PDBsum entry 1d4f

Hydrolase

PDB id: 1d4f

Contents

Protein chains

430 a.a. *

Ligands

NAD ×4

ADN ×4

Waters ×473

* Residue conservation analysis

PDB id:

1d4f

Name:

Hydrolase

Title:

Crystal structure of recombinant rat-liver d244e mutant s- adenosylhomocysteine hydrolase

Structure:

S-adenosylhomocysteine hydrolase. Chain: a, b, c, d. Engineered: yes. Mutation: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Organ: liver. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.80Å R-factor: 0.197 R-free: 0.248

Authors:

J.Komoto,Y.Huang,F.Takusagawa,T.Gomi,H.Ogawa,Y.Takata,M.Fujioka

Key ref:

J.Komoto et al. (2000). Effects of site-directed mutagenesis on structure and function of recombinant rat liver S-adenosylhomocysteine hydrolase. Crystal structure of D244E mutant enzyme. J Biol Chem, 275, 32147-32156. PubMed id: 10913437 DOI: 10.1074/jbc.M003725200

Date:

22-Jun-00 Release date: 17-Jan-01

Protein chains

P10760  (SAHH_RAT) -  Adenosylhomocysteinase from Rattus norvegicus

Seq: 432 a.a.

Struc: 430 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.13.2.1 - adenosylhomocysteinase.
• Reaction: S-adenosyl-L-homocysteine + H2O = L-homocysteine + adenosine

S-adenosyl-L-homocysteine + H2O = L-homocysteine (Bound ligand (Het Group name = ADN) corresponds exactly) + adenosine

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M003725200

J Biol Chem 275:32147-32156 (2000)

PubMed id: 10913437

Effects of site-directed mutagenesis on structure and function of recombinant rat liver S-adenosylhomocysteine hydrolase. Crystal structure of D244E mutant enzyme.

J.Komoto, Y.Huang, T.Gomi, H.Ogawa, Y.Takata, M.Fujioka, F.Takusagawa.

ABSTRACT

A site-directed mutagenesis, D244E, of S-adenosylhomocysteine hydrolase (AdoHcyase) changes drastically the nature of the protein, especially the NAD(+) binding affinity. The mutant enzyme contained NADH rather than NAD(+) (Gomi, T., Takata, Y., Date, T., Fujioka, M., Aksamit, R. R., Backlund, P. S., and Cantoni, G. L. (1990) J. Biol. Chem. 265, 16102-16107). In contrast to the site-directed mutagenesis study, the crystal structures of human and rat AdoHcyase recently determined have shown that the carboxyl group of Asp-244 points in a direction opposite to the bound NAD molecule and does not participate in any hydrogen bonds with the NAD molecule. To explain the discrepancy between the mutagenesis study and the x-ray studies, we have determined the crystal structure of the recombinant rat-liver D244E mutant enzyme to 2.8-A resolution. The D244E mutation changes the enzyme structure from the open to the closed conformation by means of a approximately 17 degrees rotation of the individual catalytic domains around the molecular hinge sections. The D244E mutation shifts the catalytic reaction from a reversible to an irreversible fashion. The large affinity difference between NAD(+) and NADH is mainly due to the enzyme conformation, but not to the binding-site geometry; an NAD(+) in the open conformation is readily released from the enzyme, whereas an NADH in the closed conformation is trapped and cannot leave the enzyme. A catalytic mechanism of AdoHcyase has been proposed on the basis of the crystal structures of the wild-type and D244E enzymes.

Selected figure(s)

Figure 2.
Fig. 2. Ribbon drawing of a single subunit of AdoHcyase showing three domains: catalytic domain, NAD^+-binding domain, and C-terminal domain. The C-terminal domain from the subunit B is illustrated with white. The bound NAD molecule and Ado* are illustrated by ball-and-stick modes. A, WT structure (open conformation); B, D244E structure (closed conformation).

Figure 7.
Fig. 7. A movement of the section of C-terminal domain (residues: 420B-430B) of subunit B. A, WT structure (open conformation); B, D244E structure (closed conformation). The NAD-binding domains are aligned by a least-squares method.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2000, 275, 32147-32156) copyright 2000.

Figures were selected by an automated process.