2FBZ

Heme-No complex in a bacterial Nitric Oxide Synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Nitrosyl-heme structures of Bacillus subtilis nitric oxide synthase have implications for understanding substrate oxidation.

Pant, K.Crane, B.R.

(2006) Biochemistry 45: 2537-2544

  • DOI: https://doi.org/10.1021/bi0518848
  • Primary Citation of Related Structures:  
    2FBZ, 2FC1, 2FC2

  • PubMed Abstract: 

    The crystal structures of nitrosyl-heme complexes of a prokaryotic nitric oxide synthase (NOS) from Bacillus subtilis (bsNOS) reveal changes in active-site hydrogen bonding in the presence of the intermediate N(omega)-hydroxy-l-arginine (NOHA) compared to the substrate l-arginine (l-Arg). Correlating with a Val-to-Ile residue substitution in the bsNOS heme pocket, the Fe(II)-NO complex with both l-Arg and NOHA is more bent than the Fe(II)-NO, l-Arg complex of mammalian eNOS [Li, H., Raman, C. S., Martasek, P., Masters, B. S. S., and Poulos, T. L. (2001) Biochemistry 40, 5399-5406]. Structures of the Fe(III)-NO complex with NOHA show a nearly linear nitrosyl group, and in one subunit, partial nitrosation of bound NOHA. In the Fe(II)-NO complexes, the protonated NOHA N(omega) atom forms a short hydrogen bond with the heme-coordinated NO nitrogen, but active-site water molecules are out of hydrogen bonding range with the distal NO oxygen. In contrast, the l-Arg guanidinium interacts more weakly and equally with both NO atoms, and an active-site water molecule hydrogen bonds to the distal NO oxygen. This difference in hydrogen bonding to the nitrosyl group by the two substrates indicates that interactions provided by NOHA may preferentially stabilize an electrophilic peroxo-heme intermediate in the second step of NOS catalysis.


  • Organizational Affiliation

    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
MoleculeChains Sequence LengthOrganismDetailsImage
Nitric oxide synthase oxygenaseA [auth X]363Bacillus subtilisMutation(s): 0 
Gene Names: nos
EC: 1.14.14.47
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth X]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
H2B
Query on H2B

Download Ideal Coordinates CCD File 
C [auth X]2-AMINO-6-(1,2-DIHYDROXY-PROPYL)-7,8-DIHYDRO-6H-PTERIDIN-4-ONE
C9 H13 N5 O3
ZHQJVZLJDXWFFX-RPDRRWSUSA-N
HAR
Query on HAR

Download Ideal Coordinates CCD File 
E [auth X]N-OMEGA-HYDROXY-L-ARGININE
C6 H14 N4 O3
FQWRAVYMZULPNK-BYPYZUCNSA-N
NO
Query on NO

Download Ideal Coordinates CCD File 
D [auth X]NITRIC OXIDE
N O
ODUCDPQEXGNKDN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.995α = 90
b = 93.503β = 90
c = 62.769γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations