Reviewed, UniProtKB/Swiss-Prot P0ABK9 (NRFA_ECOLI)

Names and origin

Protein names

Recommended name:
    Cytochrome c-552
    EC=1.7.2.2
Alternative name(s):
    Ammonia-forming cytochrome c nitrite reductase
      Short name=Cytochrome c nitrite reductase

Gene names

Name:	nrfA
Ordered Locus Names:	b4070, JW4031

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	478 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Plays a role in nitrite reduction. HAMAP MF_01182
Catalytic activity	NH3 + 2 H2O + 6 ferricytochrome c = nitrite + 6 ferrocytochrome c + 7 H+. HAMAP MF_01182
Cofactor	Binds 1 calcium ion per monomer. HAMAP MF_01182 Binds 5 heme groups covalently per monomer. Ref.6
Pathway	Nitrogen metabolism; nitrate reduction (assimilation). HAMAP MF_01182
Subcellular location	Periplasm. HAMAP MF_01182
Induction	Full induction attained in the presence of nitrite. Subject to glucose and nitrate repression. HAMAP MF_01182
Sequence similarities	Belongs to the cytochrome c-552 family.
Mass spectrometry	Molecular mass is 53590 Da from positions 27 - 478. Determined by MALDI. Ref.6

Ontologies

Keywords
Biological process	Electron transport Transport
Cellular component	Periplasm
Domain	Signal
Ligand	Calcium Heme Iron Metal-binding
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	electron transport chain Inferred from electronic annotation. Source: UniProtKB-KW nitrogen compound metabolic process Inferred from electronic annotation. Source: HAMAP transport Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	periplasmic space Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	calcium ion binding Inferred from electronic annotation. Source: UniProtKB-KW heme binding Inferred from electronic annotation. Source: InterPro nitrite reductase (cytochrome, ammonia-forming) activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 26

26

Ref.1

Chain

27 – 478

452

Cytochrome c-552 HAMAP MF_01182

PRO_0000006578

Sites

Metal binding

94

1

Iron (heme 3 axial ligand) HAMAP MF_01182

Metal binding

126

1

Iron (heme 1 axial ligand) HAMAP MF_01182

Metal binding

164

1

Iron (heme 2 axial ligand) HAMAP MF_01182

Metal binding

213

1

Iron (heme 3 axial ligand) HAMAP MF_01182

Metal binding

215

1

Calcium HAMAP MF_01182

Metal binding

216

1

Calcium; via carbonyl oxygen HAMAP MF_01182

Metal binding

261

1

Calcium; via carbonyl oxygen HAMAP MF_01182

Metal binding

263

1

Calcium HAMAP MF_01182

Metal binding

275

1

Iron (heme 5 axial ligand) HAMAP MF_01182

Metal binding

286

1

Iron (heme 4 axial ligand) HAMAP MF_01182

Metal binding

301

1

Iron (heme 2 axial ligand) HAMAP MF_01182

Metal binding

318

1

Iron (heme 5 axial ligand) HAMAP MF_01182

Metal binding

393

1

Iron (heme 4 axial ligand) HAMAP MF_01182

Binding site

122

1

Heme 1 (covalent) HAMAP MF_01182

Binding site

125

1

Heme 1 (covalent) HAMAP MF_01182

Binding site

160

1

Heme 2 (covalent) HAMAP MF_01182

Binding site

163

1

Heme 2 (covalent) HAMAP MF_01182

Binding site

209

1

Heme 3 (covalent) HAMAP MF_01182

Binding site

212

1

Heme 3 (covalent) HAMAP MF_01182

Binding site

216

1

Substrate By similarity

Binding site

264

1

Substrate By similarity

Binding site

282

1

Heme 4 (covalent) HAMAP MF_01182

Binding site

285

1

Heme 4 (covalent) HAMAP MF_01182

Binding site

314

1

Heme 5 (covalent) HAMAP MF_01182

Binding site

317

1

Heme 5 (covalent) HAMAP MF_01182

Experimental info

Mutagenesis

126

1

K → H, I or L: Almost complete loss of nitrite reductase activity. Ref.6

Secondary structure

1

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478

Helix Strand Turn

Details...

Helix

42 – 45

4

Turn

46 – 48

3

Helix

50 – 57

8

Helix

58 – 61

4

Helix

68 – 71

4

Helix

74 – 78

5

Turn

79 – 81

3

Helix

83 – 85

3

Helix

94 – 96

3

Helix

97 – 103

7

Helix

105 – 107

3

Beta strand

116 – 119

4

Helix

120 – 123

4

Turn

124 – 126

3

Helix

129 – 137

9

Helix

139 – 143

5

Beta strand

144 – 146

3

Helix

147 – 150

4

Turn

151 – 153

3

Helix

160 – 163

4

Helix

169 – 172

4

Helix

183 – 191

9

Helix

196 – 198

3

Helix

201 – 209

9

Turn

210 – 212

3

Beta strand

217 – 219

3

Turn

220 – 223

4

Beta strand

224 – 226

3

Helix

235 – 244

10

Beta strand

249 – 251

3

Turn

253 – 255

3

Helix

266 – 272

7

Helix

274 – 277

4

Helix

282 – 286

5

Beta strand

289 – 291

3

Beta strand

297 – 299

3

Helix

306 – 312

7

Helix

314 – 316

3

Helix

322 – 359

38

Helix

364 – 385

22

Helix

390 – 393

4

Helix

395 – 422

28

Helix

437 – 443

7

Helix

448 – 472

25

Sequences

	Sequence		Length	Mass (Da)
	P0ABK9-1 [UniParc]. Last modified November 8, 2005. Version 1. Checksum: F965E986412A0456	FASTA	478	53,703
	10 20 30 40 50 60 MTRIKINARR IFSLLIPFFF FTSVHAEQTA APAKPVTVEA KNETFAPQHP DQYLSWKATS 70 80 90 100 110 120 EQSERVDALA EDPRLVILWA GYPFSRDYNK PRGHAFAVTD VRETLRTGAP KNAEDGPLPM 130 140 150 160 170 180 ACWSCKSPDV ARLIQKDGED GYFHGKWARG GPEIVNNLGC ADCHNTASPE FAKGKPELTL 190 200 210 220 230 240 SRPYAARAME AIGKPFEKAG RFDQQSMVCG QCHVEYYFDG KNKAVKFPWD DGMKVENMEQ 250 260 270 280 290 300 YYDKIAFSDW TNSLSKTPML KAQHPEYETW TAGIHGKNNV TCIDCHMPKV QNAEGKLYTD 310 320 330 340 350 360 HKIGNPFDNF AQTCANCHTQ DKAALQKVVA ERKQSINDLK IKVEDQLVHA HFEAKAALDA 370 380 390 400 410 420 GATEAEMKPI QDDIRHAQWR WDLAIASHGI HMHAPEEGLR MLGTAMDKAA DARTKLARLL 430 440 450 460 470 ATKGITHEIQ IPDISTKEKA QQAIGLNMEQ IKAEKQDFIK TVIPQWEEQA RKNGLLSQ

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Regulation and sequence of the structural gene for cytochrome c552 from Escherichia coli: not a hexahaem but a 50 kDa tetrahaem nitrite reductase." Darwin A., Hussain H.A., Griffiths L., Grove J., Sambongi Y., Busby S., Cole J. Mol. Microbiol. 9:1255-1265(1993) [PubMed: 7934939] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 27-42 AND 150-167. Strain: K12.
[2]	"Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes." Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L. Nucleic Acids Res. 21:5408-5417(1993) [PubMed: 8265357] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, 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. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"A reassessment of the range of c-type cytochromes synthesized by Escherichia coli K-12." Iobbi-Nivol C., Crooke H., Griffiths L., Grov J., Hussain H., Pommier J., Mejean V., Cole J.A. FEMS Microbiol. Lett. 119:89-94(1994) [PubMed: 8039676] [Abstract] Cited for: CHARACTERIZATION AS A CYTOCHROME C.
[6]	"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." Eaves D.J., Grove J., Staudenmann W., James P., Poole R.K., White S.A., Griffiths I., Cole J.A. Mol. Microbiol. 28:205-216(1998) [PubMed: 9593308] [Abstract] Cited for: HEME-BINDING, MASS SPECTROMETRY, MUTAGENESIS OF LYS-126.
[7]	"Structure and spectroscopy of the periplasmic cytochrome c nitrite reductase from Escherichia coli." Bamford V.A., Angove H.C., Seward H.E., Thomson A.J., Cole J.A., Butt J.N., Hemmings A.M., Richardson D.J. Biochemistry 41:2921-2931(2002) [PubMed: 11863430] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS), MAGNETIC CIRCULAR DICHROISM, EPR SPECTROSCOPY.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

X72298 Genomic DNA. Translation: CAA51048.1.
U00006 Genomic DNA. Translation: AAC43164.1.
U00096 Genomic DNA. Translation: AAC77040.1.
AP009048 Genomic DNA. Translation: BAE78072.1.

PIR

S39590.

RefSeq

AP_004571.1.
NP_418494.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1GU6	X-ray	2.50	A/C/E/G	27-478	[»]
2RDZ	X-ray	1.74	A/B/C/D	27-478	[»]
2RF7	X-ray	2.04	A/B/C/D	37-477	[»]

ModBase

Search...

Genome annotation databases

GeneID

948571.

GenomeReviews

Gene locus JW4031 in contig AP009048_GR.
Gene locus b4070 in contig U00096_GR.

KEGG

ecj:JW4031.
eco:b4070.

Organism-specific databases

EchoBASE

EB1729.

EcoGene

EG11781. nrfA.

CMR

Search...

Phylogenomic databases

HOGENOM

P0ABK9.

OMA

P0ABK9. CHDQSKE.

Enzyme and pathway databases

BioCyc

EcoCyc:CYTOCHROMEC552-MON.

Family and domain databases

HAMAP

MF_01182.
[Tree]

InterPro

IPR003321. Cyt_c552.
IPR017570. Cyt_c_NO2Rdtase_formate-dep.
IPR011031. Multihaem_cyt.
[Graphical view]

Pfam

PF02335. Cytochrom_C552. 1 hit.
[Graphical view]

PIRSF

PIRSF000243. Cyt_c552. 1 hit.

TIGRFAMs

TIGR03152. cyto_c552_HCOOH. 1 hit.

PROSITE

PS51008. MULTIHEME_CYTC. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

NRFA_ECOLI

Accession

Primary (citable) accession number: P0ABK9
Secondary accession number(s): P32050, Q2M6N4

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 8, 2005
Last sequence update:	November 8, 2005
Last modified:	June 16, 2009
This is version 41 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)