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Article

Crystal Structure of S-Adenosylhomocysteine Hydrolase from Rat Liver^†^,^‡

Supporting Info

Yongbo Hu,^§ Junichi Komoto,^§ Yafei Huang,^§ Tomoharu Gomi, Hirofumi Ogawa, Yoshimi Takata, Motoji Fujioka, and Fusao Takusagawa*^§

Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045-2106, and Department of Biochemistry, Toyama Medical and Pharmaceutical University, Faculty of Medicine, Sugitani, Toyama 930-0194, Japan

Biochemistry, 1999, 38 (26), pp 8323–8333

DOI: 10.1021/bi990332k

Publication Date (Web): June 6, 1999

†

The works carried out at the University of Kansas have been supported by NIH Grant GM37233.

‡

The atomic coordinates have been deposited in the Brookhaven Protein Data Bank (file name 1B3R).

University of Kansas.

Toyama Medical and Pharmaceutical University.

To whom all correspondence should be addressed: Department of Molecular Biosciences, 3042 Haworth Hall, University of Kansas, Lawrence, KS 66045-2106. Telephone: (785) 864-4727. Fax: (785) 864-5321. E-mail: xraymain@kuhub.cc.ukans.edu.

Abstract

The crystal structure of rat liver S-adenosyl-l-homocysteine hydrolase (AdoHcyase, EC 3.3.1.1) which catalyzes the reversible hydrolysis of S-adenosylhomocysteine (AdoHcy) has been determined at 2.8 Å resolution. AdoHcyase from rat liver is a tetrameric enzyme with 431 amino acid residues in each identical subunit. The subunit is composed of the catalytic domain, the NAD⁺-binding domain, and the small C-terminal domain. Both catalytic and NAD⁺-binding domains are folded into an ellipsoid with a typical α/β twisted open sheet structure. The C-terminal section is far from the main body of the subunit and extends into the opposite subunit. An NAD⁺ molecule binds to the consensus NAD⁺-binding cleft of the NAD⁺-binding domain. The peptide folding pattern of the catalytic domain is quite similar to the patterns observed in many methyltransferases. Although the crystal structure does not contain AdoHcy or its analogue, there is a well-formed AdoHcy-binding crevice in the catalytic domain. Without introducing any major structural changes, an AdoHcy molecule can be placed in the catalytic domain. In the structure described here, the catalytic and NAD⁺-binding domains are quite far apart from each other. Thus, the enzyme appears to have an “open” conformation in the absence of substrate. It is likely that binding of AdoHcy induces a large conformational change so as to place the ribose moiety of AdoHcy in close proximity to the nicotinamide moiety of NAD⁺. A catalytic mechanism of AdoHcyase has been proposed on the basis of this crystal structure. Glu155 acts as a proton acceptor from the O3‘-H when the proton of C3‘-H is abstracted by NAD⁺. His54 or Asp130 acts as a general acid−base catalyst, while Cys194 modulates the oxidation state of the bound NAD⁺. The polypeptide folding pattern of the catalytic domain suggests that AdoHcy molecules can travel freely to and from AdoHcyase and methyltransferases to properly regulate methyltransferase activities. We believe that the crystal structure described here can provide insight into the molecular architecture of this important regulatory enzyme.