PDBsum entry 1s8h

Hydrolase, toxin

PDB id: 1s8h

Contents

Protein chain

121 a.a. *

Ligands

SO4

Waters ×139

* Residue conservation analysis

PDB id:

1s8h

Name:

Hydrolase, toxin

Title:

Crystal structure of lys49-phospholipase a2 from agkistrodon contortrix laticinctus, first fatty acid free form

Structure:

Phospholipase a2 homolog. Chain: a. Synonym: myotoxin. Ec: 3.1.1.4

Source:

Agkistrodon contortrix laticinctus. Broad-banded copperhead. Organism_taxid: 37195. Strain: laticinctus. Other_details: snake venom protein

Resolution:

1.80Å R-factor: 0.193 R-free: 0.229

Authors:

A.L.B.Ambrosio,D.H.F.De Souza,M.C.Nonato,H.S.Selistre De Araujo, C.L.Ownby,R.C.Garratt

Key ref:

A.L.Ambrosio et al. (2005). A molecular mechanism for Lys49-phospholipase A2 activity based on ligand-induced conformational change. J Biol Chem, 280, 7326-7335. PubMed id: 15596433 DOI: 10.1074/jbc.M410588200

Date:

02-Feb-04 Release date: 10-Feb-04

Protein chain

P49121  (PA2H1_AGKCL) -  Basic phospholipase A2 homolog MT1 from Agkistrodon contortrix laticinctus

Seq: 137 a.a.

Struc: 121 a.a.

Enzyme reactions

• Enzyme class: 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+)

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

reference

DOI no: 10.1074/jbc.M410588200

J Biol Chem 280:7326-7335 (2005)

PubMed id: 15596433

A molecular mechanism for Lys49-phospholipase A2 activity based on ligand-induced conformational change.

A.L.Ambrosio, M.C.Nonato, H.S.de Araújo, R.Arni, R.J.Ward, C.L.Ownby, D.H.de Souza, R.C.Garratt.

ABSTRACT

Agkistrodon contortrix laticinctus myotoxin is a Lys(49)-phospholipase A(2) (EC 3.1.1.4) isolated from the venom of the serpent A. contortrix laticinctus (broad-banded copperhead). We present here three monomeric crystal structures of the myotoxin, obtained under different crystallization conditions. The three forms present notable structural differences and reveal that the presence of a ligand in the active site (naturally presumed to be a fatty acid) induces the exposure of a hydrophobic surface (the hydrophobic knuckle) toward the C terminus. The knuckle in A. contortrix laticinctus myotoxin involves the side chains of Phe(121) and Phe(124) and is a consequence of the formation of a canonical structure for the main chain within the region of residues 118-125. Comparison with other Lys(49)-phospholipase A(2) myotoxins shows that although the knuckle is a generic structural motif common to all members of the family, it is not readily recognizable by simple sequence analyses. An activation mechanism is proposed that relates fatty acid retention at the active site to conformational changes within the C-terminal region, a part of the molecule that has long been associated with Ca(2+)-independent membrane damaging activity and myotoxicity. This provides, for the first time, a direct structural connection between the phospholipase "active site" and the C-terminal "myotoxic site," justifying the otherwise enigmatic conservation of the residues of the former in supposedly catalytically inactive molecules.

Selected figure(s)

Figure 4.
FIG. 4. Stereo view ribbon representation of the C terminus and calcium binding loops of the 18 available structures. Thirteen of the 18 available structures of Lys49-PLA[2] present the canonical conformation. Red, form I of ACL myotoxin (PDB code 1S8G [PDB] ), chains A and B of piratoxin-II (PDB code 1QLL [PDB] ), chains A and B of myotoxin-II (PDB code 1CLP [PDB] ), chain A of structure 1, and chains A and B of structure 2, a monomer of structure 3 (with stearic acid bound), where a slight difference in the conformation of residues Tyr120 and Leu121 is observed, and monomer of structure 4 (complexed with a PEG fragment) of BthTX-I, acutohemolysin (PDB code 1MC2 [PDB] ), and chains A and B for NumMT-I, both in complex with stearic acid. The Lys122 (C- shown as balls) interacts with the Cys29-Gly30 peptide bond at the Ca^2+ binding loop. Moreover, seven of these present a fatty acid molecule inside the hydrophobic channel. The remaining five structures where the Lys122 points toward the solvent region and the C terminus show a high degree of variability: in white, form II of ACL myotoxin (PDB code 1S8H [PDB] ) and A. piscivorus piscivorus (PDB code 1PPA [PDB] ); in yellow, chain B of structure I from BthTX-I; in green, form III of ACL myotoxin (PDB code 1S8I [PDB] ), and in blue, GodMT-II (1GOD).

Figure 6.
FIG. 6. The hydrophobic knuckle. a, presence of a large non-polar surface exposed to the solvent (potential surface map, calculated by GRASP (89)), formed by hydrophobic residues surrounding Lys122, and constituting the hydrophobic knuckle. In all cases, Lys122 interacts with the Cys29-Gly30 peptide bond, and a ligand is bound to the hydrophobic channel. Positive charges surround the base of the knuckle. b, the knuckle can also be observed in ligand-free structures that present the canonical conformation for the C-terminal region, where Lys122 interacts with Cys29-Gly30 peptide bond. c, structures where Lys122 is exposed to the solvent, the hydrophobic knuckle is not observed.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 7326-7335) copyright 2005.

Figures were selected by the author.