PDBsum entry 2e80

Oxidoreductase

PDB id

2e80

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Contents

			Protein chain

					471 a.a. *

			Ligands

					NO2


					ACT ×3


					HEM ×5

			Metals

					_CA


					YT3 ×3

			Waters ×653

* Residue conservation analysis

PDB id:

2e80

Links

Name:

Oxidoreductase

Title:

CytochromE C nitrite reductase from wolinella succinogenes with bound substrate nitrite

Structure:

CytochromE C-552. Chain: a. Synonym: ammonia-forming cytochromE C nitrite reductase, cytochromE C nitrite reductase. Ec: 1.7.2.2

Source:

Wolinella succinogenes. Organism_taxid: 273121. Strain: dsm 1740

Resolution:

1.60Å

R-factor:

0.186

R-free:

0.210

Authors:

O.Einsle,P.M.H.Kroneck

Key ref:

O.Einsle et al. (2002). Mechanism of the six-electron reduction of nitrite to ammonia by cytochrome c nitrite reductase. J Am Chem Soc, 124, 11737-11745. PubMed id: 12296741 DOI: 10.1021/ja0206487

Date:

15-Jan-07

Release date:

30-Jan-07

PROCHECK

	Headers

	References

Protein chain

Q9S1E5 (NRFA_WOLSU) - Cytochrome c-552 from Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / CCUG 13145 / JCM 31913 / LMG 7466 / NCTC 11488 / FDC 602W)

Seq: Struc:					507 a.a. 471 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.1.7.2.2 - nitrite reductase (cytochrome; ammonia-forming).

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

6 Fe(III)-[cytochrome c] + NH4⁺ + 2 H2O = 6 Fe(II)-[cytochrome c] + nitrite + 8 H⁺

6 × Fe(III)-[cytochrome c]	+	NH4(+)	+	2 × H2O	=	6 × Fe(II)-[cytochrome c]	+	nitrite	+	8 × H(+) Bound ligand (Het Group name = NO2) corresponds exactly

Cofactor:

Ca(2+); Heme

Ca(2+)

Heme
Bound ligand (Het Group name = HEM) matches with 95.45% similarity

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1021/ja0206487	J Am Chem Soc 124:11737-11745 (2002)
PubMed id: 12296741

Mechanism of the six-electron reduction of nitrite to ammonia by cytochrome c nitrite reductase.
O.Einsle, A.Messerschmidt, R.Huber, P.M.Kroneck, F.Neese.

ABSTRACT

Cytochrome c nitrite reductase catalyzes the six-electron reduction of nitrite to ammonia without the release of potential reaction intermediates, such as NO or hydroxylamine. On the basis of the crystallographic observation of reaction intermediates and of density functional calculations, we present a working hypothesis for the reaction mechanism of this multiheme enzyme which carries a novel lysine-coordinated heme group (Fe-Lys). It is proposed that nitrite reduction starts with a heterolytic cleavage of the N-O bond which is facilitated by a pronounced back-bonding interaction of nitrite coordinated through nitrogen to the reduced (Fe(II)) but not the oxidized (Fe(III)) active site iron. This step leads to the formation of an [FeNO](6) species and a water molecule and is further facilitated by a hydrogen bonding network that induces an electronic asymmetry in the nitrite molecule that weakens one N-O bond and strengthens the other. Subsequently, two rapid one-electron reductions lead to an [FeNO](8) form and, by protonation, to an Fe(II)-HNO adduct. Hereafter, hydroxylamine will be formed by a consecutive two-electron two-proton step which is dehydrated in the final two-electron reduction step to give ammonia and an additional water molecule. A single electron reduction of the active site closes the catalytic cycle.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21125303

D.Bykov, and F.Neese (2011).
Substrate binding and activation in the active site of cytochrome c nitrite reductase: a density functional study.

J Biol Inorg Chem, 16, 417-430.

21265772

S.Rinaldo, G.Giardina, N.Castiglione, V.Stelitano, and F.Cutruzzolà (2011).
The catalytic mechanism of Pseudomonas aeruginosa cd1 nitrite reductase.

Biochem Soc Trans, 39, 195-200.

20689707

C.M.Silveira, S.Besson, I.Moura, J.J.Moura, and M.G.Almeida (2010).
Measuring the cytochrome C nitrite reductase activity-practical considerations on the enzyme assays.

Bioinorg Chem Appl, (), 0.

20629638

G.L.Kemp, T.A.Clarke, S.J.Marritt, C.Lockwood, S.R.Poock, A.M.Hemmings, D.J.Richardson, M.R.Cheesman, and J.N.Butt (2010).
Kinetic and thermodynamic resolution of the interactions between sulfite and the pentahaem cytochrome NrfA from Escherichia coli.

Biochem J, 431, 73-80.

PDB code:

3l1t

19919672

M.Kern, F.Eisel, J.Scheithauer, R.G.Kranz, and J.Simon (2010).
Substrate specificity of three cytochrome c haem lyase isoenzymes from Wolinella succinogenes: unconventional haem c binding motifs are not sufficient for haem c attachment by NrfI and CcsA1.

Mol Microbiol, 75, 122-137.

19924902

J.Yi, J.Heinecke, H.Tan, P.C.Ford, and G.B.Richter-Addo (2009).
The distal pocket histidine residue in horse heart myoglobin directs the O-binding mode of nitrite to the heme iron.

J Am Chem Soc, 131, 18119-18128.

PDB codes:

3hc9 3hen 3heo 3hep

19322490

M.M.Gutiérrez, G.B.Alluisetti, C.Gaviglio, F.Doctorovich, J.A.Olabe, and V.T.Amorebieta (2009).
Catalytic disproportionation of N-alkylhydroxylamines bound to pentacyanoferrates.

Dalton Trans, (), 1187-1194.

18274790

C.Xu, and G.S.Thomas (2008).
Ambidentate H-bonding by heme-bound NO: structural and spectral effects of -O versus -N H-bonding.

J Biol Inorg Chem, 13, 613-621.

18245085

J.H.van Wonderen, B.Burlat, D.J.Richardson, M.R.Cheesman, and J.N.Butt (2008).
The nitric oxide reductase activity of cytochrome c nitrite reductase from Escherichia coli.

J Biol Chem, 283, 9587-9594.

18553112

J.Kostera, M.D.Youngblut, J.M.Slosarczyk, and A.A.Pacheco (2008).
Kinetic and product distribution analysis of NO* reductase activity in Nitrosomonas europaea hydroxylamine oxidoreductase.

J Biol Inorg Chem, 13, 1073-1083.

18298372

T.V.Tikhonova, E.S.Slutskaya, A.A.Filimonenkov, K.M.Boyko, S.Y.Kleimenov, P.V.Konarev, K.M.Polyakov, D.I.Svergun, A.A.Trofimov, V.G.Khomenkov, R.A.Zvyagilskaya, and V.O.Popov (2008).
Isolation and oligomeric composition of cytochrome c nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens.

Biochemistry (Mosc), 73, 164-170.

17905436

Z.N.Zahran, L.Chooback, D.M.Copeland, A.H.West, and G.B.Richter-Addo (2008).
Crystal structures of manganese- and cobalt-substituted myoglobin in complex with NO and nitrite reveal unusual ligand conformations.

J Inorg Biochem, 102, 216-233.

PDB codes:

2o58 2o5b 2o5l 2o5m 2o5o 2o5q 2o5s 2o5t

16754983

M.L.Rodrigues, T.Oliveira, P.M.Matias, I.C.Martins, F.M.Valente, I.A.Pereira, and M.Archer (2006).
Crystallization and preliminary structure determination of the membrane-bound complex cytochrome c nitrite reductase from Desulfovibrio vulgaris Hildenborough.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 565-568.

16234915

C.G.Mowat, and S.K.Chapman (2005).
Multi-heme cytochromes--new structures, new chemistry.

Dalton Trans, (), 3381-3389.

16234919

J.W.Allen, P.D.Barker, O.Daltrop, J.M.Stevens, E.J.Tomlinson, N.Sinha, Y.Sambongi, and S.J.Ferguson (2005).
Why isn't 'standard' heme good enough for c-type and d1-type cytochromes?

Dalton Trans, (), 3410-3418.

16155964

S.Kura, S.Kuwata, and T.Ikariya (2005).
N-Methylhydroxylamido(1-)- and nitrosomethaneruthenium complexes derived from nitrosyl complexes: reversible N-protonation of an N-coordinated nitrosoalkane.

Angew Chem Int Ed Engl, 44, 6406-6409.

15106981

H.Nasri, M.K.Ellison, M.Shang, C.E.Schulz, and W.R.Scheidt (2004).
Variable pi-bonding in iron(II) porphyrinates with nitrite, CO, and tert-butyl isocyanide: characterization of [Fe(TpivPP)(NO2)(CO)]-.

Inorg Chem, 43, 2932-2942.

15322098

P.Cabello, C.Pino, M.F.Olmo-Mira, F.Castillo, M.D.Roldán, and C.Moreno-Vivián (2004).
Hydroxylamine assimilation by Rhodobacter capsulatus E1F1. requirement of the hcp gene (hybrid cluster protein) located in the nitrate assimilation nas gene region for hydroxylamine reduction.

J Biol Chem, 279, 45485-45494.

15280383

T.A.Clarke, V.Dennison, H.E.Seward, B.Burlat, J.A.Cole, A.M.Hemmings, and D.J.Richardson (2004).
Purification and spectropotentiometric characterization of Escherichia coli NrfB, a decaheme homodimer that transfers electrons to the decaheme periplasmic nitrite reductase complex.

J Biol Chem, 279, 41333-41339.

12618432

C.A.Cunha, S.Macieira, J.M.Dias, G.Almeida, L.L.Goncalves, C.Costa, J.Lampreia, R.Huber, J.J.Moura, I.Moura, and M.J.Romão (2003).
Cytochrome c nitrite reductase from Desulfovibrio desulfuricans ATCC 27774. The relevance of the two calcium sites in the structure of the catalytic subunit (NrfA).

J Biol Chem, 278, 17455-17465.

PDB code:

1oah

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.