6TSI

cd1 nitrite reductase NirS with bound dihydro-heme d1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

Starting Model: experimental
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Literature

Structure of heme d 1 -free cd 1 nitrite reductase NirS.

Klunemann, T.Blankenfeldt, W.

(2020) Acta Crystallogr F Struct Biol Commun 76: 250-256

  • DOI: https://doi.org/10.1107/S2053230X20006676
  • Primary Citation of Related Structures:  
    6TPO, 6TSI

  • PubMed Abstract: 

    A key step in anaerobic nitrate respiration is the reduction of nitrite to nitric oxide, which is catalysed by the cd 1 nitrite reductase NirS in, for example, the Gram-negative opportunistic pathogen Pseudomonas aeruginosa. Each subunit of this homodimeric enzyme consists of a cytochrome c domain and an eight-bladed β-propeller that binds the uncommon isobacteriochlorin heme d 1 as an essential part of its active site. Although NirS has been well studied mechanistically and structurally, the focus of previous studies has been on the active heme d 1 -bound form. The heme d 1 -free form of NirS reported here, which represents a premature state of the reductase, adopts an open conformation with the cytochrome c domains moved away from each other with respect to the active enzyme. Further, the movement of a loop around Trp498 seems to be related to a widening of the propeller, allowing easier access to the heme d 1 -binding side. Finally, a possible link between the open conformation of NirS and flagella formation in P. aeruginosa is discussed.


  • Organizational Affiliation

    Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Niedersachsen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrite reductase
A, B
543Pseudomonas aeruginosa PAO1Mutation(s): 0 
EC: 1.7.2.1 (PDB Primary Data), 1.7.99.1 (PDB Primary Data)
UniProt
Find proteins for P24474 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore P24474 
Go to UniProtKB:  P24474
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24474
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DHE (Subject of Investigation/LOI)
Query on DHE

Download Ideal Coordinates CCD File 
D [auth A],
K [auth B]
HEME D
C34 H32 Fe N4 O10
XLQCGNUTSJTZNF-YDXXJHAFSA-L
HEC
Query on HEC

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
L [auth B],
M [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
N [auth B],
O [auth B],
P [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.762α = 90
b = 91.093β = 90
c = 112.706γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
autoPROCdata collection
STARANISOdata scaling
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyGRK2223/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-18
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description