3SCE

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase with a covalent bond between the CE1 atom of Tyr303 and the CG atom of Gln360 (TvNiRb)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.125 

Starting Model: experimental
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Literature

Covalent modifications of the catalytic tyrosine in octahaem cytochrome c nitrite reductase and their effect on the enzyme activity.

Trofimov, A.A., Polyakov, K.M., Tikhonova, T.V., Tikhonov, A.V., Safonova, T.N., Boyko, K.M., Dorovatovskii, P.V., Popov, V.O.

(2012) Acta Crystallogr D Biol Crystallogr 68: 144-153

  • DOI: https://doi.org/10.1107/S0907444911052632
  • Primary Citation of Related Structures:  
    3LG1, 3LGQ, 3RKH, 3SCE, 3UU9

  • PubMed Abstract: 

    Octahaem cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens (TvNiR), like the previously characterized pentahaem nitrite reductases (NrfAs), catalyzes the six-electron reductions of nitrite to ammonia and of sulfite to sulfide. The active site of both TvNiR and NrfAs is formed by the lysine-coordinated haem and His, Tyr and Arg residues. The distinguishing structural feature of TvNiR is the presence of a covalent bond between the CE2 atom of the catalytic Tyr303 and the S atom of Cys305, which might be responsible for the higher nitrite reductase activity of TvNiR compared with NrfAs. In the present study, a new modified form of the enzyme (TvNiRb) that contains an additional covalent bond between Tyr303 CE1 and Gln360 CG is reported. Structures of TvNiRb in complexes with phosphate (1.45 Å resolution) and sulfite (1.8 Å resolution), the structure of TvNiR in a complex with nitrite (1.83 Å resolution) and several additional structures were determined. The formation of the second covalent bond by Tyr303 leads to a decrease in both the nitrite and sulfite reductase activities of the enzyme. Tyr303 is located at the exit from the putative proton-transport channel to the active site, which is absent in NrfAs. This is an additional argument in favour of the involvement of Tyr303 as a proton donor in catalysis. The changes in the activity of cytochrome c nitrite reductases owing to the formation of Tyr-Cys and Tyr-Gln bonds may be associated with changes in the pK(a) value of the catalytic tyrosine.

    • Organizational Affiliation: 

    Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow 119991, Russian Federation. [email protected]


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Eight-heme nitrite reductase
A, B
519Thioalkalivibrio nitratireducensMutation(s): 0 
EC: 1.7.2 (PDB Primary Data), 1.7.2.2 (UniProt)
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
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC
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AA [auth B]
BA [auth B]
C [auth A]
CA [auth B]
D [auth A]
AA [auth B],
BA [auth B],
C [auth A],
CA [auth B],
D [auth A],
DA [auth B],
E [auth A],
EA [auth B],
F [auth A],
FA [auth B],
G [auth A],
GA [auth B],
H [auth A],
HA [auth B],
I [auth A],
J [auth A]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
PG6
Query on PG6
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MA [auth B],
NA [auth B],
O [auth A],
OA [auth B],
P [auth A]		1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
C12 H26 O6
DMDPGPKXQDIQQG-UHFFFAOYSA-N
PG4
Query on PG4
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LA [auth B]
N [auth A]
Q [auth A]
QA [auth B]
RA [auth B]
LA [auth B],
N [auth A],
Q [auth A],
QA [auth B],
RA [auth B],
S [auth A],
SA [auth B],
T [auth A],
TA [auth B],
U [auth A],
UA [auth B],
V [auth A],
VA [auth B],
W [auth A],
WA [auth B],
X [auth A]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PO4
Query on PO4
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IA [auth B],
K [auth A],
PA [auth B],
R [auth A]		PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CA
Query on CA
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JA [auth B],
KA [auth B],
L [auth A],
M [auth A]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA
Query on NA
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Y [auth A],
Z [auth A]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.125 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 193α = 90
b = 193β = 90
c = 193γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-07-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-01-25
    Changes: Database references
  • Version 1.3: 2012-03-28
    Changes: Database references
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-11-06
    Changes: Structure summary