STRUCTURE OF ISOCITRATE DEHYDROGENASE WITH ISOCITRATE, NICOTINAMIDE ADENINE-DINUCLEOTIDE PHOSPHATE, AND CALCIUM AT 2.5-ANGSTROM RESOLUTION - A PSEUDO-MICHAELIS TERNARY COMPLEX

被引:111
作者
STODDARD, BL [1 ]
DEAN, A [1 ]
KOSHLAND, DE [1 ]
机构
[1] UNIV CALIF BERKELEY,DEPT MOLEC & CELLULAR BIOL,DIV BIOCHEM,229 STANLEY HALL,BERKELEY,CA 94720
关键词
D O I
10.1021/bi00087a008
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The structure of isocitrate dehydrogenase (IDH) with a bound complex of isocitrate, NADP+, and Ca2+ was solved at 2.5-angstrom resolution and compared by difference mapping against previously determined enzymatic complexes. Calcium replaces magnesium in the binding of metal-substrate chelate complex, resulting in a substantially reduced turnover rate. The structure shows the following: (i) A complete, structurally ordered ternary complex (enzyme, isocitrate, NADP+, and Ca2+) is observed in the active site, with the nicotinamide ring of NADP+ exhibiting a specific salt bridge with isocitrate. The binding of the cofactor nicotinamide ring is dependent on this interaction. (ii) Isocitrate is bound by the enzyme with the same interactions as those found for the magnesium/substrate binary complex, but the entire molecule is shifted in the active site by approximately 1 angstrom in order to accommodate the larger metal species and to interact with the nicotinamide ring. The distances from isocitrate to the bound calcium are substantially longer than those previously found with magnesium. (iii) NADP in the Escherichia coli IDH has a novel binding site and conformation as compared to previously solved dehydrogenases. (iv) The orientation and interactions of the nicotinamide ring with the substrate are consistent with the stereospecificity of the enzyme-catalyzed reaction.
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页码:9310 / 9316
页数:7
相关论文
共 32 条
[1]   STRUCTURE OF LACTATE DEHYDROGENASE AT 2.8A RESOLUTION [J].
ADAMS, MJ ;
FORD, GC ;
KOEKOEK, R ;
LENTZ, PJ ;
MCPHERSON, A ;
ROSSMANN, MG ;
SMILEY, IE ;
SCHEVITZ, RW ;
WONACOTT, AJ .
NATURE, 1970, 227 (5263) :1098-+
[2]   STRUCTURE OF CALMODULIN REFINED AT 2.2 A RESOLUTION [J].
BABU, YS ;
BUGG, CE ;
COOK, WJ .
JOURNAL OF MOLECULAR BIOLOGY, 1988, 204 (01) :191-204
[3]   PROTEIN DATA BANK - COMPUTER-BASED ARCHIVAL FILE FOR MACROMOLECULAR STRUCTURES [J].
BERNSTEIN, FC ;
KOETZLE, TF ;
WILLIAMS, GJB ;
MEYER, EF ;
BRICE, MD ;
RODGERS, JR ;
KENNARD, O ;
SHIMANOUCHI, T ;
TASUMI, M .
JOURNAL OF MOLECULAR BIOLOGY, 1977, 112 (03) :535-542
[4]   REFINED CRYSTAL-STRUCTURE OF CYTOPLASMIC MALATE-DEHYDROGENASE AT 2.5-A RESOLUTION [J].
BIRKTOFT, JJ ;
RHODES, G ;
BANASZAK, LJ .
BIOCHEMISTRY, 1989, 28 (14) :6065-6081
[5]   CRYSTALLOGRAPHIC R-FACTOR REFINEMENT BY MOLECULAR-DYNAMICS [J].
BRUNGER, AT ;
KURIYAN, J ;
KARPLUS, M .
SCIENCE, 1987, 235 (4787) :458-460
[6]   ELECTROSTATIC AND STERIC CONTRIBUTIONS TO REGULATION AT THE ACTIVE-SITE OF ISOCITRATE DEHYDROGENASE [J].
DEAN, AM ;
KOSHLAND, DE .
SCIENCE, 1990, 249 (4972) :1044-1046
[7]  
DEAN AM, 1993, BIOCHEMISTRY-US, V32
[8]   CRYSTALLOGRAPHIC INVESTIGATIONS OF NICOTINAMIDE ADENINE-DINUCLEOTIDE BINDING TO HORSE LIVER ALCOHOL-DEHYDROGENASE [J].
EKLUND, H ;
SAMAMA, JP ;
JONES, TA .
BIOCHEMISTRY, 1984, 23 (25) :5982-5996
[9]  
EKLUND H, 1981, J MOL BIOL, V146, P561, DOI 10.1016/0022-2836(81)90047-4
[10]   STRUCTURE OF THE ACTIVE TERNARY COMPLEX OF PIG-HEART LACTATE-DEHYDROGENASE WITH S-LAC-NAD AT 2.7 A RESOLUTION [J].
GRAU, UM ;
TROMMER, WE ;
ROSSMANN, MG .
JOURNAL OF MOLECULAR BIOLOGY, 1981, 151 (02) :289-307