Crystal Structure of Serine Dehydratase from Rat Liver
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- 作者：Taro Yamada ; Junichi Komoto ; Yoshimi Takata ; Hirofumi Ogawa ; Henry C. Pitot ; and Fusao Takusagawa
- 刊名：Biochemistry
- 出版年：2003
- 出版时间：November 11, 2003
- 年：2003
- 卷：42
- 期：44
- 页码：12854 - 12865
- 全文大小：872K
- 年卷期：v.42,no.44(November 11, 2003)
- ISSN：1520-4995
文摘
SDH (L-serine dehydratase, EC 4.3.1.17) catalyzes the pyridoxal 5'-phosphate (PLP)-dependentdehydration of L-serine to yield pyruvate and ammonia. Liver SDH plays an important role ingluconeogenesis. Formation of pyruvate by SDH is a two-step reaction in which the hydroxyl group ofserine is cleaved to produce aminoacrylate, and then the aminoacrylate is deaminated by nonenzymatichydrolysis to produce pyruvate. The crystal structure of rat liver apo-SDH was determined by singleisomorphous replacement at 2.8 Å resolution. The holo-SDH crystallized with O-methylserine (OMS)was also determined at 2.6 Å resolution by molecular replacement. SDH is composed of two domains,and each domain has a typical 
-open structure. The active site is located in the cleft between the twodomains. The holo-SDH contained PLP-OMS aldimine in the active site, indicating that OMS can formthe Schiff base linkage with PLP, but the subsequent dehydration did not occur. Apo-SDH forms a dimerby inserting the small domain into the catalytic cleft of the partner subunit so that the active site is closed.Holo-SDH also forms a dimer by making contacts at the back of the clefts so that the dimerization doesnot close the catalytic cleft. The phosphate group of PLP is surrounded by a characteristic G-rich sequence(168GGGGL172) and forms hydrogen bonds with the amide groups of those amino acid residues, suggestingthat the phosphate group can be protonated. N1 of PLP participates in a hydrogen bond with Cys303, andsimilar hydrogen bonds with N1 participating are seen in other -elimination enzymes. These hydrogenbonding schemes indicate that N1 is not protonated, and thus, the pyridine ring cannot take a quinone-likestructure. These characteristics of the bound PLP suggest that SDH catalysis is not facilitated by formingthe resonance-stabilized structure of the PLP-Ser aldimine as seen in aminotransferases. A possible catalyticmechanism involves the phosphate group, surrounded by the characteristic sequence, acting as a generalacid to donate a proton to the leaving hydroxyl group of serine.
-open structure. The active site is located in the cleft between the twodomains. The holo-SDH contained PLP-OMS aldimine in the active site, indicating that OMS can formthe Schiff base linkage with PLP, but the subsequent dehydration did not occur. Apo-SDH forms a dimerby inserting the small domain into the catalytic cleft of the partner subunit so that the active site is closed.Holo-SDH also forms a dimer by making contacts at the back of the clefts so that the dimerization doesnot close the catalytic cleft. The phosphate group of PLP is surrounded by a characteristic G-rich sequence(168GGGGL172) and forms hydrogen bonds with the amide groups of those amino acid residues, suggestingthat the phosphate group can be protonated. N1 of PLP participates in a hydrogen bond with Cys303, andsimilar hydrogen bonds with N1 participating are seen in other -elimination enzymes. These hydrogenbonding schemes indicate that N1 is not protonated, and thus, the pyridine ring cannot take a quinone-likestructure. These characteristics of the bound PLP suggest that SDH catalysis is not facilitated by formingthe resonance-stabilized structure of the PLP-Ser aldimine as seen in aminotransferases. A possible catalyticmechanism involves the phosphate group, surrounded by the characteristic sequence, acting as a generalacid to donate a proton to the leaving hydroxyl group of serine.