ECMDB: Cytochrome c-552 (P0ABK9)

Identification

Name:

Cytochrome c-552

Synonyms:

Ammonia-forming cytochrome c nitrite reductase
Cytochrome c nitrite reductase

Gene Name:

nrfA

Enzyme Class:

1.7.2.2

Biological Properties

General Function:

Involved in nitrogen compound metabolic process

Specific Function:

Plays a role in nitrite reduction

Cellular Location:

Periplasm

SMPDB Pathways:

Nitrogen metabolism PW000755
Phenylalanine metabolism PW000921

KEGG Pathways:

Microbial metabolism in diverse environments ec01120
Nitrogen metabolism ec00910
Phenylalanine metabolism ec00360

KEGG Reactions:

1.0

2.0

6.0Ferricytochrome c

1.0

↔

1.0

6.0Ferrocytochrome c

6.0

1.0

1.0Ammonia + 2.0Water + 6.0Ferricytochrome c + 1.0Ferricytochrome c ↔ 1.0Nitrite + 6.0Ferrocytochrome c + 6.0Hydrogen ion + 1.0Ferrocytochrome c
ReactionCard

SMPDB Reactions:

1.0Nitrite

6.0ferrocytochrome c

7.0

1.0

6.0

↔

1.0

6.0ferricytochrome c

2.0

6.0

1.0Nitrite + 6.0ferrocytochrome c + 7.0Hydrogen ion + 1.0Nitrite + 6.0Ferrocytochrome c ↔ 1.0Ammonia + 6.0ferricytochrome c + 2.0Water + 6.0Ferricytochrome c
ReactionCard

Complex Reactions:

3.0

2.0

1.0

→

3.0

2.0

1.0

3.0Ubiquinol-8 + 2.0Hydrogen ion + 1.0Nitrite → 3.0Ubiquinone-8 + 2.0Water + 1.0Ammonium
ReactionCard

3.0

2.0

1.0

→

3.0Menaquinone 8

2.0

1.0

3.0Menaquinol 8 + 2.0Hydrogen ion + 1.0Nitrite → 3.0Menaquinone 8 + 2.0Water + 1.0Ammonium
ReactionCard

1.0

2.0

6.0

→

1.0

6.0

7.0

1.0Ammonia + 2.0Water + 6.0Ferricytochrome c → 1.0Nitrite + 6.0Ferrocytochrome c + 7.0Hydrogen ion
ReactionCard

Metabolites:

ECMDB ID	Name	View
ECMDB00051	Ammonia	MetaboCard
ECMDB21186	Ammonium	MetaboCard
ECMDB21652	Ferricytochrome c	MetaboCard
ECMDB23135	Ferrocytochrome c	MetaboCard
ECMDB21225	Hydrogen ion	MetaboCard
ECMDB21245	Menaquinol 8	MetaboCard
ECMDB02786	Nitrite	MetaboCard
ECMDB01060	Ubiquinol-8	MetaboCard
ECMDB21296	Ubiquinone-8	MetaboCard
ECMDB00494	Water	MetaboCard

GO Classification:

Component
cell part
periplasmic space
Function
binding
calcium ion binding
catalytic activity
cation binding
heme binding
ion binding
iron ion binding
metal ion binding
nitrite reductase (cytochrome, ammonia-forming) activity
oxidoreductase activity
oxidoreductase activity, acting on other nitrogenous compounds as donors
oxidoreductase activity, acting on other nitrogenous compounds as donors, cytochrome as acceptor
transition metal ion binding
Process
metabolic process
nitrogen compound metabolic process
oxidation reduction

Gene Properties

Blattner:

b4070

Gene Orientation

Clockwise

Centisome Percentage:

92.37

Left Sequence End

4285787

Right Sequence End

4287223

Gene Sequence:

>1437 bp
ATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTT
TTCACTTCTGTTCACGCTGAACAAACGGCTGCTCCCGCAAAACCTGTAACTGTGGAAGCG
AAGAATGAAACCTTTGCCCCGCAGCATCCCGATCAATATCTCTCCTGGAAAGCCACCTCG
GAACAGTCAGAGCGTGTTGACGCCCTGGCGGAAGATCCACGGCTGGTGATCCTGTGGGCG
GGGTATCCCTTCTCGCGCGATTACAACAAGCCGCGTGGACATGCTTTTGCTGTGACCGAT
GTGCGTGAAACCCTGCGTACCGGTGCGCCGAAAAACGCTGAAGATGGTCCGCTACCGATG
GCATGCTGGAGTTGTAAAAGCCCGGATGTGGCGCGTCTGATCCAGAAAGACGGCGAAGAT
GGCTACTTCCACGGTAAATGGGCGCGCGGCGGTCCGGAAATCGTCAACAACTTAGGTTGT
GCCGATTGCCATAACACCGCCTCTCCAGAGTTCGCCAAAGGCAAACCGGAGTTAACCCTT
TCCCGTCCGTATGCGGCTCGCGCGATGGAAGCCATTGGTAAACCTTTTGAGAAAGCCGGA
CGTTTCGACCAGCAATCGATGGTTTGCGGTCAGTGCCATGTGGAGTATTACTTCGACGGC
AAAAACAAAGCGGTTAAATTCCCGTGGGATGACGGCATGAAAGTCGAAAATATGGAGCAG
TATTACGACAAAATTGCCTTCTCTGACTGGACTAACTCCCTGTCGAAAACGCCAATGCTG
AAAGCGCAGCACCCGGAATATGAAACCTGGACAGCGGGCATTCACGGTAAAAACAACGTG
ACCTGTATCGACTGCCATATGCCAAAAGTGCAGAACGCCGAAGGCAAACTCTACACCGAC
CATAAAATTGGTAATCCGTTTGATAACTTCGCCCAGACTTGTGCGAACTGCCATACCCAG
GACAAAGCTGCCTTGCAAAAAGTGGTCGCGGAACGTAAGCAGTCGATTAACGACCTGAAA
ATCAAGGTTGAAGATCAACTGGTTCACGCTCACTTCGAAGCGAAAGCAGCGCTGGATGCA
GGCGCGACGGAAGCTGAAATGAAGCCAATTCAGGACGATATCCGTCATGCCCAGTGGCGC
TGGGATCTGGCGATCGCTTCCCACGGCATTCATATGCACGCACCGGAAGAAGGTTTACGG
ATGCTCGGTACGGCGATGGATAAAGCGGCGGATGCACGCACCAAACTGGCGCGCCTGCTG
GCGACCAAAGGCATCACCCATGAAATCCAGATCCCGGATATCTCAACCAAAGAGAAAGCC
CAGCAGGCCATTGGCCTGAACATGGAACAAATCAAGGCCGAGAAGCAGGACTTCATCAAA
ACGGTGATCCCGCAGTGGGAAGAACAGGCACGTAAAAACGGTCTGTTAAGCCAATAA

Protein Properties

Pfam Domain Function:

Cytochrom_C552 (PF02335 )

Protein Residues:

478

Protein Molecular Weight:

53703

Protein Theoretical pI:

PDB File:

1GU6

Signaling Regions:

1-26

Transmembrane Regions:

None

Protein Sequence:

>Cytochrome c-552
MTRIKINARRIFSLLIPFFFFTSVHAEQTAAPAKPVTVEAKNETFAPQHPDQYLSWKATS
EQSERVDALAEDPRLVILWAGYPFSRDYNKPRGHAFAVTDVRETLRTGAPKNAEDGPLPM
ACWSCKSPDVARLIQKDGEDGYFHGKWARGGPEIVNNLGCADCHNTASPEFAKGKPELTL
SRPYAARAMEAIGKPFEKAGRFDQQSMVCGQCHVEYYFDGKNKAVKFPWDDGMKVENMEQ
YYDKIAFSDWTNSLSKTPMLKAQHPEYETWTAGIHGKNNVTCIDCHMPKVQNAEGKLYTD
HKIGNPFDNFAQTCANCHTQDKAALQKVVAERKQSINDLKIKVEDQLVHAHFEAKAALDA
GATEAEMKPIQDDIRHAQWRWDLAIASHGIHMHAPEEGLRMLGTAMDKAADARTKLARLL
ATKGITHEIQIPDISTKEKAQQAIGLNMEQIKAEKQDFIKTVIPQWEEQARKNGLLSQ

References

External Links:

Resource	Link
Uniprot ID:	P0ABK9
Uniprot Name:	NRFA_ECOLI
GenBank Gene ID:	AP009048
Genebank Protein ID:	85676822
PDB ID:	1GU6
Ecogene ID:	EG11781
Ecocyc:	EG11781
ColiBase:	b4070
Kegg Gene:	b4070
EchoBASE ID:	EB1729
CCDB:	NRFA_ECOLI
BacMap:	16131896

General Reference:

Bamford, V. A., Angove, H. C., Seward, H. E., Thomson, A. J., Cole, J. A., Butt, J. N., Hemmings, A. M., Richardson, D. J. (2002). "Structure and spectroscopy of the periplasmic cytochrome c nitrite reductase from Escherichia coli." Biochemistry 41:2921-2931. Pubmed: 11863430
Blattner, F. R., Burland, V., Plunkett, G. 3rd, Sofia, H. J., Daniels, D. L. (1993). "Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes." Nucleic Acids Res 21:5408-5417. Pubmed: 8265357
Blattner, F. R., Plunkett, G. 3rd, Bloch, C. A., Perna, N. T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C. K., Mayhew, G. F., Gregor, J., Davis, N. W., Kirkpatrick, H. A., Goeden, M. A., Rose, D. J., Mau, B., Shao, Y. (1997). "The complete genome sequence of Escherichia coli K-12." Science 277:1453-1462. Pubmed: 9278503
Darwin, A., Hussain, H., Griffiths, L., Grove, J., Sambongi, Y., Busby, S., Cole, J. (1993). "Regulation and sequence of the structural gene for cytochrome c552 from Escherichia coli: not a hexahaem but a 50 kDa tetrahaem nitrite reductase." Mol Microbiol 9:1255-1265. Pubmed: 7934939
Eaves, D. J., Grove, J., Staudenmann, W., James, P., Poole, R. K., White, S. A., Griffiths, I., Cole, J. A. (1998). "Involvement of products of the nrfEFG genes in the covalent attachment of haem c to a novel cysteine-lysine motif in the cytochrome c552 nitrite reductase from Escherichia coli." Mol Microbiol 28:205-216. Pubmed: 9593308
Hayashi, K., Morooka, N., Yamamoto, Y., Fujita, K., Isono, K., Choi, S., Ohtsubo, E., Baba, T., Wanner, B. L., Mori, H., Horiuchi, T. (2006). "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Mol Syst Biol 2:2006.0007. Pubmed: 16738553
Iobbi-Nivol, C., Crooke, H., Griffiths, L., Grove, J., Hussain, H., Pommier, J., Mejean, V., Cole, J. A. (1994). "A reassessment of the range of c-type cytochromes synthesized by Escherichia coli K-12." FEMS Microbiol Lett 119:89-94. Pubmed: 8039676