2ZO5

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with azide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

High-resolution structural analysis of a novel octaheme cytochrome c nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens

Polyakov, K.M.Boyko, K.M.Tikhonova, T.V.Slutsky, A.Antipov, A.N.Zvyagilskaya, R.A.Popov, A.N.Bourenkov, G.P.Lamzin, V.S.Popov, V.O.

(2009) J.Mol.Biol. 389: 846-862

  • DOI: 10.1016/j.jmb.2009.04.037
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacterial pentaheme cytochrome c nitrite reductases (NrfAs) are key enzymes involved in the terminal step of dissimilatory nitrite reduction of the nitrogen cycle. Their structure and functions are well studied. Recently, a novel octaheme cytochrome ...

    Bacterial pentaheme cytochrome c nitrite reductases (NrfAs) are key enzymes involved in the terminal step of dissimilatory nitrite reduction of the nitrogen cycle. Their structure and functions are well studied. Recently, a novel octaheme cytochrome c nitrite reductase (TvNiR) has been isolated from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens. Here we present high-resolution crystal structures of the apoenzyme and its complexes with the substrate (nitrite) and the inhibitor (azide). Both in the crystalline state and in solution, TvNiR exists as a stable hexamer containing 48 hemes-the largest number of hemes accommodated within one protein molecule known to date. The subunit of TvNiR consists of two domains. The N-terminal domain has a unique fold and contains three hemes. The catalytic C-terminal domain hosts the remaining five hemes, their arrangement, including the catalytic heme, being identical to that found in NrfAs. The complete set of eight hemes forms a spatial pattern characteristic of other multiheme proteins, including structurally characterized octaheme cytochromes. The catalytic machinery of TvNiR resembles that of NrfAs. It comprises the lysine residue at the proximal position of the catalytic heme, the catalytic triad of tyrosine, histidine, and arginine at the distal side, channels for the substrate and product transport with a characteristic gradient of electrostatic potential, and, finally, two conserved Ca(2+)-binding sites. However, TvNiR has a number of special structural features, including a covalent bond between the catalytic tyrosine and the adjacent cysteine and the unusual topography of the product channels that open into the void interior space of the protein hexamer. The role of these characteristic structural features in the catalysis by this enzyme is discussed.


    Related Citations: 
    • Molecular and catalytic properties of a novel cytochrome c nitrite reductase from nitrate-reducing haloalkaliphilic sulfur-oxidizing bacterium Thioalkalivibrio nitratireducens
      Tikhonova, T.V.,Slutsky, A.,Antipov, A.N.,Boyko, K.M.,Polyakov, K.M.,Sorokin, D.Y.,Zvyagilskaya, R.A.,Popov, V.O.
      (2006) Biochim.Biophys.Acta 1764: 715
    • Crystallization and preliminary X-ray analysis of cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens
      Boyko, K.M.,Polyakov, K.M.,Tikhonova, T.V.,Slutsky, A.,Antipov, A.N.,Zvyagilskaya, R.A.,Bourenkov, G.P.,Popov, A.N.,Lamzin, V.S.,Popov, V.O.
      (2006) Acta Crystallogr.,Sect.F 62: 215


    Organizational Affiliation

    A. N. Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Eight-heme nitrite reductase
A, B
525Thioalkalivibrio nitratireducens (strain DSM 14787 / UNIQEM 213 / ALEN2)Mutation(s): 0 
Gene Names: nir
EC: 1.7.2.2
Find proteins for L0DSL2 (Thioalkalivibrio nitratireducens (strain DSM 14787 / UNIQEM 213 / ALEN2))
Go to UniProtKB:  L0DSL2
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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A, B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
AZI
Query on AZI

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A, B
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
HEC
Query on HEC

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A, B
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
PG6
Query on PG6

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A, B
1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
C12 H26 O6
DMDPGPKXQDIQQG-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

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A, B
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.151 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 193.027α = 90.00
b = 193.027β = 90.00
c = 193.027γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance