1FS8 | pdb_00001fs8

CYTOCHROME C NITRITE REDUCTASE FROM WOLINELLA SUCCINOGENES-SULFATE COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.206 (Depositor) 
  • R-Value Work: 
    0.184 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1FS8

This is version 2.1 of the entry. See complete history

Literature

Cytochrome c nitrite reductase from Wolinella succinogenes. Structure at 1.6 A resolution, inhibitor binding, and heme-packing motifs.

Einsle, O.Stach, P.Messerschmidt, A.Simon, J.Kroger, A.Huber, R.Kroneck, P.M.

(2000) J Biological Chem 275: 39608-39616

  • DOI: https://doi.org/10.1074/jbc.M006188200
  • Primary Citation Related Structures: 
    1FS7, 1FS8, 1FS9

  • PubMed Abstract: 

    Cytochrome c nitrite reductase catalyzes the 6-electron reduction of nitrite to ammonia. This second part of the respiratory pathway of nitrate ammonification is a key step in the biological nitrogen cycle. The x-ray structure of the enzyme from the epsilon-proteobacterium Wolinella succinogenes has been solved to a resolution of 1.6 A. It is a pentaheme c-type cytochrome whose heme groups are packed in characteristic motifs that also occur in other multiheme cytochromes. Structures of W. succinogenes nitrite reductase have been obtained with water bound to the active site heme iron as well as complexes with two inhibitors, sulfate and azide, whose binding modes and inhibitory functions differ significantly. Cytochrome c nitrite reductase is part of a highly optimized respiratory system found in a wide range of Gram-negative bacteria. It reduces both anionic and neutral substrates at the distal side of a lysine-coordinated high-spin heme group, which is accessible through two different channels, allowing for a guided flow of reaction educt and product. Based on sequence comparison and secondary structure prediction, we have demonstrated that cytochrome c nitrite reductases constitute a protein family of high structural similarity.


  • Organizational Affiliation
    • Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, 82152 Martinsried, Germany. einsle@biochem.mpg.de

Macromolecule Content 

  • Total Structure Weight: 59.18 kDa 
  • Atom Count: 4,661 
  • Modeled Residue Count: 471 
  • Deposited Residue Count: 485 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CYTOCHROME C NITRITE REDUCTASE485Wolinella succinogenesMutation(s): 0 
EC: 1.7.2.2
UniProt
Find proteins for Q9S1E5 (Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / CCUG 13145 / JCM 31913 / LMG 7466 / NCTC 11488 / FDC 602W))
Explore Q9S1E5 
Go to UniProtKB:  Q9S1E5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9S1E5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC

Query on HEC



Download:Ideal Coordinates CCD File
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
I [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Y1

Query on Y1



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A],
F [auth A]
YTTRIUM ION
Y
KAJPZYFHSCFBCI-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
J [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA

Query on CA



Download:Ideal Coordinates CCD File
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.206 (Depositor) 
  • R-Value Work:  0.184 (Depositor) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.01α = 90
b = 119.01β = 90
c = 186.525γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-01-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2021-03-03
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-11-13
    Changes: Advisory, Data collection, Database references, Structure summary