4XYD

Nitric oxide reductase from Roseobacter denitrificans (RdNOR)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the Membrane-intrinsic Nitric Oxide Reductase from Roseobacter denitrificans.

Crow, A.Matsuda, Y.Arata, H.Oubrie, A.

(2016) Biochemistry 55: 3198-3203

  • DOI: 10.1021/acs.biochem.6b00332

  • PubMed Abstract: 
  • Membrane-intrinsic nitric oxide reductases (NORs) are key components of bacterial denitrification pathways with a close evolutionary relationship to the cytochrome oxidase (COX) complex found in aerobic respiratory chains. A key distinction between C ...

    Membrane-intrinsic nitric oxide reductases (NORs) are key components of bacterial denitrification pathways with a close evolutionary relationship to the cytochrome oxidase (COX) complex found in aerobic respiratory chains. A key distinction between COX and NOR is the identity of the metal directly opposite heme b3 within the active site. In NOR, this metal is iron (FeB), whereas in COX, it is copper (CuB). The purified NOR of Roseobacter denitrificans contains copper and has modest oxidase activity, raising the possibility that a COX-like active site might have independently arisen within the context of a NOR-like protein scaffold. Here we present the crystal structure of the Roseobacter denitrificans NorBC complex and anomalous scattering experiments probing the identity of each metal center. Our results refute the hypothesis that copper occupies the active site and instead reveal a new metal center in the small subunit not seen in any other NOR or COX.


    Organizational Affiliation

    Department of Biology, Kyushu University , Fukuoka, Japan.,Department of Pathology, University of Cambridge , Cambridge, U.K.,Lead Pharma , Pivot Park, 5349AC Oss, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nitric-oxide reductase subunit B
A
456Roseobacter denitrificans (strain ATCC 33942 / OCh 114)Mutation(s): 0 
Gene Names: norB
EC: 1.7.2.5
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Nitric Oxide Reductases
Protein: 
Nitric Oxide Reductase BC complex
Find proteins for Q16A04 (Roseobacter denitrificans (strain ATCC 33942 / OCh 114))
Go to UniProtKB:  Q16A04
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NorC-like protein
B
150Roseobacter denitrificans (strain ATCC 33942 / OCh 114)Mutation(s): 0 
Gene Names: norC
EC: 1.7.2.5
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Nitric Oxide Reductases
Protein: 
Nitric Oxide Reductase BC complex
Find proteins for Q16A03 (Roseobacter denitrificans (strain ATCC 33942 / OCh 114))
Go to UniProtKB:  Q16A03
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
FE
Query on FE

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Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

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B
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
HEC
Query on HEC

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Download CCD File 
B
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.188 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.220α = 90.00
b = 98.830β = 90.00
c = 126.780γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-02-02 
  • Released Date: 2016-05-25 
  • Deposition Author(s): Crow, A.

Revision History 

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2016-06-01
    Type: Database references
  • Version 1.2: 2016-06-22
    Type: Database references