1A3D

PHOSPHOLIPASE A2 (PLA2) FROM NAJA NAJA VENOM

Summary for 1A3D

• Entry DOI: 10.2210/pdb1a3d/pdb
• Descriptor: PHOSPHOLIPASE A2, SODIUM ION (3 entities in total)
• Functional Keywords: phospholipase, trimer, calcium binding, activator site, carboxylic ester hydrolase
• Biological source: Naja naja (Indian cobra)
• Cellular location: Secreted: P15445
• Total number of polymer chains: 1
• Total formula weight: 13380.84

Authors

Segelke, B.W.,Nguyen, D.,Chee, R.,Xuong, H.N.,Dennis, E.A. (deposition date: 1998-01-20, release date: 1998-04-29, Last modification date: 2024-10-23)

Primary citation

Segelke, B.W.,Nguyen, D.,Chee, R.,Xuong, N.H.,Dennis, E.A.
Structures of two novel crystal forms of Naja naja naja phospholipase A2 lacking Ca2+ reveal trimeric packing.
J.Mol.Biol., 279:223-232, 1998

PubMed Abstract: Three crystal forms of Naja naja naja phospholipase A2 were discovered through random crystallization screening, including two heretofore uncharacterized forms. The crystallization conditions for both of these novel crystal forms are Ca(2+)-free whereas previously reported conditions include Ca2+. One of the new crystal forms has a cubic lattice in the space group P2(1)3 (a = b = c = 69.24 A), the other has an orthorhombic lattice in the space group P2(1)2(1)2(1) (a = 67.22 A, b = 73.48 A, c = 87.52 A) and a previously characterized crystal belong to the tetragonal space group P4(3)2(1)2 (a = b = 88.6 A, c = 107.4 A). The structure from the cubic crystal form has been determined to 1.8 A and refined to an R-factor of 17% while the structure from the orthorhombic form has been determined to 2.65 A and has been refined to an R-factor of 21%. The determination of the cubic structure extends the resolution to which structures of this molecule have been determined from 2.3 A to 1.8 A. The two newly determined structures, in combination with the previously determined structure, generate an informative structural ensemble from which structural changes due to Ca2+, which is required for catalysis, and the effect of crystal contacts on side-chain conformations and oligomeric association can be inferred. Both of the newly determined structures reveal a trimeric oligomer as observed in the tetragonal structure; this appears to be a unique feature of the Naja naja naja enzyme.

PubMed: 9636712
DOI: 10.1006/jmbi.1998.1759

Experimental method

X-RAY DIFFRACTION (1.8 Å)