PDBsum entry 1p6h

Oxidoreductase

PDB id: 1p6h

Contents

Protein chains

407 a.a. *

Ligands

ACT ×2

HEM ×2

H4B ×2

DP1 ×2

Metals

_ZN

Waters ×487

* Residue conservation analysis

PDB id:

1p6h

Name:

Oxidoreductase

Title:

Rat neuronal nos heme domain with l-n(omega)-nitroarginine-2,4-l- diaminobutyric amide bound

Structure:

Nitric-oxide synthase, brain. Chain: a, b. Fragment: nos heme domain. Synonym: nos, type i, neuronal nos, n-nos, nnos, constitutive nos, nc-nos, bnos. Engineered: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

1.98Å R-factor: 0.231 R-free: 0.273

Authors:

M.L.Flinspach,H.Li,J.Jamal,W.Yang,H.Huang,J.-M.Hah,J.A.Gomez-Vidal, E.A.Litzinger,R.B.Silverman,T.L.Poulos

Key ref:

M.L.Flinspach et al. (2004). Structural basis for dipeptide amide isoform-selective inhibition of neuronal nitric oxide synthase. Nat Struct Mol Biol, 11, 54-59. PubMed id: 14718923 DOI: 10.1038/nsmb704

Date:

29-Apr-03 Release date: 13-Jan-04

Protein chains

P29476  (NOS1_RAT) -  Nitric oxide synthase 1 from Rattus norvegicus

Seq: 1429 a.a.

Struc: 407 a.a.

Enzyme reactions

• Enzyme class: E.C.1.14.13.39 - nitric-oxide synthase (NADPH).
• Reaction: 2 L-arginine + 3 NADPH + 4 O2 + H⁺ = 2 L-citrulline + 2 nitric oxide + 3 NADP⁺ + 4 H2O

2 × L-arginine + 3 × NADPH (Bound ligand (Het Group name = DP1) matches with 47.83% similarity) + 4 × O2 + H(+) = 2 × L-citrulline + 2 × nitric oxide + 3 × NADP(+) + 4 × H2O

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

reference

DOI no: 10.1038/nsmb704

Nat Struct Mol Biol 11:54-59 (2004)

PubMed id: 14718923

Structural basis for dipeptide amide isoform-selective inhibition of neuronal nitric oxide synthase.

M.L.Flinspach, H.Li, J.Jamal, W.Yang, H.Huang, J.M.Hah, J.A.Gómez-Vidal, E.A.Litzinger, R.B.Silverman, T.L.Poulos.

ABSTRACT

Three nitric oxide synthase (NOS) isoforms, eNOS, nNOS and iNOS, generate nitric oxide (NO) crucial to the cardiovascular, nervous and host defense systems, respectively. Development of isoform-selective NOS inhibitors is of considerable therapeutic importance. Crystal structures of nNOS-selective dipeptide inhibitors in complex with both nNOS and eNOS were solved and the inhibitors were found to adopt a curled conformation in nNOS but an extended conformation in eNOS. We hypothesized that a single-residue difference in the active site, Asp597 (nNOS) versus Asn368 (eNOS), is responsible for the favored binding in nNOS. In the D597N nNOS mutant crystal structure, a bound inhibitor switches to the extended conformation and its inhibition of nNOS decreases >200-fold. Therefore, a single-residue difference is responsible for more than two orders of magnitude selectivity in inhibition of nNOS over eNOS by L-N(omega)-nitroarginine-containing dipeptide inhibitors.

Selected figure(s)

Figure 1.
Figure 1. Ribbon diagram of the eNOS heme domain, the active site and the dipeptide inhibitors used in this study. (a) Chemical structures of the three dipeptide amide or peptidomimetic NOS inhibitors used in this study: I, L-N^ -nitroarginine-2,4- L-diaminobutyramide; II (4S)-N-(4-amino-5-[aminoethyl]aminopentyl)-N'-nitroguanidine; III, L-N^ -nitroarginine-(4R)-amino-L-proline amide. (b) Ribbon diagram of eNOS heme domain. All three isoforms share the similar dimeric fold and have a wide open solvent-accessible channel connecting the heme active site to the molecular surface. (c) L-NNA bound in the active site of eNOS. The extensive hydrogen bonding network (dashed lines) between L-NNA and enzyme may explain its low-nanomolar potency. The active site structure and interactions between L-arginine and the protein are the same in all three mammalian NOS isoforms. The only exception is Asn368, which is aspartate in nNOS and iNOS. Even so, the aspartate and asparagine side chains are oriented in the same way in all three structures.

Figure 4.
Figure 4. Stereo diagrams of the F[o] - F[c] omit electron density maps contoured at 3 of inhibitor I binding. (a,b) Inhibitor I bound to nNOS D597N mutant (a) and eNOS N368D mutant (b). In b, the curled binding mode was observed at 70% occupancy, with the wild-type binding mode present at 30% (data not shown). Occupancies were empirically determined by adjusting occupancies of the two alternate conformations until F[o] - F[c] electron density maps indicated no further changes were required. For nNOS only one conformation was observed.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2004, 11, 54-59) copyright 2004.

Figures were selected by an automated process.