylate
• Cofactor: Calcium

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular region (2 terms)
• Biological process: lipid catabolic process (4 terms)
• Biochemical function: hydrolase activity (4 terms)

reference

DOI no: 10.1006/jmbi.2001.4550

J Mol Biol 307:1049-1059 (2001)

PubMed id: 11286555

Sequence and crystal structure determination of a basic phospholipase A2 from common krait (Bungarus caeruleus) at 2.4 A resolution: identification and characterization of its pharmacological sites.

G.Singh, S.Gourinath, S.Sharma, M.Paramasivam, A.Srinivasan, T.P.Singh.

ABSTRACT

This is the first phospholipase A2 (PLA2) structure from the family of kraits. The protein was isolated from Bungarus caeruleus (common krait) and the primary sequence was determined using cDNA approach. Three-dimensional structure of this presynaptic neurotoxic PLA2 from group I has been determined by molecular replacement method using the model of PLA2 component of beta2-bungarotoxin (Bungarus multicinctus) and refined using CNS package to a final R-factor of 20.1 % for all the data in resolution range 20.0-2.4 A. The final refined model comprises 897 protein atoms and 77 water molecules. The overall framework of krait phospholipase A2 with three long helices and two short antiparallel beta-strands is extremely similar to those observed for other group I PLA2s. However, the critical parts of PLA2 folding are concerned with its various functional loops. The conformations of these loops determine the efficiency of enzyme action and presence/absence of various pharmacological functions. In the present structure calcium-binding loop is occupied by a sodium ion with a 7-fold co-ordination. The conformation of loop 55-75 in krait PLA2 corresponds to a very high activity of the enzyme. A comparison of its sequence with multimeric PLA2s clearly shows the absence of critical residues such as Tyr3, Trp61 and Phe64, which are involved in the multimerization of PLA2 molecules. The protein shows anticoagulant and neurotoxic activities.

Selected figure(s)

Figure 2.
Figure 2. Stereoview of a representative region of the electron density map (2F[o] - F[c]) with a final refined model superimposed on it. The map was contoured at 1.6 s.

Figure 5.
Figure 5. Superimposition of C^a tracing of KPLA2 (continuous lines) on the C^a tracing of (a) NPLA2, (b) APLA2, (c) PPLA2, (d) SPLA2, (e) GPLA2, (f) EPLA2 and (g) BPLA2 (broken lines). L1-L6 indicate various loops, and N and C correspond to N and C termini.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 307, 1049-1059) copyright 2001.

Figures were selected by an automated process.