PDBsum entry 1a3f

Carboxylic ester hydrolase

PDB id: 1a3f

Contents

Protein chains

119 a.a. *

* Residue conservation analysis

PDB id:

1a3f

Name:

Carboxylic ester hydrolase

Title:

Phospholipase a2 (pla2) from naja naja venom

Structure:

Phospholipase a2. Chain: a, b, c. Ec: 3.1.1.4

Source:

Naja naja. Indian cobra. Organism_taxid: 35670. Cellular_location: venom sack

Biol. unit:

Monomer (from PDB file)

Resolution:

2.65Å R-factor: 0.210 R-free: 0.260

Authors:

B.W.Segelke,D.Nguyen,R.Chee,H.N.Xuong,E.A.Dennis

Key ref:

B.W.Segelke et al. (1998). Structures of two novel crystal forms of Naja naja naja phospholipase A2 lacking Ca2+ reveal trimeric packing. J Mol Biol, 279, 223-232. PubMed id: 9636712 DOI: 10.1006/jmbi.1998.1759

Date:

21-Jan-98 Release date: 29-Apr-98

Protein chains

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

Seq: 119 a.a.

Struc: 119 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: 10.1006/jmbi.1998.1759

J Mol Biol 279:223-232 (1998)

PubMed id: 9636712

Structures of two novel crystal forms of Naja naja naja phospholipase A2 lacking Ca2+ reveal trimeric packing.

B.W.Segelke, D.Nguyen, R.Chee, N.H.Xuong, E.A.Dennis.

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.

Selected figure(s)

Figure 4.
Figure 4. Average deviation of atomic position for side-chain atoms versus ���������������� �B=8p

Figure 5.
Figure 5. Conformational changes. (a) Conformational change at residue 73 due to crystal contacts. A stereo view of the crystal contact environment for glutamine 73 of subunit B in the tetragonal structure (shown in yellow) is shown with the cubic structure (shown in cyan) superimposed. Bonds are shown as thin tubes and polar or charged atoms of interest are shown as spheres colored according to atom type (nitrogen blue and oxygen red). Proposed hydrogen bonds are shown as broken gray lines. Glutamine 73 from subunit B of the tetragonal structure is hydrogen bonding with lysine 65 and asparagine 83 of subunit C of a symmetry-related molecule in the crystal packing of the tetragonal struc- ture. Glutamine 73 from the cubic structure clashes severely with atoms in the symmetry-related molecules in the crystal packing of the tetragonal structure. Gluta- mine 73 from subunit C (not shown) is also involved in crystal contacts, hydrogen bonding with asparagine 83 of a symmetry-related subunit A and to a water mol- ecule hydrogen bonding to lysine 65 of subunit A. This Figure was generated with MIDAS (UCSF & MGL, 1995). (b) Conformational change at residue 42 due to crystal contacts. Shown in cyan, residues 39, 42, and 45 are shown with the backbone helical segment and superimposed with the same residues of the tetragonal structure (shown in yellow). Backbone C a trace is shown as thick tubes while bonds are shown as thin tubes and polar or charged atoms of interest are shown as spheres colored according to atom type (nitrogen blue and oxy- gen red). Proposed hydrogen bonds are shown as bro- ken gray lines. Also shown are two symmetry-related residues 39 and a proposed sodium ion coordinated to the three acid groups that approach each other in the crystal packing. A thin green line is shown which is coincident with the crystallographic 3-fold axis. The con- formational change in residue 42 is due to shielding of the charge on the acidic group of aspartate 39 upon binding to the ammonium ion, which causes the charge

The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 279, 223-232) copyright 1998.

Figures were selected by an automated process.