PDBsum entry 1psh

Carboxylic ester hydrolase

PDB id

1psh

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Contents

			Protein chains

					119 a.a. *

			Metals

					_CA ×3

			Waters ×148

* Residue conservation analysis

PDB id:

1psh

Links

Name:

Carboxylic ester hydrolase

Title:

Crystal structure of phospholipase a2 from indian cobra reveals a trimeric association

Structure:

Phospholipase a2. Chain: a, b, c. Engineered: yes

Source:

Naja naja. Indian cobra. Organism_taxid: 35670

Biol. unit:

Trimer (from PQS)

Resolution:

2.30Å

R-factor:

0.174

Authors:

D.Fremont,N.-H.Xuong,I.Wilson

Key ref:

D.H.Fremont et al. (1993). Crystal structure of phospholipase A2 from Indian cobra reveals a trimeric association. Proc Natl Acad Sci U S A, 90, 342-346. PubMed id: 8419939 DOI: 10.1073/pnas.90.1.342

Date:

28-Jul-92

Release date:

31-Jan-94

PROCHECK

	Headers

	References

Protein chains

P15445 (PA2A2_NAJNA) - Acidic phospholipase A2 2 from Naja naja

Seq: Struc:					119 a.a. 119 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.3.1.1.4 - phospholipase A2.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

a 1,2-diacyl-sn-glycero-3-phosphocholine + H2O = a 1-acyl-sn-glycero-3- phosphocholine + a fatty acid + H⁺

1,2-diacyl-sn-glycero-3-phosphocholine	+	H2O	=	1-acyl-sn-glycero-3- phosphocholine	+	fatty acid	+	H(+)

Cofactor:

Ca(2+)

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

reference

DOI no: 10.1073/pnas.90.1.342	Proc Natl Acad Sci U S A 90:342-346 (1993)
PubMed id: 8419939

Crystal structure of phospholipase A2 from Indian cobra reveals a trimeric association.
D.H.Fremont, D.H.Anderson, I.A.Wilson, E.A.Dennis, N.H.Xuong.

ABSTRACT

Phospholipase A2 (PLA2) from Indian cobra venom (Naja naja naja) was crystallized from ethanol in space group P4(3)2(1)2 in the presence of Ca2+. The x-ray crystal structure was determined to 2.3-A resolution by molecular replacement techniques using a theoretical model constructed from homologous segments of the bovine pancreatic, porcine pancreatic, and rattlesnake venom crystal structures. The structure was refined to an R value of 0.174 for 17,542 reflections between 6.0- and 2.3-A resolution (F > 2 sigma), including 148 water molecules. The 119-amino acid enzyme has an overall architecture strikingly similar to the other known PLA2 structures with regions implicated in catalysis showing the greatest structural conservation. Unexpectedly, three monomers were found to occupy the asymmetric unit and are oriented with their catalytic sites facing the pseudo-threefold axis with approximately 15% of the solvent accessible surface of each monomer buried in trimer contacts. The majority of the interactions at the subunit interfaces are made by residues unique to PLA2 sequences from cobra and krait venoms. The possible relevance of this unique trimeric structure is considered.

Literature references that cite this PDB file's key reference

PubMed id

Reference

19604472

D.S.Glazer, R.J.Radmer, and R.B.Altman (2009).
Improving structure-based function prediction using molecular dynamics.

Structure, 17, 919-929.

18931897

J.E.Burke, and E.A.Dennis (2009).
Phospholipase a(2) biochemistry.

Cardiovasc Drugs Ther, 23, 49-59.

19297324

W.Xu, L.Yi, Y.Feng, L.Chen, and J.Liu (2009).
Structural insight into the activation mechanism of human pancreatic prophospholipase A2.

J Biol Chem, 284, 16659-16666.

PDB code:

3elo

18500818

J.E.Burke, M.J.Karbarz, R.A.Deems, S.Li, V.L.Woods, and E.A.Dennis (2008).
Interaction of group IA phospholipase A2 with metal ions and phospholipid vesicles probed with deuterium exchange mass spectrometry.

Biochemistry, 47, 6451-6459.

18247353

P.Hu, L.Sun, Z.Q.Zhu, X.W.Hou, S.Wang, S.S.Yu, H.L.Wang, P.Zhang, M.Wang, L.W.Niu, M.K.Teng, and D.Y.Ruan (2008).
Crystal structure of Natratoxin, a novel snake secreted phospholipaseA2 neurotoxin from Naja atra venom inhibiting A-type K+ currents.

Proteins, 72, 673-683.

PDB code:

2osh

16287060

T.Jabeen, N.Singh, R.K.Singh, J.Jasti, S.Sharma, P.Kaur, A.Srinivasan, and T.P.Singh (2006).
Crystal structure of a heterodimer of phospholipase A2 from Naja naja sagittifera at 2.3 A resolution reveals the presence of a new PLA2-like protein with a novel cys 32-Cys 49 disulphide bridge with a bound sugar at the substrate-binding site.

Proteins, 62, 329-337.

PDB code:

1y75

16508078

G.Singh, S.Gourinath, K.Saravanan, S.Sharma, S.Bhanumathi, C.h.Betzel, A.Srinivasan, and T.P.Singh (2005).
Sequence-induced trimerization of phospholipase A2: structure of a trimeric isoform of PLA2 from common krait (Bungarus caeruleus) at 2.5 A resolution.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 8.

PDB code:

1g2x

15720395

S.M.Lok, R.Gao, M.Rouault, G.Lambeau, P.Gopalakrishnakone, and K.Swaminathan (2005).
Structure and function comparison of Micropechis ikaheka snake venom phospholipase A2 isoenzymes.

FEBS J, 272, 1211-1220.

PDB codes:

1ozy 1p7o 1pwo

16301791

T.Jabeen, N.Singh, R.K.Singh, S.Sharma, R.K.Somvanshi, S.Dey, and T.P.Singh (2005).
Non-steroidal anti-inflammatory drugs as potent inhibitors of phospholipase A2: structure of the complex of phospholipase A2 with niflumic acid at 2.5 Angstroms resolution.

Acta Crystallogr D Biol Crystallogr, 61, 1579-1586.

PDB code:

1td7

12554936

D.J.Rigden, L.W.Hwa, S.Marangoni, M.H.Toyama, and I.Polikarpov (2003).
The structure of the D49 phospholipase A2 piratoxin III from Bothrops pirajai reveals unprecedented structural displacement of the calcium-binding loop: possiblerelationship to cooperative substrate binding.

Acta Crystallogr D Biol Crystallogr, 59, 255-262.

PDB code:

1gmz

11566873

E.Soragni, A.Bolchi, R.Balestrini, C.Gambaretto, R.Percudani, P.Bonfante, and S.Ottonello (2001).
A nutrient-regulated, dual localization phospholipase A(2) in the symbiotic fungus Tuber borchii.

EMBO J, 20, 5079-5090.

11264594

M.C.Nonato, R.C.Garratt, Y.P.Mascarenhas, W.D.Jesus, M.T.Assakura, S.M.Serrano, and G.Oliva (2001).
Crystallization and preliminary crystallographic studies of a phospholipase A2 from the venom of the Brazilian snake Bothrops moojeni.

Acta Crystallogr D Biol Crystallogr, 57, 599-601.

10673441

A.Dessen (2000).
Phospholipase A(2) enzymes: structural diversity in lipid messenger metabolism.

Structure, 8, R15-R22.

11080672

D.A.Six, and E.A.Dennis (2000).
The expanding superfamily of phospholipase A(2) enzymes: classification and characterization.

Biochim Biophys Acta, 1488, 1.

10704197

J.P.Cartailler, H.T.Haigler, and H.Luecke (2000).
Annexin XII E105K crystal structure: identification of a pH-dependent switch for mutant hexamerization.

Biochemistry, 39, 2475-2483.

PDB code:

1dm5

10329797

A.Nagpal, V.Chandra, P.Kaur, and T.P.Singh (1999).
Purification, crystallization and preliminary crystallographic analysis of a natural complex of phospholipase A2 from Echis carinatus (saw-scaled viper).

Acta Crystallogr D Biol Crystallogr, 55, 1240-1241.

10092841

V.Puri, A.Arora, and C.M.Gupta (1999).
Probing the role of C-1 ester group in Naja naja phospholipase A2-phospholipid interactions using butanetriol-containing phosphatidylcholine analogues.

Eur J Biochem, 259, 586-591.

7612854

L.J.Reynolds, E.S.Kempner, L.L.Hughes, and E.A.Dennis (1995).
Inactivation of secretory phospholipase A2 by ionizing radiation.

Biophys J, 68, 2108-2114.

8590005

P.D.Kwong, N.Q.McDonald, P.B.Sigler, and W.A.Hendrickson (1995).
Structure of beta 2-bungarotoxin: potassium channel binding by Kunitz modules and targeted phospholipase action.

Structure, 3, 1109-1119.

PDB code:

1bun

7948668

D.L.Scott, A.M.Mandel, P.B.Sigler, and B.Honig (1994).
The electrostatic basis for the interfacial binding of secretory phospholipases A2.

Biophys J, 67, 493-504.

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.