4UQR | pdb_00004uqr

Structure of Bacillus subtilis Nitric Oxide Synthase in complex with N-omega-Nitro-L-Arginine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 
    0.199 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

Identification of Redox Partners and Development of a Novel Chimeric Bacterial Nitric Oxide Synthase for Structure Activity Analyses.

Holden, J.K.Lim, N.Poulos, T.L.

(2014) J Biological Chem 289: 29437

  • DOI: https://doi.org/10.1074/jbc.M114.595165
  • Primary Citation Related Structures: 
    4UQR, 4UQS

  • PubMed Abstract: 

    Production of nitric oxide (NO) by nitric oxide synthase (NOS) requires electrons to reduce the heme iron for substrate oxidation. Both FAD and FMN flavin groups mediate the transfer of NADPH derived electrons to NOS. Unlike mammalian NOS that contain both FAD and FMN binding domains within a single polypeptide chain, bacterial NOS is only composed of an oxygenase domain and must rely on separate redox partners for electron transfer and subsequent activity. Here, we report on the native redox partners for Bacillus subtilis NOS (bsNOS) and a novel chimera that promotes bsNOS activity. By identifying and characterizing native redox partners, we were also able to establish a robust enzyme assay for measuring bsNOS activity and inhibition. This assay was used to evaluate a series of established NOS inhibitors. Using the new assay for screening small molecules led to the identification of several potent inhibitors for which bsNOS-inhibitor crystal structures were determined. In addition to characterizing potent bsNOS inhibitors, substrate binding was also analyzed using isothermal titration calorimetry giving the first detailed thermodynamic analysis of substrate binding to NOS.


  • Organizational Affiliation
    • From the Departments of Molecular Biology and Biochemistry.

Macromolecule Content 

  • Total Structure Weight: 43.6 kDa 
  • Atom Count: 3,391 
  • Modeled Residue Count: 362 
  • Deposited Residue Count: 363 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NITRIC OXIDE SYNTHASE OXYGENASE363Bacillus subtilisMutation(s): 3 
EC: 1.14.13.165 (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
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / 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
H4B

Query on H4B



Download:Ideal Coordinates CCD File
C [auth A]5,6,7,8-TETRAHYDROBIOPTERIN
C9 H15 N5 O3
FNKQXYHWGSIFBK-RPDRRWSUSA-N
NRG

Query on NRG



Download:Ideal Coordinates CCD File
D [auth A]N-OMEGA-NITRO-L-ARGININE
C6 H13 N5 O4
MRAUNPAHJZDYCK-BYPYZUCNSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A],
H [auth A],
L [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
POL

Query on POL



Download:Ideal Coordinates CCD File
K [auth A]N-PROPANOL
C3 H8 O
BDERNNFJNOPAEC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free:  0.199 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.606α = 90
b = 94.82β = 90
c = 62.892γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-17
    Type: Initial release
  • Version 1.1: 2014-10-29
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other
  • Version 2.1: 2024-01-10
    Changes: Refinement description