PDBsum entry 1d1v

Oxidoreductase

PDB id: 1d1v

Contents

Protein chains

416 a.a. *

Ligands

ACT ×4

HEM ×2

H4B ×2

PTU ×2

CAD ×2

GOL ×2

Metals

_ZN

Waters ×627

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Implications for isoform-Selective inhibitor design derived from the binding mode of bulky isothioureas to the heme domain of endothelial nitric-Oxide synthase.

Authors

C.S.Raman, H.Li, P.Martásek, B.R.Babu, O.W.Griffith, B.S.Masters, T.L.Poulos.

Ref.

J Biol Chem, 2001, 276, 26486-26491. [DOI no: 10.1074/jbc.M102255200]

PubMed id

11331290

Abstract

Nitric oxide produced by nitric-oxide synthase (NOS) is not only involved in a wide range of physiological functions but also in a variety of pathological conditions. Isoform-selective NOS inhibitors are highly desirable to regulate the NO production of one isoform beneficial to normal physiological functions from the uncontrolled NO production of another isoform that accompanies certain pathological states. Crystal structures of the heme domain of the three NOS isoforms have revealed a very high degree of similarity in the immediate vicinity of the heme active site illustrating the challenge of isoform-selective inhibitor design. Isothioureas are potent NOS inhibitors, and the structures of the endothelial NOS heme domain complexed with isothioureas bearing small S-alkyl substituents have been determined (Li, H., Raman, C.S., Martásek, P., Král, V., Masters, B.S.S., and Poulos, T.L. (2000) J. Inorg. Biochem. 81, 133--139). In the present communication, the binding mode of larger bisisothioureas complexed to the endothelial NOS heme domain has been determined. These structures afford a structural rationale for the known inhibitory activities. In addition, these structures provide clues on how to exploit the longer inhibitor substituents that extend out of the active site pocket for isoform-selective inhibitor design.

Figure 3.
Fig. 3. The chemical structures and the abbreviations of compounds discussed in the text.

Figure 5.
Fig. 5. The space-filling drawing of eNOS heme domain with long chain bisisothiourea inhibitor 1,14-BITU modeled in the substrate access channel. The surface residues expected to interact with the ureido of the ligand are labeled.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 26486-26491) copyright 2001.

Secondary reference #1

Title

Crystal structure of constitutive endothelial nitric oxide synthase: a paradigm for pterin function involving a novel metal center.

Authors

C.S.Raman, H.Li, P.Martásek, V.Král, B.S.Masters, T.L.Poulos.

Ref.

Cell, 1998, 95, 939-950. [DOI no: 10.1016/S0092-8674(00)81718-3]

PubMed id

9875848

Figure 5.
Figure 5. Cooperativity and Molecular Mimicry in eNOS(A) Cross talk between H[4]B and L-Arg mediated by the heme propionate (Se-edge data). The guanidinium and amino groups of L-Arg are held in place by H-bonding with the conserved Glu-363. The amino group also H-bonds with a heme propionate. H[4]B H-bonds directly with the heme propionate, while the pteridine ring is sandwiched between Phe-462 in one monomer and Trp-449 in another, respectively.(B) L-Arg is a structural mimic of H[4]B at the pterin-binding site when SEITU is bound at the active site (-H[4]B, +SEITU data). L-Arg binds to the pterin site and exquisitely mimics the H[4]B interaction with eNOS ([A] and Figure 4). The specific interaction of the potent inhibitor, SEITU, at the active site is mediated by a pair of bifurcated H-bonds to Glu-363. Two water molecules bridge between the inhibitor and heme propionate. The ethyl group of the inhibitor forms nonbonded contacts with Val-338 and Phe-355. The ureido sulfur is positioned 3.5 Å and 4.0 Å above heme pyrrole B-ring nitrogen and the heme iron, respectively.

Figure 7.
Figure 7. Proposed Mechanism for Pterin in NO BiosynthesisThe uniqueness of the H[4]B–eNOS interaction (Figure 4) and the ability to bind L-Arg at the pterin site present a strong case for the involvement of a pterin radical in NOS catalysis and rule out the possibility of H[4]B ↔ qH[2]B cycling during NO biosynthesis. R represents the dihydroxypropyl side chain at the C6 position on the pterin ring.

The above figures are reproduced from the cited reference with permission from Cell Press

Secondary reference #2

Title

Structure of nitric oxide synthase oxygenase dimer with pterin and substrate.

Authors

B.R.Crane, A.S.Arvai, D.K.Ghosh, C.Wu, E.D.Getzoff, D.J.Stuehr, J.A.Tainer.

Ref.

Science, 1998, 279, 2121-2126. [DOI no: 10.1126/science.279.5359.2121]

PubMed id

9516116

Figure 1.
Fig. 1. NOS[ox] - fold, dimer assembly, and likely interaction surface for NOS[red] and caveolin. (A) The symmetric iNOS[ox] dimer viewed along the crystallographic twofold axis, showing left (and^ right) subunits with orange (yellow) winged sheets and flanking blue (cyan) helices. Ball-and-stick models (white bonds with red^ oxygen, blue nitrogen, yellow sulfur, and purple iron atoms) highlight active-center hemes (left-most and right-most), interchain disulfide^ bonds (center, foreground), pterin cofactors (white, left-center and right-center), and substrate L-Arg (green left and magenta^ right). The NH[2]-terminal ends contribute hairpins (center top and bottom) to the dimer interface, and the COOH-termini (lower left and upper right) lie 85 Å apart. Gray loops (residues 101^ to 107) are disordered. (B) iNOS[ox] dimer shown rotated^ 90° about a horizontal axis from (A). Each heme is cupped between the inward-facing palm (webbed sheet) and thumb (magenta loop in front of left heme and green loop behind right heme) of the^ "catcher's mitt" subunit fold. (C) Solvent-accessible surface^ (29) of the iNOS[ox] dimer (one subunit red, one subunit blue) oriented as in (B) and color-coded by residue conservation (paler to more saturated represents less conserved to more conserved) in NOS[ox] sequences of known species and isozymes. The heme (white^ tubes) is also solvent-exposed on the side (left subunit) opposite^ the active-center channel (right subunit) and surrounded by a^ highly conserved hydrophobic surface for NOS[red] and caveolin binding. (Stereo variations of Figs.

Figure 5.
Fig. 5. Proposed L-Arg-assisted NOS oxygen activation. First, substrate L-Arg (only guanidinium shown) donates a proton to peroxo-iron, facilitating O-O bond cleavage and conversion to a proposed oxo-iron(IV) -cation radical species, which then rapidly hydroxylates the^ neutral guanidinium to NOH-L-Arg, possibly through a radical-based^ mechanism (3).

The above figures are reproduced from the cited reference with permission from the AAAs