PDBsum entry 1rlw

Hydrolase

PDB id: 1rlw

Contents

Protein chain

126 a.a. *

Metals

_CD ×2

_CA ×2

Waters ×151

* Residue conservation analysis

PDB id:

1rlw

Name:

Hydrolase

Title:

Calcium-phospholipid binding domain from cytosolic phospholipase a2

Structure:

Phospholipase a2. Chain: a. Fragment: c2 domain, residues 17 - 141 from cpla2. Synonym: calb domain. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Cellular_location: cytosol. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: de3.

Resolution:

2.40Å R-factor: 0.227 R-free: 0.273

Authors:

O.Perisic,R.L.Williams

Key ref:

O.Perisic et al. (1998). Crystal structure of a calcium-phospholipid binding domain from cytosolic phospholipase A2. J Biol Chem, 273, 1596-1604. PubMed id: 9430701 DOI: 10.1074/jbc.273.3.1596

Date:

28-Oct-97 Release date: 25-Feb-98

Protein chain

P47712  (PA24A_HUMAN) -  Cytosolic phospholipase A2 from Homo sapiens

Seq: 749 a.a.

Struc: 126 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: E.C.3.1.1.4 - phospholipase A2.
• Reaction: a 1,2-diacyl-sn-glycero-3-phosphocholine + H2O = a 1-acyl-sn-glycero-3- phosphocholine + a fatty acid + H⁺
• Cofactor: Ca(2+)
• Enzyme class 3: E.C.3.1.1.5 - lysophospholipase.
• Reaction: a 1-acyl-sn-glycero-3-phosphocholine + H2O = sn-glycerol 3-phosphocholine + a fatty acid + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1074/jbc.273.3.1596

J Biol Chem 273:1596-1604 (1998)

PubMed id: 9430701

Crystal structure of a calcium-phospholipid binding domain from cytosolic phospholipase A2.

O.Perisic, S.Fong, D.E.Lynch, M.Bycroft, R.L.Williams.

ABSTRACT

Cytosolic phospholipase A2 (cPLA2) is a calcium-sensitive 85-kDa enzyme that hydrolyzes arachidonic acid-containing membrane phospholipids to initiate the biosynthesis of eicosanoids and platelet-activating factor, potent inflammatory mediators. The calcium-dependent activation of the enzyme is mediated by an N-terminal C2 domain, which is responsible for calcium-dependent translocation of the enzyme to membranes and that enables the intact enzyme to hydrolyze membrane-resident substrates. The 2.4-A x-ray crystal structure of this C2 domain was solved by multiple isomorphous replacement and reveals a beta-sandwich with the same topology as the C2 domain from phosphoinositide-specific phospholipase C delta 1. Two clusters of exposed hydrophobic residues surround two adjacent calcium binding sites. This region, along with an adjoining strip of basic residues, appear to constitute the membrane binding motif. The structure provides a striking insight into the relative importance of hydrophobic and electrostatic components of membrane binding for cPLA2. Although hydrophobic interactions predominate for cPLA2, for other C2 domains such as in "conventional" protein kinase C and synaptotagmins, electrostatic forces prevail.

Selected figure(s)

Figure 4.
Fig. 4. A surface representation of cPLA2 C2 domain and a comparison with SytI-C2A. A, the entire domain of cPLA2 oriented^ to illustrate the strikingly hydrophobic CBRs and a prominent strip of basic residues on strand 3. The residues are colored^ by type. Basic residues are blue, acidic are red, and hydrophobic^ (Ala, Pro, Val, Leu, Ile, Met, Phe, Tyr, and Trp) are colored^ green. B, an expanded view of the CBRs in either the same orientation as A (right) or rotated 90° around a horizontal axis (left). C, views of the SytI-C2A domain in orientations equivalent to those^ shown in B. The figures were created with the program GRASP.

Figure 5.
Fig. 5. A model of the proposed interaction of cPLA2 C2 domain with a phospholipid membrane (rendered with POV-RAYTM). The membrane lipids are taken from a crystal structure^ of a 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine bilayer (73). The domain was approximately oriented so that 1) the hydrophobic^ tip of CBR3 penetrated into the membrane, displacing 2-3 phospholipids from the membrane, 2) the phosphate group of one phospholipid^ makes a direct interaction with calcium ions bound in sites I and II, 3) the hydrophobic residues of CBR1 are in the interface^ region of the membrane and interacting with the methyl groups of the phosphatidylcholine headgroups, and 4) the strip of basic^ residues along strand 3 shown in the CPK representation (dark blue spheres) is near the surface of the membrane layer to facilitate^ electrostatic interactions with the phospholipid head groups.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (1998, 273, 1596-1604) copyright 1998.

Figures were selected by an automated process.