PDBsum entry 3b6h

Isomerase

PDB id: 3b6h

Contents

Protein chain

469 a.a. *

Ligands

BOG ×2

MXD-HEM ×2

Waters ×765

* Residue conservation analysis

PDB id:

3b6h

Name:

Isomerase

Title:

Crystal structure of human prostacyclin synthase in complex with inhibitor minoxidil

Structure:

Prostacyclin synthase. Chain: a, b. Fragment: unp residues 18-500. Synonym: cytochrome p450 8a1, prostaglandin i2 synthase. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ptgis, cyp8, cyp8a1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.62Å R-factor: 0.204 R-free: 0.228

Authors:

Y.-C.Li,C.-W.Chiang,H.-C.Yeh,P.-Y.Hsu,F.G.Whitby,L.-H.Wang,N.-L.Chan

Key ref:

Y.C.Li et al. (2008). Structures of Prostacyclin Synthase and Its Complexes with Substrate Analog and Inhibitor Reveal a Ligand-specific Heme Conformation Change. J Biol Chem, 283, 2917-2926. PubMed id: 18032380 DOI: 10.1074/jbc.M707470200

Date:

29-Oct-07 Release date: 20-Nov-07

Protein chains

Q16647  (PTGIS_HUMAN) -  Prostacyclin synthase from Homo sapiens

Seq: 500 a.a.

Struc: 469 a.a.

Enzyme reactions

• Enzyme class 1: E.C.4.2.1.152 - hydroperoxy icosatetraenoate dehydratase.
• Reaction: a hydroperoxyeicosatetraenoate = an oxoeicosatetraenoate + H2O
• Cofactor: Fe(2+)
• Enzyme class 2: E.C.5.3.99.4 - prostaglandin-I synthase.
• Reaction: prostaglandin H2 = prostaglandin I2

prostaglandin H2 (Bound ligand (Het Group name = HEM) matches with 51.11% similarity) = prostaglandin I2

• Cofactor: Heme-thiolate

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

Added reference

DOI no: 10.1074/jbc.M707470200

J Biol Chem 283:2917-2926 (2008)

PubMed id: 18032380

Structures of Prostacyclin Synthase and Its Complexes with Substrate Analog and Inhibitor Reveal a Ligand-specific Heme Conformation Change.

Y.C.Li, C.W.Chiang, H.C.Yeh, P.Y.Hsu, F.G.Whitby, L.H.Wang, N.L.Chan.

ABSTRACT

Prostacyclin synthase (PGIS) is a cytochrome P450 (P450) enzyme that catalyzes production of prostacyclin from prostaglandin H(2). PGIS is unusual in that it catalyzes an isomerization rather than a monooxygenation, which is typical of P450 enzymes. To understand the structural basis for prostacyclin biosynthesis in greater detail, we have determined the crystal structures of ligand-free, inhibitor (minoxidil)-bound and substrate analog U51605-bound PGIS. These structures demonstrate a stereo-specific substrate binding and suggest features of the enzyme that facilitate isomerization. Unlike most microsomal P450s, where large substrate-induced conformational changes take place at the distal side of the heme, conformational changes in PGIS are observed at the proximal side and in the heme itself. The conserved and extensive heme propionate-protein interactions seen in all other P450s, which are largely absent in the ligand-free PGIS, are recovered upon U51605 binding accompanied by water exclusion from the active site. In contrast, when minoxidil binds, the propionate-protein interactions are not recovered and water molecules are largely retained. These findings suggest that PGIS represents a divergent evolution of the P450 family, in which a heme barrier has evolved to ensure strict binding specificity for prostaglandin H(2), leading to a radical-mediated isomerization with high product fidelity. The U51605-bound structure also provides a view of the substrate entrance and product exit channels.

Selected figure(s)

Figure 1.
FIGURE 1. Proposed mechanism for PGI[2] biosynthesis. A, chemical structures of substrate PGH[2], substrate analog U51605, and inhibitor minoxidil. B, a proposed mechanism for the reaction catalyzed by PGIS (R1, CH[2]-(CH[2])[2]-COOH; R2, CH-CHOH-(CH[2])[4]-CH[3]) (6).

Figure 5.
FIGURE 5. The minoxidil-bound hPGIS. A, a F[o] - F[c] omit map contoured at 2.7 shows unbiased electron density for minoxidil. B, structural changes around the active site, Cys ligand loop, and B' helix upon minoxidil binding. The ligand-free (blue) and minoxidil-bound (gold) structures were superimposed over all equivalent C atom pairs. The minoxidil-induced stacking between Phe^96 and His^438 is indicated by the dashed lines.

The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2008, 283, 2917-2926) copyright 2008.

Figures were selected by an automated process.