High-resolution refinement of orthorhombic bovine pancreatic phospholipase A2

被引:26
作者
Sekar, K
Sundaralingam, M
机构
[1] Ohio State Univ, Dept Chem, Biol Macromol Struct Ctr, Columbus, OH 43210 USA
[2] Ohio State Univ, Dept Biochem, Columbus, OH 43210 USA
来源
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY | 1999年 / 55卷
关键词
D O I
10.1107/S0907444998006568
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
The X-ray structure of recombinant bovine pancreatic phospholipase A(2) (PLA2), which specifically catalyzes the cleavage of the sn-2 acylester bond of phospholipids, has been refined at 1.5 Angstrom resolution. The crystal belongs to the space group P2(1)2(1)2(1) with unit-cell parameters a = 47.12, b = 64.59 and c = 38.14 Angstrom similar to the native enzyme reported previously by Dijkstra et nl. [J. Mel. Biol. (1981), 147, 97-123]. The refinement converged to an R value of 18.4% (R-free = 22.8%) for 16 374 reflections between 10.0 and 1.5 Angstrom resolution. The surface-loop residues (60-70) art: ordered in the present orthorhombic recombinant enzyme, but disordered in the trigonal recombinant enzyme. The active-site residues, His48, Asp99, and the catalytic water superimpose well with the trigonal form. Besides the catalytic water which is hydrogen bonded to His48, it is often seen that there is a second water attached to the same N atom of His48 and simultaneously hydrogen bonded to the O atom of Asp49. It is thought that the second water facilitates the tautomerism of His48 for enzyme catalysis, The catalytic water is also hydrogen bonded to the equatorial water coordinated to the calcium ion, In addition to the equatorial water, there is also an axial calcium water and the additional structural water. These five common water molecules are hydrogen bonded to the additional 16 water molecules in the present orthorhombic structure which may further enhance the structural integrity of the active site. Besides the protein and one calcium ion, a total of 134 water molecules were located in the present high-resolution refinement.
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页码:46 / 50
页数:5
相关论文
共 15 条
[1]  
Brunger A.T., 1992, X-Plor Manual Version 3.1
[2]   FREE R-VALUE - A NOVEL STATISTICAL QUANTITY FOR ASSESSING THE ACCURACY OF CRYSTAL-STRUCTURES [J].
BRUNGER, AT .
NATURE, 1992, 355 (6359) :472-475
[3]   EVOLUTIONARY RELATIONSHIPS AND IMPLICATIONS FOR THE REGULATION OF PHOSPHOLIPASE-A2 FROM SNAKE-VENOM TO HUMAN SECRETED FORMS [J].
DAVIDSON, FF ;
DENNIS, EA .
JOURNAL OF MOLECULAR EVOLUTION, 1990, 31 (03) :228-238
[4]   STRUCTURE OF BOVINE PANCREATIC PHOSPHOLIPASE-A2 AT 1.7A RESOLUTION [J].
DIJKSTRA, BW ;
KALK, KH ;
HOL, WGJ ;
DRENTH, J .
JOURNAL OF MOLECULAR BIOLOGY, 1981, 147 (01) :97-123
[5]   RAT SUBMAXILLARY-GLAND SERINE PROTEASE, TONIN - STRUCTURE SOLUTION AND REFINEMENT AT 1.8 A RESOLUTION [J].
FUJINAGA, M ;
JAMES, MNG .
JOURNAL OF MOLECULAR BIOLOGY, 1987, 195 (02) :373-396
[6]   FUNCTIONAL-ASPECTS OF HEPATIC SINUSOIDAL CELLS [J].
JONES, EA ;
SUMMERFIELD, JA .
SEMINARS IN LIVER DISEASE, 1985, 5 (02) :157-174
[7]   MOLSCRIPT - A PROGRAM TO PRODUCE BOTH DETAILED AND SCHEMATIC PLOTS OF PROTEIN STRUCTURES [J].
KRAULIS, PJ .
JOURNAL OF APPLIED CRYSTALLOGRAPHY, 1991, 24 :946-950
[8]   PROCHECK - A PROGRAM TO CHECK THE STEREOCHEMICAL QUALITY OF PROTEIN STRUCTURES [J].
LASKOWSKI, RA ;
MACARTHUR, MW ;
MOSS, DS ;
THORNTON, JM .
JOURNAL OF APPLIED CRYSTALLOGRAPHY, 1993, 26 :283-291
[9]  
LIU X, 1995, BIOCHEMISTRY-US, V35, P7322
[10]   TRAITEMENT STATISTIQUE DES ERREURS DANS LA DETERMINATION DES STRUCTURES CRISTALLINES [J].
LUZZATI, V .
ACTA CRYSTALLOGRAPHICA, 1952, 5 (06) :802-810