1M7Z

Structure of Nitric Oxide Synthase Heme Protein from Bacillus Subtilis with N-Hydroxy-Arginine and Tetrahydrofolate Bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a nitric oxide synthase heme protein from Bacillus subtilis.

Pant, K.Bilwes, A.M.Adak, S.Stuehr, D.J.Crane, B.R.

(2002) Biochemistry 41: 11071-11079

  • DOI: 10.1021/bi0263715
  • Primary Citation of Related Structures:  
    1M7V, 1M7Z

  • PubMed Abstract: 
  • Eukaryotic nitric oxide synthases (NOSs) produce nitric oxide to mediate intercellular signaling and protect against pathogens. Recently, proteins homologous to mammalian NOS oxygenase domains have been found in prokaryotes and one from Bacillus subtilis (bsNOS) has been demonstrated to produce nitric oxide [Adak, S ...

    Eukaryotic nitric oxide synthases (NOSs) produce nitric oxide to mediate intercellular signaling and protect against pathogens. Recently, proteins homologous to mammalian NOS oxygenase domains have been found in prokaryotes and one from Bacillus subtilis (bsNOS) has been demonstrated to produce nitric oxide [Adak, S., Aulak, K. S., and Stuehr, D. J. (2002) J. Biol. Chem. 277, 16167-16171]. We present structures of bsNOS complexed with the active cofactor tetrahydrofolate and the substrate L-arginine (L-Arg) or the intermediate N(omega)-hydroxy-L-arginine (NHA) to 1.9 or 2.2 A resolution, respectively. The bsNOS structure is similar to those of the mammalian NOS oxygenase domains (mNOS(ox)) except for the absence of an N-terminal beta-hairpin hook and zinc-binding region that interact with pterin and stabilize the mNOS(ox) dimer. Changes in patterns of residue conservation between bacterial and mammalian NOSs correlate to different binding modes for pterin side chains. Residue conservation on a surface patch surrounding an exposed heme edge indicates a likely interaction site for reductase proteins in all NOSs. The heme pockets of bsNOS and mNOS(ox) recognize L-Arg and NHA similarly, although a change from Val to Ile beside the substrate guanidinium may explain the 10-20-fold slower dissociation of product NO from the bacterial enzyme. Overall, these structures suggest that bsNOS functions naturally to produce nitrogen oxides from L-Arg and NHA in a pterin-dependent manner, but that the regulation and purpose of NO production by NOS may be quite different in B. subtilis than in mammals.


    Organizational Affiliation

    The Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nitric oxide synthaseA361Bacillus subtilisMutation(s): 0 
EC: 1.14.13.39 (PDB Primary Data), 1.14.14.47 (UniProt)
UniProt
Find proteins for O34453 (Bacillus subtilis (strain 168))
Explore O34453 
Go to UniProtKB:  O34453
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34453
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
THG
Query on THG

Download Ideal Coordinates CCD File 
D [auth A](6S)-5,6,7,8-TETRAHYDROFOLATE
C19 H23 N7 O6
MSTNYGQPCMXVAQ-RYUDHWBXSA-N
 Ligand Interaction
HAR
Query on HAR

Download Ideal Coordinates CCD File 
C [auth A]N-OMEGA-HYDROXY-L-ARGININE
C6 H14 N4 O3
FQWRAVYMZULPNK-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.085α = 90
b = 93.068β = 90
c = 62.769γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-10-30
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance