P11349 (NARH_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Respiratory nitrate reductase 1 beta chain
EC=1.7.99.4

Alternative name(s):
Nitrate reductase A subunit beta
Quinol-nitrate oxidoreductase subunit beta

Gene names

Name:	narH
Ordered Locus Names:	b1225, JW1216

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	512 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	The nitrate reductase enzyme complex allows E.coli to use nitrate as an electron acceptor during anaerobic growth. The beta chain is an electron transfer unit containing four cysteine clusters involved in the formation of iron-sulfur centers. Electrons are transferred from the gamma chain to the molybdenum cofactor of the alpha subunit.
Catalytic activity	Nitrite + acceptor = nitrate + reduced acceptor.
Cofactor	Binds 3 4Fe-4S clusters per subunit. Binds 1 3Fe-4S cluster per subunit.
Subunit structure	Dimer of heterotrimers each composed of an alpha, a beta and a gamma chain. Alpha and beta are catalytic chains; gamma chains are involved in binding the enzyme complex to the cytoplasmic membrane.
Subcellular location	Cell membrane; Peripheral membrane protein.
Induction	By nitrate.
Sequence similarities	Contains 3 4Fe-4S ferredoxin-type domains.

Ontologies

Keywords
Biological process	Electron transport Nitrate assimilation Transport
Cellular component	Cell membrane Membrane
Domain	Repeat
Ligand	3Fe-4S 4Fe-4S Iron Iron-sulfur Metal-binding
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	anaerobic respiration Inferred from expression pattern PubMed 7050087. Source: EcoCyc cytochrome complex assembly Inferred from direct assay Ref.7. Source: EcoCyc electron transport chain Inferred from electronic annotation. Source: UniProtKB-KW nitrate assimilation Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	intrinsic to membrane Inferred from direct assay PubMed 5996. Source: EcoCyc nitrate reductase complex Inferred from electronic annotation. Source: InterPro plasma membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	3 iron, 4 sulfur cluster binding Inferred from physical interaction Ref.11. Source: EcoCyc 4 iron, 4 sulfur cluster binding Inferred from direct assay Ref.14. Source: EcoCyc electron carrier activity Inferred from physical interaction PubMed 10504245. Source: EcoCyc metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW nitrate reductase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
narG	P09152	10	EBI-555067,EBI-547248
narZ	P19319	3	EBI-555067,EBI-547262

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 512

512

Respiratory nitrate reductase 1 beta chain

PRO_0000096720

Regions

Domain

7 – 35

29

4Fe-4S ferredoxin-type 1

Domain

175 – 206

32

4Fe-4S ferredoxin-type 2

Domain

208 – 237

30

4Fe-4S ferredoxin-type 3

Sites

Metal binding

16

1

Iron-sulfur 1 (4Fe-4S)

Metal binding

19

1

Iron-sulfur 1 (4Fe-4S)

Metal binding

22

1

Iron-sulfur 1 (4Fe-4S)

Metal binding

26

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

184

1

Iron-sulfur 3 (4Fe-4S)

Metal binding

187

1

Iron-sulfur 3 (4Fe-4S)

Metal binding

192

1

Iron-sulfur 3 (4Fe-4S)

Metal binding

196

1

Iron-sulfur 4 (3Fe-4S)

Metal binding

217

1

Iron-sulfur 4 (3Fe-4S)

Metal binding

223

1

Iron-sulfur 4 (3Fe-4S)

Metal binding

227

1

Iron-sulfur 3 (4Fe-4S)

Metal binding

244

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

247

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

259

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

263

1

Iron-sulfur 1 (4Fe-4S)

Experimental info

Sequence conflict

398 – 417

20

DTKPV…RHYKR → EYQTGTARTETYAGDASLQT in AAA24195. Ref.6

Secondary structure

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512

Helix Strand Turn

Details...

Beta strand

3 – 12

10

Turn

13 – 15

3

Helix

21 – 30

10

Beta strand

41 – 49

9

Turn

51 – 57

7

Helix

59 – 62

4

Beta strand

65 – 68

4

Beta strand

74 – 76

3

Helix

81 – 85

5

Turn

86 – 89

4

Helix

97 – 100

4

Beta strand

104 – 106

3

Helix

109 – 113

5

Beta strand

126 – 128

3

Turn

129 – 131

3

Turn

142 – 148

7

Helix

152 – 155

4

Helix

159 – 161

3

Helix

167 – 170

4

Helix

172 – 174

3

Beta strand

178 – 182

5

Helix

191 – 194

4

Beta strand

201 – 204

4

Turn

205 – 207

3

Beta strand

210 – 212

3

Turn

214 – 216

3

Helix

223 – 226

4

Beta strand

232 – 235

4

Turn

236 – 239

4

Beta strand

240 – 243

4

Helix

248 – 251

4

Turn

252 – 254

3

Helix

258 – 261

4

Beta strand

268 – 276

9

Helix

277 – 279

3

Helix

280 – 284

5

Helix

289 – 291

3

Helix

292 – 297

6

Helix

306 – 314

9

Helix

319 – 325

7

Helix

329 – 334

6

Beta strand

341 – 343

3

Helix

345 – 347

3

Beta strand

352 – 356

5

Beta strand

366 – 368

3

Helix

380 – 382

3

Beta strand

383 – 385

3

Helix

387 – 394

8

Helix

399 – 420

22

Helix

428 – 432

5

Helix

437 – 447

11

Helix

452 – 455

4

Turn

463 – 466

4

Helix

469 – 475

7

Sequences

	Sequence		Length	Mass (Da)
	P11349 [UniParc]. Last modified February 1, 1996. Version 3. Checksum: 2E7719C8D078BAEA	FASTA	512	58,066
	10 20 30 40 50 60 MKIRSQVGMV LNLDKCIGCH TCSVTCKNVW TSREGVEYAW FNNVETKPGQ GFPTDWENQE 70 80 90 100 110 120 KYKGGWIRKI NGKLQPRMGN RAMLLGKIFA NPHLPGIDDY YEPFDFDYQN LHTAPEGSKS 130 140 150 160 170 180 QPIARPRSLI TGERMAKIEK GPNWEDDLGG EFDKLAKDKN FDNIQKAMYS QFENTFMMYL 190 200 210 220 230 240 PRLCEHCLNP ACVATCPSGA IYKREEDGIV LIDQDKCRGW RMCITGCPYK KIYFNWKSGK 250 260 270 280 290 300 SEKCIFCYPR IEAGQPTVCS ETCVGRIRYL GVLLYDADAI ERAASTENEK DLYQRQLDVF 310 320 330 340 350 360 LDPNDPKVIE QAIKDGIPLS VIEAAQQSPV YKMAMEWKLA LPLHPEYRTL PMVWYVPPLS 370 380 390 400 410 420 PIQSAADAGE LGSNGILPDV ESLRIPVQYL ANLLTAGDTK PVLRALKRML AMRHYKRAET 430 440 450 460 470 480 VDGKVDTRAL EEVGLTEAQA QEMYRYLAIA NYEDRFVVPS SHRELAREAF PEKNGCGFTF 490 500 510 GDGCHGSDTK FNLFNSRRID AIDVTSKTEP HP

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nitrate reductase of Escherichia coli: completion of the nucleotide sequence of the nar operon and reassessment of the role of the alpha and beta subunits in iron binding and electron transfer." Blasco F., Iobbi C., Giordano G., Chippaux M., Bonnefoy V. Mol. Gen. Genet. 218:249-256(1989) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12 / TG1.
[2]	Blasco F. Submitted (JUL-1991) to the EMBL/GenBank/DDBJ databases Cited for: SEQUENCE REVISION TO 398-417. Strain: K12 / TG1.
[3]	"A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map." Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K. , Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M., Horiuchi T. DNA Res. 3:137-155(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[5]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]	"narI region of the Escherichia coli nitrate reductase (nar) operon contains two genes." Sodergren E.J., Demoss J.A. J. Bacteriol. 170:1721-1729(1988) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 365-512.
[7]	"Roles of the narJ and narI gene products in the expression of nitrate reductase in Escherichia coli." Sodergren E.J., Hsu P.Y., Demoss J.A. J. Biol. Chem. 263:16156-16162(1988) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-10.
[8]	"EPR and redox characterization of iron-sulfur centers in nitrate reductases A and Z from Escherichia coli. Evidence for a high-potential and a low-potential class and their relevance in the electron-transfer mechanism." Guigliarelli B., Asso M., More C., Augier V., Blasco F., Pommier J., Giordano G., Bertrand P. Eur. J. Biochem. 207:61-68(1992) [PubMed] [Europe PMC] [Abstract] Cited for: EPR SPECTROSCOPY OF IRON-SULFUR CLUSTERS.
[9]	"Site-directed mutagenesis of conserved cysteine residues within the beta subunit of Escherichia coli nitrate reductase. Physiological, biochemical, and EPR characterization of the mutated enzymes." Augier V., Guigliarelli B., Asso M., Bertrand P., Frixon C., Giordano G., Chippaux M., Blasco F. Biochemistry 32:2013-2023(1993) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF CYSTEINE RESIDUES, EPR SPECTROSCOPY OF IRON-SULFUR CLUSTERS.
[10]	"Removal of the high-potential [4Fe-4S] center of the beta-subunit from Escherichia coli nitrate reductase. Physiological, biochemical, and EPR characterization of site-directed mutated enzymes." Augier V., Asso M., Guigliarelli B., More C., Bertrand P., Santini C.-L., Blasco F., Chippaux M., Giordano G. Biochemistry 32:5099-5108(1993) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF CYSTEINE RESIDUES, EPR SPECTROSCOPY OF IRON-SULFUR CLUSTERS.
[11]	"Complete coordination of the four Fe-S centers of the beta subunit from Escherichia coli nitrate reductase. Physiological, biochemical, and EPR characterization of site-directed mutants lacking the highest or lowest potential [4Fe-4S] clusters." Guigliarelli B., Magalon A., Asso M., Bertrand P., Frixon C., Giordano G., Blasco F. Biochemistry 35:4828-4836(1996) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF CYSTEINE RESIDUES, EPR SPECTROSCOPY OF IRON-SULFUR CLUSTERS.
[12]	"The molybdenum cofactor of Escherichia coli nitrate reductase A (NarGHI). Effect of a mobAB mutation and interactions with [Fe-S] clusters." Rothery R.A., Magalon A., Giordano G., Guigliarelli B., Blasco F., Weiner J.H. J. Biol. Chem. 273:7462-7469(1998) [PubMed] [Europe PMC] [Abstract] Cited for: EPR SPECTROSCOPY, REDOX POTENTIOMETRY OF IRON-SULFUR CLUSTERS.
[13]	"Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A." Bertero M.G., Rothery R.A., Palak M., Hou C., Lim D., Blasco F., Weiner J.H., Strynadka N.C.J. Nat. Struct. Biol. 10:681-687(2003) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
[14]	"Architecture of NarGH reveals a structural classification of Mo-bisMGD enzymes." Jormakka M., Richardson D., Byrne B., Iwata S. Structure 12:95-104(2004) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 43-512.
+	Additional computationally mapped references.

Web resources

Worthington enzyme manual

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M20147 Genomic DNA. Translation: AAA24195.1.
U00096 Genomic DNA. Translation: AAC74309.1.
AP009048 Genomic DNA. Translation: BAA36095.1.
X16181 Genomic DNA. Translation: CAA34304.1.

PIR

RDECNB. F64869.

RefSeq

NP_415743.1. NC_000913.2.
YP_489495.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1Q16	X-ray	1.90	B	1-512	[»]
1R27	X-ray	2.00	B/D	1-512	[»]
1SIW	X-ray	2.20	B	1-512	[»]
1Y4Z	X-ray	2.00	B	1-512	[»]
1Y5I	X-ray	1.90	B	1-512	[»]
1Y5L	X-ray	2.50	B	1-512	[»]
1Y5N	X-ray	2.50	B	1-512	[»]
3EGW	X-ray	1.90	B	1-509	[»]
3IR5	X-ray	2.30	B	1-512	[»]
3IR6	X-ray	2.80	B	1-512	[»]
3IR7	X-ray	2.50	B	1-512	[»]

ProteinModelPortal

P11349.

SMR

P11349. Positions 1-509.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10312N.

IntAct

P11349. 12 interactions.

MINT

MINT-1260007.

STRING

511145.b1225.

Protein family/group databases

TCDB

5.A.3.1.1. prokaryotic molybdopterin-containing oxidoreductase (PMO) family.

Proteomic databases

PaxDb

P11349.

PRIDE

P11349.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC74309; AAC74309; b1225.
BAA36095; BAA36095; BAA36095.

GeneID

12933237.
945780.

KEGG

ecj:Y75_p1200.
eco:b1225.

PATRIC

32117710. VBIEscCol129921_1277.

Organism-specific databases

EchoBASE

EB0633.

EcoGene

EG10639. narH.

Phylogenomic databases

eggNOG

COG1140.

HOGENOM

HOG000237353.

KO

K00371.

OMA

EYAENAF.

ProtClustDB

CLSK868287.

Enzyme and pathway databases

BioCyc

EcoCyc:NARH-MONOMER.
ECOL316407:JW1216-MONOMER.
MetaCyc:NARH-MONOMER.

Gene expression databases

Genevestigator

P11349.

Family and domain databases

InterPro

IPR017896. 4Fe4S_Fe-S-bd.
IPR006547. NO3_Rdtase_bsu.
[Graphical view]

Pfam

PF13247. Fer4_11. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01660. narH. 1 hit.

PROSITE

PS00198. 4FE4S_FER_1. False negative.
PS51379. 4FE4S_FER_2. 3 hits.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P11349.

Entry information

Entry name

NARH_ECOLI

Accession

Primary (citable) accession number: P11349

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 1989
Last sequence update:	February 1, 1996
Last modified:	May 1, 2013
This is version 139 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program