2OT4

Structure of a hexameric multiheme c nitrite reductase from the extremophile bacterium Thiolkalivibrio nitratireducens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.127 

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Ligand Structure Quality Assessment 


This is version 1.2 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:  
    2OT4, 2ZO5, 3D1I

  • 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 c nitrite reductase (TvNiR) has been isolated from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens ...

    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: 
    • Crystallization and preliminary X-ray analysis of cytochrome c nitrite reductase from Thialkalivibrio nitraterecense.
      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 Struct Biol Cryst Commun 26: 215
    • Molecular and catalytic properties of a novel cytochrome c nitrite reductase from nitrate-reducing haloalkaliphic sulfur-oxidixing 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
    • Structures of complexes of octahaem cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens with sulfite and cyanide.
      Trofimov, A.A., Polyakov, K.M., Boyko, K.M., Tikhonova, T.V., Safonova, T.N., Tikhonov, A.V., Popov, A.N., Popov, V.O.
      (2010) Acta Crystallogr D Biol Crystallogr 66: 1043
    • Structure of octaheme cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens in a complex with phosphate
      Trofimov, A.A., Polyakov, K.M., Boiko, K.M., Filimonenkov, A.A., Dorovatovskii, P.V., Tikhonova, T.V., Popov, V.O., Kovalchuk, M.V.
      (2010) Crystallogr Rep 55: 58

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Eight-heme nitrite reductaseA, B525Thioalkalivibrio nitratireducensMutation(s): 0 
EC: 1.7.2.2
UniProt
Find proteins for L0DSL2 (Thioalkalivibrio nitratireducens (strain DSM 14787 / UNIQEM 213 / ALEN2))
Explore L0DSL2 
Go to UniProtKB:  L0DSL2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL0DSL2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
CIT
Query on CIT

Download Ideal Coordinates CCD File 
X [auth B]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
AA [auth B],
BA [auth B],
N [auth A]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
MRD
Query on MRD

Download Ideal Coordinates CCD File 
L [auth A],
M [auth A],
Y [auth B],
Z [auth B]
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A],
O [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.127 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 193.917α = 90
b = 193.917β = 90
c = 193.917γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
SHELXSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Refinement description