7CCX

Crystal structure of the holo form of human hydroxymethylbilane synthase

Summary for 7CCX

• Entry DOI: 10.2210/pdb7ccx/pdb
• Descriptor: Porphobilinogen deaminase, 3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid (3 entities in total)
• Functional Keywords: porphyrin synthesis, transferase
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 2
• Total formula weight: 79606.85

Authors

Sato, H.,Sugishima, M.,Wada, K.,Hirabayashi, K.,Tsukaguchi, M. (deposition date: 2020-06-18, release date: 2021-03-17, Last modification date: 2023-11-29)

Primary citation

Sato, H.,Sugishima, M.,Tsukaguchi, M.,Masuko, T.,Iijima, M.,Takano, M.,Omata, Y.,Hirabayashi, K.,Wada, K.,Hisaeda, Y.,Yamamoto, K.
Crystal structures of hydroxymethylbilane synthase complexed with a substrate analog: a single substrate-binding site for four consecutive condensation steps.
Biochem.J., 478:1023-1042, 2021

PubMed Abstract: Hydroxymethylbilane synthase (HMBS), which is involved in the heme biosynthesis pathway, has a dipyrromethane cofactor and combines four porphobilinogen (PBG) molecules to form a linear tetrapyrrole, hydroxymethylbilane. Enzyme kinetic study of human HMBS using a PBG-derivative, 2-iodoporphobilinogen (2-I-PBG), exhibited noncompetitive inhibition with the inhibition constant being 5.4 ± 0.3 µM. To elucidate the reaction mechanism of HMBS in detail, crystal structure analysis of 2-I-PBG-bound holo-HMBS and its reaction intermediate possessing two PBG molecules (ES2), and inhibitor-free ES2 was performed at 2.40, 2.31, and 1.79 Å resolution, respectively. Their overall structures are similar to that of inhibitor-free holo-HMBS, and the differences are limited near the active site. In both 2-I-PBG-bound structures, 2-I-PBG is located near the terminus of the cofactor or the tetrapyrrole chain. The propionate group of 2-I-PBG interacts with the side chain of Arg173, and its acetate group is associated with the side chains of Arg26 and Ser28. Furthermore, the aminomethyl group and pyrrole nitrogen of 2-I-PBG form hydrogen bonds with the side chains of Gln34 and Asp99, respectively. These amino acid residues form a single substrate-binding site, where each of the four PBG molecules covalently binds to the cofactor (or oligopyrrole chain) consecutively, ultimately forming a hexapyrrole chain. Molecular dynamics simulation of the ES2 intermediate suggested that the thermal fluctuation of the lid and cofactor-binding loops causes substrate recruitment and oligopyrrole chain shift needed for consecutive condensation. Finally, the hexapyrrole chain is hydrolyzed self-catalytically to produce hydroxymethylbilane.

PubMed: 33600566
DOI: 10.1042/BCJ20200996

Experimental method

X-RAY DIFFRACTION (1.84 Å)