Reviewed, UniProtKB/Swiss-Prot Q9S1E5 (NRFA_WOLSU)

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:	WS0969

Organism

Wolinella succinogenes [Complete proteome] [HAMAP]

Taxonomic identifier

844 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Epsilonproteobacteria › Campylobacterales › Helicobacteraceae › Wolinella

Protein attributes

Sequence length	507 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. Ref.1
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. HAMAP MF_01182
Pathway	Nitrogen metabolism; nitrate reduction (assimilation). HAMAP MF_01182
Subunit structure	Heterodimer with nrfH. Ref.1
Subcellular location	Periplasm Ref.1.
Miscellaneous	X-ray crystallographic determinations include sulfate or azide ions at what is thought to be the substrate binding site. HAMAP MF_01182
Sequence similarities	Belongs to the cytochrome c-552 family.

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 Ref.1 Inferred from direct assay. Source: UniProtKB transport Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	outer membrane-bounded periplasmic space Ref.1 Inferred from direct assay. Source: UniProtKB
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 – 22

22

Ref.1

Chain

23 – 507

485

Cytochrome c-552 HAMAP MF_01182

PRO_0000006584

Sites

Metal binding

102

1

Iron (heme 3 axial ligand) HAMAP MF_01182

Metal binding

134

1

Iron (heme 1 axial ligand) HAMAP MF_01182

Metal binding

172

1

Iron (heme 2 axial ligand) HAMAP MF_01182

Metal binding

215

1

Iron (heme 3 axial ligand) HAMAP MF_01182

Metal binding

217

1

Calcium HAMAP MF_01182

Metal binding

218

1

Calcium; via carbonyl oxygen HAMAP MF_01182

Metal binding

274

1

Calcium; via carbonyl oxygen HAMAP MF_01182

Metal binding

276

1

Calcium HAMAP MF_01182

Metal binding

288

1

Iron (heme 5 axial ligand) HAMAP MF_01182

Metal binding

299

1

Iron (heme 4 axial ligand) HAMAP MF_01182

Metal binding

313

1

Iron (heme 2 axial ligand) HAMAP MF_01182

Metal binding

330

1

Iron (heme 5 axial ligand) HAMAP MF_01182

Metal binding

405

1

Iron (heme 4 axial ligand) HAMAP MF_01182

Binding site

130

1

Heme 1 (covalent) HAMAP MF_01182

Binding site

133

1

Heme 1 (covalent) HAMAP MF_01182

Binding site

168

1

Heme 2 (covalent) HAMAP MF_01182

Binding site

171

1

Heme 2 (covalent) HAMAP MF_01182

Binding site

211

1

Heme 3 (covalent) HAMAP MF_01182

Binding site

214

1

Heme 3 (covalent) HAMAP MF_01182

Binding site

218

1

Substrate HAMAP MF_01182

Binding site

277

1

Substrate HAMAP MF_01182

Binding site

295

1

Heme 4 (covalent) HAMAP MF_01182

Binding site

298

1

Heme 4 (covalent) HAMAP MF_01182

Binding site

326

1

Heme 5 (covalent) HAMAP MF_01182

Binding site

329

1

Heme 5 (covalent) HAMAP MF_01182

Experimental info

Sequence conflict

45

1

E → K in CAB53160. Ref.1

Secondary structure

1

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507

Helix Strand Turn

Details...

Turn

39 – 42

4

Turn

45 – 48

4

Helix

50 – 53

4

Turn

54 – 56

3

Helix

58 – 65

8

Helix

66 – 69

4

Helix

76 – 79

4

Helix

82 – 86

5

Turn

87 – 89

3

Helix

91 – 93

3

Helix

102 – 104

3

Helix

105 – 111

7

Helix

113 – 115

3

Beta strand

124 – 127

4

Helix

128 – 131

4

Helix

137 – 145

9

Helix

147 – 150

4

Beta strand

152 – 154

3

Helix

155 – 158

4

Turn

159 – 161

3

Helix

168 – 171

4

Turn

174 – 176

3

Helix

185 – 192

8

Turn

198 – 200

3

Helix

203 – 212

10

Beta strand

219 – 226

8

Beta strand

232 – 239

8

Helix

248 – 257

10

Beta strand

262 – 264

3

Turn

266 – 268

3

Helix

279 – 283

5

Helix

287 – 290

4

Helix

295 – 299

5

Beta strand

302 – 305

4

Beta strand

308 – 311

4

Helix

318 – 321

4

Helix

322 – 325

4

Turn

326 – 329

4

Helix

334 – 372

39

Helix

376 – 397

22

Helix

402 – 405

4

Helix

407 – 434

28

Helix

448 – 454

7

Helix

459 – 471

13

Helix

473 – 483

11

Helix

489 – 492

4

Turn

493 – 496

4

Sequences

	Sequence		Length	Mass (Da)
	Q9S1E5-1 [UniParc]. Last modified September 26, 2003. Version 2. Checksum: D5CE7E841E3E7AB3	FASTA	507	57,511
	10 20 30 40 50 60 MTKFKLLLAG SLVAIVSMGL LASNINEREK ERVALNKTAH SQGIEGKAMS EEWARYYPRQ 70 80 90 100 110 120 FDSWKKTKES DNITDMLKEK PALVVAWAGY PFSKDYNAPR GHYYALQDNI NTLRTGAPVD 130 140 150 160 170 180 GKTGPLPSAC WTCKSPDVPR IIEQDGELEY FTGKWAKYGD EIVNTIGCYN CHDDKSAELK 190 200 210 220 230 240 SKVPYLDRGL SAAGFKTFAE STHQEKRSLV CAQCHVEYYF KKTEWKDDKG VDKTAMVVTL 250 260 270 280 290 300 PWSKGISTEQ MEAYYDEINF ADWTHGISKT PMLKAQHPDW ELYKTGIHGQ KGVSCADCHM 310 320 330 340 350 360 PYTQEGAVKY SDHKVGNPLD NMDKSCMNCH RESEQKLKDI VKQKFERKEF LQDIAFDNIG 370 380 390 400 410 420 KAHLETGKAM ELGATDAELK EIRTHIRHAQ WRADMAIAGH GSFFHAPEEV LRLLASGNEE 430 440 450 460 470 480 AQKARIKLVK VLAKYGAIDY VAPDFETKEK AQKLAKVDME AFIAEKLKFK QTLEQEWKKQ 490 500 AIAKGRLNPE SLKGVDEKSS YYDKTKK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"A NapC/NirT-type cytochrome c (NrfH) is the mediator between the quinone pool and the cytochrome c nitrite reductase of Wolinella succinogenes." Simon J., Gross R., Einsle O., Kroneck P.M.H., Kroeger A., Klimmek O. Mol. Microbiol. 35:686-696(2000) [PubMed: 10672190] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 23-30, FUNCTION, SUBCELLULAR LOCATION, SUBUNIT.
[2]	"Complete genome sequence and analysis of Wolinella succinogenes." Baar C., Eppinger M., Raddatz G., Simon J., Lanz C., Klimmek O., Nandakumar R., Gross R., Rosinus A., Keller H., Jagtap P., Linke B., Meyer F., Lederer H., Schuster S.C. Proc. Natl. Acad. Sci. U.S.A. 100:11690-11695(2003) [PubMed: 14500908] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: DSMZ 1740.
[3]	"Cytochrome c nitrite reductase from Wolinella succinogenes. Structure at 1.6 A resolution, inhibitor binding, and heme-packing motifs." Einsle O., Stach P., Messerschmidt A., Simon J., Kroeger A., Huber R., Kroneck P.M.H. J. Biol. Chem. 275:39608-39616(2000) [PubMed: 10984487] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 37-507.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AJ245540 Genomic DNA. Translation: CAB53160.1.
BX571659 Genomic DNA. Translation: CAE10072.1.

RefSeq

NP_907172.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1FS7	X-ray	1.60	A	23-507	[»]
1FS8	X-ray	1.60	A	23-507	[»]
1FS9	X-ray	2.00	A	1-507	[»]
2E80	X-ray	1.60	A	23-507	[»]
2E81	X-ray	2.00	A	23-507	[»]
3BNF	X-ray	1.70	A	23-507	[»]
3BNG	X-ray	1.50	A	23-507	[»]
3BNH	X-ray	1.75	A	23-507	[»]
3BNJ	X-ray	1.30	A	23-507	[»]

ModBase

Search...

Genome annotation databases

GeneID

2555567.

KEGG

wsu:WS0969.

NMPDR

fig|273121.1.peg.899.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

HBG488281.

OMA

CGQCHAS.

Enzyme and pathway databases

BioCyc

WSUC273121:WS0969-MONOMER.

BRENDA

1.7.2.2. 191624.

Family and domain databases

HAMAP

MF_01182. Cytochrom_C552.
[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.

PROSITE

PS51008. MULTIHEME_CYTC. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

NRFA_WOLSU

Accession

Primary (citable) accession number: Q9S1E5

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 19, 2002
Last sequence update:	September 26, 2003
Last modified:	February 9, 2010
This is version 84 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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