3TTB

Structure of the Thioalkalivibrio paradoxus cytochrome c nitrite reductase in complex with sulfite


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.135 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Comparative structural and functional analysis of two octaheme nitrite reductases from closely related Thioalkalivibrio species.

Tikhonova, T.Tikhonov, A.Trofimov, A.Polyakov, K.Boyko, K.Cherkashin, E.Rakitina, T.Sorokin, D.Popov, V.

(2012) FEBS J 279: 4052-4061

  • DOI: 10.1111/j.1742-4658.2012.08811.x
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Octaheme nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio paradoxus was isolated and characterized. A comparative structural and functional analysis of two homologous octaheme nitrite reductases from closely related Thioalkalivi ...

    Octaheme nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio paradoxus was isolated and characterized. A comparative structural and functional analysis of two homologous octaheme nitrite reductases from closely related Thioalkalivibrio species was performed. It was shown that both enzymes have similar catalytic properties, owing to high structural similarity. Both enzymes are characterized by specific structural features distinguishing them from pentaheme cytochrome c nitrite reductases, such as the Tyr-Cys bond in the active site, the hexameric structure resulting in the formation of a void space inside the hexamer, and the product channel that opens into the void interior space of the hexamer. It is suggested that these specific structural features are responsible for the higher nitrite reductase activity, the greater preference for nitrite than for sulfite as a substrate, and the wider pH range of the catalytic activity of octaheme nitrite reductases than of pentaheme homologs.


    Organizational Affiliation

    Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia. ttikhonova@inbi.ras.ru



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Eight-heme nitrite reductase
A, B
525Thioalkalivibrio paradoxusMutation(s): 0 
EC: 1.7.2.2
Find proteins for E7EDQ7 (Thioalkalivibrio paradoxus)
Go to UniProtKB:  E7EDQ7
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download CCD File 
A, B
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SO3
Query on SO3

Download CCD File 
A, B
SULFITE ION
O3 S
LSNNMFCWUKXFEE-UHFFFAOYSA-L
 Ligand Interaction
CO
Query on CO

Download CCD File 
A, B
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.135 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 190.99α = 90
b = 190.99β = 90
c = 190.99γ = 90
Software Package:
Software NamePurpose
AUTOMARdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-05
    Type: Initial release
  • Version 1.1: 2012-09-26
    Changes: Database references
  • Version 1.2: 2012-12-19
    Changes: Database references
  • Version 1.3: 2019-11-20
    Changes: Advisory, Derived calculations