PDBsum entry 3bnh

Oxidoreductase

PDB id

3bnh

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Contents

			Protein chain

					471 a.a. *

			Ligands

					NO2


					ACT ×2


					SO4


					HEM ×5

			Metals

					_CA


					_Y1 ×3

			Waters ×646

* Residue conservation analysis

PDB id:

3bnh

Links

Name:

Oxidoreductase

Title:

W. Succinogenes nrfa y218f nitrite complex

Structure:

CytochromE C-552. Chain: a. Synonym: ammonia-forming cytochromE C nitrite reductase, cytochromE C nitrite reductase. Engineered: yes. Mutation: yes

Source:

Wolinella succinogenes. Organism_taxid: 844. Gene: nrfa y218f. Expressed in: wolinella succinogenes. Expression_system_taxid: 844

Resolution:

1.75Å

R-factor:

0.179

R-free:

0.215

Authors:

P.Lukat,O.Einsle

Key ref:

P.Lukat et al. (2008). Binding and reduction of sulfite by cytochrome c nitrite reductase. Biochemistry, 47, 2080-2086. PubMed id: 18201106

Date:

14-Dec-07

Release date:

26-Feb-08

PROCHECK

	Headers

	References

Protein chain

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

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

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)



		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

	Biochemistry 47:2080-2086 (2008)
PubMed id: 18201106

Binding and reduction of sulfite by cytochrome c nitrite reductase.
P.Lukat, M.Rudolf, P.Stach, A.Messerschmidt, P.M.Kroneck, J.Simon, O.Einsle.

ABSTRACT

Pentaheme cytochrome c nitrite reductase (ccNiR) catalyzes the six-electron reduction of nitrite to ammonia as the final step in the dissimilatory pathway of nitrate ammonification. It has also been shown to reduce sulfite to sulfide, thus forming the only known link between the biogeochemical cycles of nitrogen and of sulfur. We have found the sulfite reductase activity of ccNiR from Wolinella succinogenes to be significantly smaller than its nitrite reductase activity but still several times higher than the one described for dissimilatory, siroheme-containing sulfite reductases. To compare the sulfite reductase activity of ccNiR with our previous data on nitrite reduction, we determined the binding mode of sulfite to the catalytic heme center of ccNiR from W. succinogenes at a resolution of 1.7 A. Sulfite and nitrite both provide a pair of electrons to form the coordinative bond to the Fe(III) active site of the enzyme, and the oxygen atoms of sulfite are found to interact with the three active site protein residues conserved within the enzyme family. Furthermore, we have characterized the active site variant Y218F of ccNiR that exhibited an almost complete loss of nitrite reductase activity, while sulfite reduction remained unaffected. These data provide a first direct insight into the role of the first sphere of protein ligands at the active site in ccNiR catalysis.

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.

21199252

S.Shirodkar, S.Reed, M.Romine, and D.Saffarini (2011).
The octahaem SirA catalyses dissimilatory sulfite reduction in Shewanella oneidensis MR-1.

Environ Microbiol, 13, 108-115.

20944237

A.A.Trofimov, K.M.Polyakov, K.M.Boyko, T.V.Tikhonova, T.N.Safonova, A.V.Tikhonov, A.N.Popov, and V.O.Popov (2010).
Structures of complexes of octahaem cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens with sulfite and cyanide.

Acta Crystallogr D Biol Crystallogr, 66, 1043-1047.

PDB codes:

3fo3 3mmo

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

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

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 codes are shown on the right.