PDBsum entry 7cd0

Transferase

PDB id: 7cd0

Contents

Protein chains

323 a.a.

Ligands

7J8 ×2

FWL

Waters ×76

PDB id:

7cd0

Name:

Transferase

Title:

Crystal structure of the 2-iodoporphobilinogen-bound es2 intermediate form of human hydroxymethylbilane synthase

Structure:

Porphobilinogen deaminase. Chain: a, b. Synonym: pbg-d,hydroxymethylbilane synthase,hmbs,pre-uroporphyrinogen synthase. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: hmbs, pbgd, ups. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.31Å R-factor: 0.230 R-free: 0.277

Authors:

H.Sato,M.Sugishima,K.Wada,K.Hirabayashi,M.Tsukaguchi

Key ref:

H.Sato et al. (2021). 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. PubMed id: 33600566 DOI: 10.1042/BCJ20200996

Date:

18-Jun-20 Release date: 17-Mar-21

Protein chains

P08397  (HEM3_HUMAN) -  Porphobilinogen deaminase from Homo sapiens

Seq: 361 a.a.

Struc: 323 a.a.

Enzyme reactions

• Enzyme class: E.C.2.5.1.61 - hydroxymethylbilane synthase.
• Pathway: Porphyrin Biosynthesis (early stages)
• Reaction: 4 porphobilinogen + H2O = hydroxymethylbilane + 4 NH4⁺

4 × porphobilinogen + H2O (Bound ligand (Het Group name = FWL) matches with 94.12% similarity) = hydroxymethylbilane (Bound ligand (Het Group name = 7J8) matches with 98.36% similarity) + 4 × NH4(+)

• Cofactor: Dipyrromethane

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

Added reference

DOI no: 10.1042/BCJ20200996

Biochem J 478:1023-1042 (2021)

PubMed id: 33600566

Crystal structures of hydroxymethylbilane synthase complexed with a substrate analog: a single substrate-binding site for four consecutive condensation steps.

H.Sato, M.Sugishima, M.Tsukaguchi, T.Masuko, M.Iijima, M.Takano, Y.Omata, K.Hirabayashi, K.Wada, Y.Hisaeda, K.Yamamoto.

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.