4OBW
crystal structure of yeast Coq5 in the SAM bound form
Summary for 4OBW
| Entry DOI | 10.2210/pdb4obw/pdb |
| Related | 4OBX |
| Descriptor | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial, TRIS(HYDROXYETHYL)AMINOMETHANE, S-ADENOSYLMETHIONINE, ... (4 entities in total) |
| Functional Keywords | rossmann fold, methyltransferase, transferase |
| Biological source | Saccharomyces cerevisiae (Baker's yeast) |
| Cellular location | Mitochondrion: P49017 |
| Total number of polymer chains | 4 |
| Total formula weight | 118929.01 |
| Authors | Dai, Y.N.,Zhou, K.,Cao, D.D.,Jiang, Y.L.,Meng, F.,Chi, C.B.,Ren, Y.M.,Chen, Y.X.,Zhou, C.Z. (deposition date: 2014-01-07, release date: 2014-08-06, Last modification date: 2024-02-28) |
| Primary citation | Dai, Y.N.,Zhou, K.,Cao, D.D.,Jiang, Y.L.,Meng, F.,Chi, C.B.,Ren, Y.M.,Chen, Y.,Zhou, C.Z. Crystal structures and catalytic mechanism of the C-methyltransferase Coq5 provide insights into a key step of the yeast coenzyme Q synthesis pathway. Acta Crystallogr.,Sect.D, 70:2085-2092, 2014 Cited by PubMed Abstract: Saccharomyces cerevisiae Coq5 is an S-adenosyl methionine (SAM)-dependent methyltransferase (SAM-MTase) that catalyzes the only C-methylation step in the coenzyme Q (CoQ) biosynthesis pathway, in which 2-methoxy-6-polyprenyl-1,4-benzoquinone (DDMQH2) is converted to 2-methoxy-5-methyl-6-polyprenyl-1,4-benzoquinone (DMQH2). Crystal structures of Coq5 were determined in the apo form (Coq5-apo) at 2.2 Å resolution and in the SAM-bound form (Coq5-SAM) at 2.4 Å resolution, representing the first pair of structures for the yeast CoQ biosynthetic enzymes. Coq5 displays a typical class I SAM-MTase structure with two minor variations beyond the core domain, both of which are considered to participate in dimerization and/or substrate recognition. Slight conformational changes at the active-site pocket were observed upon binding of SAM. Structure-based computational simulation using an analogue of DDMQH2 enabled us to identify the binding pocket and entrance tunnel of the substrate. Multiple-sequence alignment showed that the residues contributing to the dimeric interface and the SAM- and DDMQH2-binding sites are highly conserved in Coq5 and homologues from diverse species. A putative catalytic mechanism of Coq5 was proposed in which Arg201 acts as a general base to initiate catalysis with the help of a water molecule. PubMed: 25084328DOI: 10.1107/S1399004714011559 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.4 Å) |
Structure validation
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