Crystal structure of type-III geranylgeranyl pyrophosphate synthase from Saccharomyces cerevisiae and the mechanism of product chain length determination

被引:86
作者
Chang, Tao-Hsin
Guo, Rey-Ting
Ko, Tzu-Ping
Wang, Andrew H. -J.
Liang, Po-Huang
机构
[1] Acad Sinica, Inst Biol Chem, Taiwan Int Grad Program, Taipei 115, Taiwan
[2] Natl Taiwan Univ, Inst Biochem Sci, Taipei 106, Taiwan
[3] Acad Sinica, Inst Biol Chem, Taipei 115, Taiwan
关键词
D O I
10.1074/jbc.M512886200
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
Geranylgeranyl pyrophosphate synthase ( GGPPs) catalyzes a condensation reaction of farnesyl pyrophosphate with isopentenyl pyrophosphate to generate C-20 geranylgeranyl pyrophosphate, which is a precursor for carotenoids, chlorophylls, geranylgeranylated proteins, and archaeal ether-linked lipid. For short-chain trans-prenyltransferases that synthesize C-10-C-25 products, bulky amino acid residues generally occupy the fourth or fifth position upstream from the first DDXXD motif to block further elongation of the final products. However, the short-chain type-III GGPPs in eukaryotes lack any large amino acid at these positions. In this study, the first structure of type-III GGPPs from Saccharomyces cerevisiae has been determined to 1.98 (A) over circle resolution. The structure is composed entirely of 15 alpha-helices joined by connecting loops and is arranged with alpha-helices around a large central cavity. Distinct from other known structures of trans-prenyltransferases, the N-terminal 17 amino acids ( 9-amino acid helix A and the following loop) of this GGPPs protrude from the helix core into the other subunit and contribute to the tight dimer formation. Deletion of the first 9 or 17 amino acids caused the dissociation of dimer into monomer, and the Delta( 1 - 17) mutant showed abolished enzyme activity. In each subunit, an elongated hydrophobic crevice surrounded by D, F, G, H, and I alpha-helices contains two DDXXD motifs at the top for substrate binding with one Mg2+ coordinated by Asp(75), Asp(79), and four water molecules. It is sealed at the bottom with three large residues of Tyr(107), Phe(108), and His(139). Compared with the major product C-30 synthesized by mutant H139A, the products generated by mutant Y107A and F108A are predominantly C-40 and C-30, respectively, suggesting the most important role of Tyr(107) in determining the product chain length.
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页码:14991 / 15000
页数:10
相关论文
共 34 条
[1]  
Brunger AT, 1998, ACTA CRYSTALLOGR D, V54, P905, DOI 10.1107/s0907444998003254
[2]   Substrate binding mode and reaction mechanism of undecaprenyl pyrophosphate synthase deduced from crystallographic studies [J].
Chang, SY ;
Ko, TP ;
Chen, APC ;
Wang, AHJ ;
Liang, PH .
PROTEIN SCIENCE, 2004, 13 (04) :971-978
[3]  
CHEN AJ, 1994, PROTEIN SCI, V3, P600
[4]   Crystal structure of cis-prenyl chain elongating enzyme, undecaprenyl diphosphate synthase [J].
Fujihashi, M ;
Zhang, YW ;
Higuchi, Y ;
Li, XY ;
Koyama, T ;
Miki, K .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (08) :4337-4342
[5]   Production of selenomethionine-labelled proteins using simplified culture conditions and generally applicable host/vector systems [J].
Guerrero, SA ;
Hecht, HJ ;
Hofmann, B ;
Biebl, H ;
Singh, M .
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 2001, 56 (5-6) :718-723
[6]   SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling [J].
Guex, N ;
Peitsch, MC .
ELECTROPHORESIS, 1997, 18 (15) :2714-2723
[7]   Crystal structures of undecaprenyl pyrophosphate synthase in complex with magnesium, isopentenyl pyrophosphate, and farnesyl thiopyrophosphate - Roles of the metal ion and conserved residues in catalysis [J].
Guo, RT ;
Ko, TP ;
Chen, APC ;
Kuo, CJ ;
Wang, AHJ ;
Liang, PH .
JOURNAL OF BIOLOGICAL CHEMISTRY, 2005, 280 (21) :20762-20774
[8]   Crystal structure of octaprenyl pyrophosphate synthase from hyperthermophilic hyhermotoga maritima and mechanism of product chain length determination [J].
Guo, RT ;
Kuo, CJ ;
Chou, CC ;
Ko, TP ;
Shr, HL ;
Liang, PH ;
Wang, AHJ .
JOURNAL OF BIOLOGICAL CHEMISTRY, 2004, 279 (06) :4903-4912
[9]   A molecular ruler for chain elongation catalyzed by octaprenyl pyrophosphate synthase and its structure-based engineering to produce unprecedented long chain trans-prenyl products [J].
Guo, RT ;
Kuo, CJ ;
Ko, TP ;
Chou, CC ;
Liang, PH ;
Wang, AHJ .
BIOCHEMISTRY, 2004, 43 (24) :7678-7686
[10]   An alternative mechanism of product chain-length determination in type III geranylgeranyl diphosphate synthase [J].
Hemmi, H ;
Noike, M ;
Nakayama, T ;
Nishino, T .
EUROPEAN JOURNAL OF BIOCHEMISTRY, 2003, 270 (10) :2186-2194