1DWV

MURINE INDUCIBLE NITRIC OXIDE SYNTHASE OXYGENASE DIMER N-hydroxyarginine and 4-amino tetrahydrobiopterin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of the N(Omega)-Hydroxy-L-Arginine Complex of Inducible Nitric Oxide Synthase Oxygenase Dimer with Active Andinactive Pterins

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

(2000) Biochemistry 39: 4608

  • Primary Citation of Related Structures:  1DWW, 1DWX

  • PubMed Abstract: 
  • Nitric oxide synthases (NOSs) catalyze two mechanistically distinct, tetrahydrobiopterin (H(4)B)-dependent, heme-based oxidations that first convert L-arginine (L-Arg) to N(omega)-hydroxy-L-arginine (NHA) and then NHA to L-citrulline and nitric oxide ...

    Nitric oxide synthases (NOSs) catalyze two mechanistically distinct, tetrahydrobiopterin (H(4)B)-dependent, heme-based oxidations that first convert L-arginine (L-Arg) to N(omega)-hydroxy-L-arginine (NHA) and then NHA to L-citrulline and nitric oxide. Structures of the murine inducible NOS oxygenase domain (iNOS(ox)) complexed with NHA indicate that NHA and L-Arg both bind with the same conformation adjacent to the heme iron and neither interacts directly with it nor with H(4)B. Steric restriction of dioxygen binding to the heme in the NHA complex suggests either small conformational adjustments in the ternary complex or a concerted reaction of dioxygen with NHA and the heme iron. Interactions of the NHA hydroxyl with active center beta-structure and the heme ring polarize and distort the hydroxyguanidinium to increase substrate reactivity. Steric constraints in the active center rule against superoxo-iron accepting a hydrogen atom from the NHA hydroxyl in their initial reaction, but support an Fe(III)-peroxo-NHA radical conjugate as an intermediate. However, our structures do not exclude an oxo-iron intermediate participating in either L-Arg or NHA oxidation. Identical binding modes for active H(4)B, the inactive quinonoid-dihydrobiopterin (q-H(2)B), and inactive 4-amino-H(4)B indicate that conformational differences cannot explain pterin inactivity. Different redox and/or protonation states of q-H(2)B and 4-amino-H(4)B relative to H(4)B likely affect their ability to electronically influence the heme and/or undergo redox reactions during NOS catalysis. On the basis of these structures, we propose a testable mechanism where neutral H(4)B transfers both an electron and a 3,4-amide proton to the heme during the first step of NO synthesis.


    Related Citations: 
    • Inducible Nitric Oxide Synthase: Role of the N-Terminal Beta-Hairpin Hook and Pterin-Binding Segment in Dimerization and Tetrahydrobiopterin Interaction
      Ghosh, D.K.,Crane, B.R.,Ghosh, S.,Wolan, D.,Gachhui, R.,Crooks, C.,Presta, A.,Tainer, J.A.,Getzoff, E.D.,Stuehr, D.J.
      (1999) Embo J. 18: 6260
    • N-Terminal Domain Swapping and Metal Ion Binding in Nitric Oxide Synthase Dimerization
      Crane, B.R.,Rosenfeld, R.A.,Arvai, A.S.,Ghosh, D.K.,Ghosh, S.,Tainer, J.A.,Stuehr, D.J.,Getzoff, E.D.
      (1999) Embo J. 18: 6271
    • The Structure of Nitric Oxide Synthase Oxygenase Domain and Inhibitor Complexes
      Crane, B.R.,Arvai, A.S.,Gachhui, R.,Wu, C.,Ghosh, D.K.,Getzoff, E.D.,Stuehr, D.J.,Tainer, J.A.
      (1997) Science 278: 425
    • Structure of Nitric Oxide Synthase Oxygenase Dimer with Pterin and Substrate
      Crane, B.R.,Arvai, A.S.,Ghosh, D.K.,Wu, C.,Getzoff, E.D.,Stuehr, D.J.,Tainer, J.A.
      (1998) Science 279: 2121


    Organizational Affiliation

    The Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NITRIC OXIDE SYNTHASE
A, B
420Mus musculusGene Names: Nos2 (Inosl)
EC: 1.14.13.39
Find proteins for P29477 (Mus musculus)
Go to UniProtKB:  P29477
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
HAR
Query on HAR

Download SDF File 
Download CCD File 
A, B
N-OMEGA-HYDROXY-L-ARGININE
C6 H14 N4 O3
FQWRAVYMZULPNK-BYPYZUCNSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
4AB
Query on 4AB

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Download CCD File 
A, B
2,4-DIAMINO-6-[2,3-DIHYDROXY-PROP-3-YL]-5,6,7,8-TETRAHYDROPTERIDINE
4-AMINO 5,6,7,8-TETRAHYDROBIOPTERIN
C9 H16 N6 O2
NDSDGUULXHNXGA-RPDRRWSUSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4ABIC50: 1700 nM (87) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.247 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 212.980α = 90.00
b = 212.980β = 90.00
c = 114.200γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
X-PLORrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-02-06
    Type: Initial release
  • Version 1.1: 2011-05-07
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance