Reviewed, UniProtKB/Swiss-Prot P81186 (NAPA_DESDA)

Names and origin

Protein names

Recommended name:
    Periplasmic nitrate reductase
    EC=1.7.99.4

Gene names

Name:	napA
Synonyms:	nap
Ordered Locus Names:	Ddes_0616

Organism

Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949) [Complete proteome] [HAMAP]

Taxonomic identifier

525146 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Deltaproteobacteria › Desulfovibrionales › Desulfovibrionaceae › Desulfovibrio

Protein attributes

Sequence length	755 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. HAMAP MF_01630
Catalytic activity	Nitrite + acceptor = nitrate + reduced acceptor. HAMAP MF_01630
Cofactor	Binds 1 4Fe-4S cluster. HAMAP MF_01630 Binds 1 molybdenum ion per subunit. HAMAP MF_01630 Binds 2 molybdopterin guanine dinucleotide (MGD) groups per subunit. HAMAP MF_01630
Subunit structure	Monomer. HAMAP MF_01630
Subcellular location	Periplasm HAMAP MF_01630.
Induction	Nitrate reductase activity is induced by potassium and sodium and inhibited by magnesium and calcium. HAMAP MF_01630
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.

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 – 32

32

Tat-type signal Ref.4

Chain

33 – 755

723

Periplasmic nitrate reductase HAMAP MF_01630

PRO_0000019169

Sites

Metal binding

45

1

Iron-sulfur (4Fe-4S) HAMAP MF_01630

Metal binding

48

1

Iron-sulfur (4Fe-4S) HAMAP MF_01630

Metal binding

52

1

Iron-sulfur (4Fe-4S) HAMAP MF_01630

Metal binding

79

1

Iron-sulfur (4Fe-4S) HAMAP MF_01630

Secondary structure

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755

Helix Strand Turn

Details...

Beta strand

38 – 44

7

Beta strand

53 – 59

7

Beta strand

62 – 68

7

Turn

73 – 76

4

Helix

80 – 83

4

Helix

86 – 90

5

Helix

113 – 131

19

Helix

133 – 135

3

Beta strand

136 – 140

5

Helix

146 – 158

13

Beta strand

165 – 167

3

Helix

168 – 171

4

Helix

174 – 184

11

Helix

193 – 198

6

Beta strand

200 – 206

7

Helix

209 – 212

4

Helix

214 – 226

13

Beta strand

231 – 235

5

Helix

241 – 245

5

Beta strand

247 – 250

4

Helix

257 – 270

14

Helix

276 – 282

7

Beta strand

283 – 286

4

Helix

295 – 302

8

Helix

303 – 305

3

Helix

307 – 314

8

Helix

319 – 330

12

Beta strand

331 – 338

8

Helix

340 – 343

4

Helix

348 – 362

15

Beta strand

370 – 374

5

Helix

381 – 384

4

Turn

385 – 389

5

Turn

396 – 398

3

Helix

404 – 413

10

Helix

429 – 438

10

Beta strand

443 – 448

6

Helix

451 – 454

4

Beta strand

455 – 457

3

Helix

458 – 465

8

Beta strand

471 – 475

5

Helix

482 – 485

4

Beta strand

488 – 491

4

Helix

496 – 498

3

Beta strand

501 – 504

4

Beta strand

508 – 513

6

Helix

526 – 536

11

Turn

541 – 544

4

Helix

549 – 560

12

Helix

572 – 577

6

Beta strand

581 – 583

3

Turn

599 – 601

3

Beta strand

610 – 613

4

Beta strand

623 – 626

4

Beta strand

643 – 648

6

Helix

660 – 662

3

Helix

664 – 667

4

Beta strand

675 – 678

4

Helix

679 – 685

7

Beta strand

692 – 697

6

Beta strand

700 – 712

13

Beta strand

716 – 720

5

Helix

728 – 730

3

Turn

738 – 740

3

Beta strand

748 – 754

7

Sequences

	Sequence		Length	Mass (Da)
	P81186-1 [UniParc]. Last modified May 30, 2000. Version 2. Checksum: D54BDB9D1FE21DC2	FASTA	755	83,497
	10 20 30 40 50 60 MSTSRRDFLK YFAMSAAVAA ASGAGFGSLA LAADNRPEKW VKGVCRYCGT GCGVLVGVKD 70 80 90 100 110 120 GKAVAIQGDP NNHNAGLLCL KGSLLIPVLN SKERVTQPLV RRHKGGKLEP VSWDEALDLM 130 140 150 160 170 180 ASRFRSSIDM YGPNSVAWYG SGQCLTEESY VANKIFKGGF GTNNVDGNPR LCMASAVGGY 190 200 210 220 230 240 VTSFGKDEPM GTYADIDQAT CFFIIGSNTS EAHPVLFRRI ARRKQVEPGV KIIVADPRRT 250 260 270 280 290 300 NTSRIADMHV AFRPGTDLAF MHSMAWVIIN EELDNPRFWQ RYVNFMDAEG KPSDFEGYKA 310 320 330 340 350 360 FLENYRPEKV AEICRVPVEQ IYGAARAFAE SAATMSLWCM GINQRVQGVF ANNLIHNLHL 370 380 390 400 410 420 ITGQICRPGA TSFSLTGQPN ACGGVRDGGA LSHLLPAGRA IPNAKHRAEM EKLWGLPEGR 430 440 450 460 470 480 IAPEPGYHTV ALFEALGRGD VKCMIICETN PAHTLPNLNK VHKAMSHPES FIVCIEAFPD 490 500 510 520 530 540 AVTLEYADLV LPPAFWCERD GVYGCGERRY SLTEKAVDPP GQCRPTVNTL VEFARRAGVD 550 560 570 580 590 600 PQLVNFRNAE DVWNEWRMVS KGTTYDFWGM TRERLRKESG LIWPCPSEDH PGTSLRYVRG 610 620 630 640 650 660 QDPCVPADHP DRFFFYGKPD GRAVIWMRPA KGAAEEPDAE YPLYLTSMRV IDHWHTATMT 670 680 690 700 710 720 GKVPELQKAN PIAFVEINEE DAARTGIKHG DSVIVETRRD AMELPARVSD VCRPGLIAVP 730 740 750 FFDPKKLVNK LFLDATDPVS REPEYKICAA RVRKA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Crystal structure of the first dissimilatory nitrate reductase at 1.9 A solved by MAD methods." Dias J.M., Than M.E., Humm A., Huber R., Bourenkov G.P., Bartunik H.D., Bursakov S., Calvete J.J., Caldeira J., Carneiro C., Moura J.J.G., Moura I., Romao M.J. Structure 7:65-79(1999) [PubMed: 10368307] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
[2]	"Nitrate reduction by Desulfovibrio desulfuricans: a periplasmic nitrate reductase system that lacks NapB, but includes a unique tetraheme c-type cytochrome, NapM." Marietou A., Richardson D., Cole J., Mohan S. FEMS Microbiol. Lett. 248:217-225(2005) [PubMed: 15972253] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"Complete sequence of Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774." Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Tice H., Bruce D., Goodwin L., Pitluck S., Sims D., Lu M., Kiss H., Meineke L., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L. , Kyrpides N., Ovchinnikova G., Hazen T.C. Submitted (JAN-2009) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]	"Enzymatic properties and effect of ionic strength on periplasmic nitrate reductase (NAP) from Desulfovibrio desulfuricans ATCC 27774." Bursakov S.A., Carneiro C., Almendra M.J., Duarte R.O., Caldeira J., Moura I., Moura J.J.G. Biochem. Biophys. Res. Commun. 239:816-822(1997) [PubMed: 9367852] [Abstract] Cited for: PROTEIN SEQUENCE OF 33-73.
[5]	"Isolation and preliminary characterization of a soluble nitrate reductase from the sulfate-reducing bacterium Desulfovibrio desulfuricans 27774." Bursakov S., Liu M.-Y., Payne W.J., Legall J., Moura I., Moura J.J.G. Anaerobe 1:55-60(1995) [PubMed: 16887508] [Abstract] Cited for: CHARACTERIZATION.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

Y18045 Genomic DNA. Translation: CAA77019.1.
AJ920046 Genomic DNA. Translation: CAI72603.1.
CP001358 Genomic DNA. Translation: ACL48525.1.

PIR

PC4422.

RefSeq

YP_002479203.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2JIM	X-ray	2.45	A	33-755	[»]
2JIO	X-ray	2.20	A	33-755	[»]
2JIP	X-ray	2.30	A	33-755	[»]
2JIQ	X-ray	2.44	A	33-755	[»]
2JIR	X-ray	2.35	A	33-755	[»]
2NAP	X-ray	1.90	A	33-755	[»]
2V3V	X-ray	1.99	A	33-755	[»]
2V45	X-ray	2.40	A	33-755	[»]

ModBase

Search...

Genome annotation databases

GeneID

7284288.

GenomeReviews

Gene locus Ddes_0616 in contig CP001358_GR.

KEGG

dds:Ddes_0616.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

HBG715033.

Enzyme and pathway databases

BRENDA

1.7.99.4. 2407.

Family and domain databases

HAMAP

MF_01630. Nitrate_reduct.
[Tree]

InterPro

IPR009010. Asp_de-COase-like_fold.
IPR006657. MoPterin_dinucl-bd_dom.
IPR006656. Mopterin_OxRdtase.
IPR006963. Mopterin_OxRdtase_Fe4S4_dom.
IPR010051. NO3_reductase_lsu_periplasm.
IPR006311. 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.
[Graphical view]

TIGRFAMs

TIGR01409. TAT_signal_seq. 1 hit.

PROSITE

PS00551. MOLYBDOPTERIN_PROK_1. False negative.
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_DESDA

Accession

Primary (citable) accession number: P81186
Secondary accession number(s): B8IYC9, Q599G8

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 15, 1998
Last sequence update:	May 30, 2000
Last modified:	February 9, 2010
This is version 80 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)