Reviewed, UniProtKB/Swiss-Prot P33937 (NAPA_ECOLI)

Names and origin

Protein names

Recommended name:
    Periplasmic nitrate reductase
    EC=1.7.99.4

Gene names

Name:	napA
Synonyms:	yojC, yojD, yojE
Ordered Locus Names:	b2206, JW2194

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	828 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	Catalytic subunit of the periplasmic nitrate reductase (NAP). Only expressed at high levels during aerobic growth. NapAB complex receives electrons from the membrane-anchored tetraheme protein napC, thus allowing electron flow between membrane and periplasm. Essential function for nitrate assimilation and may have a role in anaerobic metabolism By similarity.
Catalytic activity	Nitrite + acceptor = nitrate + reduced acceptor. HAMAP MF_01630
Cofactor	Binds 1 4Fe-4S cluster By similarity. Binds 1 molybdenum ion per subunit By similarity. Binds 2 molybdopterin guanine dinucleotide (MGD) groups per subunit By similarity.
Subunit structure	Interacts with napB By similarity.
Subcellular location	Periplasm. Ref.6
Post-translational modification	Predicted to be exported by the Tat system. The position of the signal peptide cleavage has been experimentally proven. HAMAP MF_01630
Sequence similarities	Belongs to the prokaryotic molybdopterin-containing oxidoreductase family. NasA/napA/narB subfamily.
Sequence caution	The sequence AAA16399.1 differs from that shown. Reason: Frameshift at positions 19 and 27.

Ontologies

Keywords
Biological process	Electron transport Nitrate assimilation Transport
Cellular component	Periplasm
Domain	Signal
Ligand	4Fe-4S Iron Iron-sulfur Metal-binding Molybdenum
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	Mo-molybdopterin cofactor biosynthetic process Inferred from electronic annotation. Source: HAMAP electron transport chain Inferred from electronic annotation. Source: UniProtKB-KW nitrate assimilation 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	4 iron, 4 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW electron carrier activity Inferred from electronic annotation. Source: HAMAP iron ion binding Inferred from electronic annotation. Source: HAMAP molybdenum ion binding Inferred from electronic annotation. Source: UniProtKB-KW nitrate reductase 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 – 36

36

Tat-type signal Ref.6

Chain

37 – 828

792

Periplasmic nitrate reductase HAMAP MF_01630

PRO_0000019170

Sites

Metal binding

46

1

Iron-sulfur (4Fe-4S) By similarity

Metal binding

49

1

Iron-sulfur (4Fe-4S) By similarity

Metal binding

53

1

Iron-sulfur (4Fe-4S) By similarity

Metal binding

81

1

Iron-sulfur (4Fe-4S) By similarity

Experimental info

Sequence conflict

98

1

T → R in AAA16399. Ref.1

Secondary structure

1

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828

Helix Strand Turn

Details...

Helix

6 – 21

16

Beta strand

26 – 29

4

Beta strand

40 – 45

6

Beta strand

47 – 49

3

Beta strand

54 – 60

7

Beta strand

63 – 69

7

Turn

74 – 78

5

Helix

82 – 85

4

Helix

86 – 89

4

Beta strand

101 – 109

9

Beta strand

114 – 117

4

Helix

120 – 137

18

Helix

140 – 142

3

Beta strand

143 – 147

5

Helix

153 – 164

12

Turn

165 – 167

3

Beta strand

172 – 174

3

Helix

175 – 177

3

Turn

178 – 180

3

Helix

181 – 190

10

Helix

200 – 205

6

Beta strand

207 – 213

7

Helix

216 – 219

4

Helix

221 – 232

12

Beta strand

238 – 246

9

Helix

248 – 252

5

Beta strand

254 – 258

5

Turn

261 – 263

3

Helix

264 – 277

14

Helix

283 – 289

7

Beta strand

290 – 295

6

Helix

308 – 311

4

Beta strand

321 – 323

3

Helix

326 – 334

9

Helix

338 – 345

8

Helix

349 – 360

12

Beta strand

366 – 371

6

Helix

372 – 375

4

Helix

380 – 394

15

Beta strand

402 – 406

5

Turn

411 – 416

6

Helix

417 – 420

4

Helix

436 – 446

11

Helix

461 – 469

9

Beta strand

475 – 480

6

Helix

483 – 486

4

Turn

490 – 493

4

Helix

494 – 499

6

Beta strand

504 – 511

8

Helix

514 – 517

4

Beta strand

519 – 525

7

Helix

528 – 530

3

Beta strand

533 – 536

4

Beta strand

540 – 545

6

Helix

558 – 565

8

Helix

566 – 568

3

Helix

571 – 574

4

Helix

577 – 580

4

Helix

584 – 586

3

Helix

591 – 595

5

Turn

599 – 602

4

Helix

606 – 608

3

Helix

616 – 621

6

Helix

625 – 637

13

Turn

638 – 641

4

Helix

647 – 650

4

Beta strand

656 – 658

3

Beta strand

667 – 671

5

Turn

672 – 674

3

Beta strand

694 – 698

5

Beta strand

710 – 712

3

Beta strand

714 – 719

6

Helix

731 – 733

3

Helix

735 – 738

4

Beta strand

745 – 747

3

Helix

750 – 754

5

Turn

755 – 757

3

Beta strand

763 – 768

6

Beta strand

771 – 782

12

Beta strand

789 – 793

5

Helix

801 – 803

3

Turn

811 – 813

3

Beta strand

821 – 826

6

Sequences

	Sequence		Length	Mass (Da)
	P33937-1 [UniParc]. Last modified November 1, 1997. Version 3. Checksum: CE2D7AB000FEAFCA	FASTA	828	93,042
	10 20 30 40 50 60 MKLSRRSFMK ANAVAAAAAA AGLSVPGVAR AVVGQQEAIK WDKAPCRFCG TGCGVLVGTQ 70 80 90 100 110 120 QGRVVACQGD PDAPVNRGLN CIKGYFLPKI MYGKDRLTQP LLRMKNGKYD KEGEFTPITW 130 140 150 160 170 180 DQAFDVMEEK FKTALKEKGP ESIGMFGSGQ WTIWEGYAAS KLFKAGFRSN NIDPNARHCM 190 200 210 220 230 240 ASAVVGFMRT FGMDEPMGCY DDIEQADAFV LWGANMAEMH PILWSRITNR RLSNQNVTVA 250 260 270 280 290 300 VLSTYQHRSF ELADNGIIFT PQSDLVILNY IANYIIQNNA INQDFFSKHV NLRKGATDIG 310 320 330 340 350 360 YGLRPTHPLE KAAKNPGSDA SEPMSFEDYK AFVAEYTLEK TAEMTGVPKD QLEQLAQLYA 370 380 390 400 410 420 DPNKKVISYW TMGFNQHTRG VWANNLVYNL HLLTGKISQP GCGPFSLTGQ PSACGTAREV 430 440 450 460 470 480 GTFAHRLPAD MVVTNEKHRD ICEKKWNIPS GTIPAKIGLH AVAQDRALKD GKLNVYWTMC 490 500 510 520 530 540 TNNMQAGPNI NEERMPGWRD PRNFIIVSDP YPTVSALAAD LILPTAMWVE KEGAYGNAER 550 560 570 580 590 600 RTQFWRQQVQ APGEAKSDLW QLVQFSRRFK TEEVWPEDLL AKKPELRGKT LYEVLYATPE 610 620 630 640 650 660 VSKFPVSELA EDQLNDESRE LGFYLQKGLF EEYAWFGRGH GHDLAPFDDY HKARGLRWPV 670 680 690 700 710 720 VNGKETQWRY SEGNDPYVKA GEGYKFYGKP DGKAVIFALP FEPAAEAPDE EYDLWLSTGR 730 740 750 760 770 780 VLEHWHTGSM TRRVPELHRA FPEAVLFIHP LDAKARDLRR GDKVKVVSRR GEVISIVETR 790 800 810 820 GRNRPPQGLV YMPFFDAAQL VNKLTLDATD PLSKETDFKK CAVKLEKV

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Automated multiplex sequencing of the E.coli genome." Richterich P., Lakey N., Gryan G., Jaehn L., Mintz L., Robison K., Church G.M. Submitted (OCT-1993) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / BHB2600.
[2]	Robison K. Submitted (FEB-1994) to the EMBL/GenBank/DDBJ databases Cited for: SEQUENCE REVISION.
[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 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 40.1-50.0 min region on the linkage map." Itoh T., Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Kasai H., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S. , Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Wada C., Yamamoto Y., Horiuchi T. DNA Res. 3:379-392(1996) [PubMed: 9097040] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] OF 1-757. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]	"The periplasmic nitrate reductase from Escherichia coli: a heterodimeric molybdoprotein with a double-arginine signal sequence and an unusual leader peptide cleavage site." Thomas G., Potter L., Cole J.A. FEMS Microbiol. Lett. 174:167-171(1999) [PubMed: 10234835] [Abstract] Cited for: PROTEIN SEQUENCE OF 37-43, SUBCELLULAR LOCATION.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

U00008 Genomic DNA. Translation: AAA16399.1. Frameshift.
U00096 Genomic DNA. Translation: AAC75266.1.
AP009048 Genomic DNA. Translation: BAA15989.2.

PIR

D64990.

RefSeq

AP_002802.1.
NP_416710.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2NYA	X-ray	2.50	A/F	37-828	[»]
2PQ4	NMR	-	B	1-35	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:10304N.

Genome annotation databases

GeneID

947093.

GenomeReviews

Gene locus JW2194 in contig AP009048_GR.
Gene locus b2206 in contig U00096_GR.

KEGG

ecj:JW2194.
eco:b2206.

Organism-specific databases

EchoBASE

EB1994.

EcoGene

EG12067. napA.

CMR

Search...

Phylogenomic databases

HOGENOM

P33937.

OMA

P33937. NMLYNIH.

Enzyme and pathway databases

BioCyc

EcoCyc:NAPA-MON.
MetaCyc:NAPA-MON.

Family and domain databases

HAMAP

MF_01630.
[Tree]

InterPro

IPR009010. Asp_de-COase-like_fold.
IPR006656. Mopterin_OxRdtase.
IPR006963. Mopterin_OxRdtase_Fe4S4.
IPR006655. Mopterin_OxRdtase_prok_CS.
IPR006657. MPT_dinuc_bd.
IPR010051. NO3_reductase_lsu_periplasm.
IPR006311. Tat.
IPR019546. TAT_signal.
IPR017909. Twin_arg_translocation_Tat.
[Graphical view]

Gene3D

G3DSA:2.40.40.20. Asp_decarboxylase-like_fold. 1 hit.

Pfam

PF04879. Molybdop_Fe4S4. 1 hit.
PF00384. Molybdopterin. 1 hit.
PF01568. Molydop_binding. 1 hit.
PF10518. TAT_signal. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01706. NAPA. 1 hit.
TIGR01409. TAT_signal_seq. 1 hit.

PROSITE

PS00551. MOLYBDOPTERIN_PROK_1. 1 hit.
PS00490. MOLYBDOPTERIN_PROK_2. False negative.
PS00932. MOLYBDOPTERIN_PROK_3. False negative.
PS51318. TAT. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

NAPA_ECOLI

Accession

Primary (citable) accession number: P33937
Secondary accession number(s): P78087

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1994
Last sequence update:	November 1, 1997
Last modified:	June 16, 2009
This is version 96 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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