Reviewed, UniProtKB/Swiss-Prot Q53176 (NAPA_RHOS4)

Names and origin

Protein names

Recommended name:
    Periplasmic nitrate reductase
    EC=1.7.99.4

Gene names

Name:	napA
Ordered Locus Names:	RHOS4_40230
ORF Names:	RSP_4116

Encoded on

Plasmid pRS241c Ref.2

Organism

Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158) [Complete proteome] [HAMAP]

Taxonomic identifier

272943 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Alphaproteobacteria › Rhodobacterales › Rhodobacteraceae › Rhodobacter

Protein attributes

Sequence length	831 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 By similarity. Binds 1 molybdenum ion per subunit. HAMAP MF_01630 Binds 2 molybdopterin guanine dinucleotide (MGD) groups per subunit. HAMAP MF_01630
Subunit structure	Interacts with napB. HAMAP MF_01630
Subcellular location	Periplasm. HAMAP MF_01630
Induction	Nitrate reductase activity can be induced by nitrate and not repressed by ammonium or oxygen. HAMAP MF_01630
Post-translational modification	Predicted to be exported by the Tat system. The position of the signal peptide cleavage has not 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 Plasmid
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 – 29

29

Tat-type signal Potential

Chain

30 – 831

802

Periplasmic nitrate reductase HAMAP MF_01630

PRO_0000019171

Sites

Metal binding

48

1

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

Metal binding

51

1

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

Metal binding

55

1

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

Metal binding

83

1

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

Experimental info

Sequence conflict

135

1

R → L in CAA86827. Ref.1

Sequence conflict

141

1

G → A Ref.1

Sequence conflict

143

1

K → E Ref.1

Sequence conflict

252

1

M → S in CAA86827. Ref.1

Sequence conflict

255

1

A → S in CAA86827. Ref.1

Sequence conflict

267

1

L → R in CAA86827. Ref.1

Sequence conflict

369

1

V → W in CAA86827. Ref.1

Sequence conflict

415

1

S → F in CAA86827. Ref.1

Sequence conflict

521

1

C → A in CAA86827. Ref.1

Sequence conflict

660

1

R → H in CAA86827. Ref.1

Sequence conflict

737

1

V → W in CAA86827. Ref.1

Secondary structure

1

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831

Helix Strand Turn

Details...

Beta strand

42 – 47

6

Beta strand

56 – 62

7

Beta strand

65 – 71

7

Turn

76 – 78

3

Helix

84 – 87

4

Helix

88 – 91

4

Beta strand

103 – 105

3

Beta strand

107 – 109

3

Helix

122 – 139

18

Helix

142 – 144

3

Beta strand

145 – 149

5

Helix

155 – 166

12

Beta strand

174 – 176

3

Helix

178 – 181

4

Helix

183 – 193

11

Helix

204 – 207

4

Beta strand

209 – 215

7

Helix

218 – 221

4

Helix

223 – 235

13

Beta strand

240 – 248

9

Helix

250 – 253

4

Beta strand

256 – 260

5

Turn

263 – 265

3

Helix

266 – 279

14

Helix

285 – 291

7

Beta strand

292 – 296

5

Helix

310 – 313

4

Helix

329 – 337

9

Helix

341 – 348

8

Helix

352 – 361

10

Beta strand

369 – 374

6

Helix

375 – 378

4

Helix

383 – 397

15

Beta strand

405 – 409

5

Turn

414 – 419

6

Helix

420 – 423

4

Turn

431 – 433

3

Beta strand

434 – 437

4

Helix

439 – 448

10

Helix

464 – 472

9

Beta strand

478 – 483

6

Helix

486 – 489

4

Turn

491 – 497

7

Helix

498 – 502

5

Beta strand

507 – 514

8

Helix

517 – 520

4

Beta strand

522 – 528

7

Helix

531 – 533

3

Beta strand

536 – 539

4

Beta strand

543 – 548

6

Helix

561 – 569

9

Helix

574 – 577

4

Helix

580 – 585

6

Beta strand

587 – 591

5

Turn

594 – 599

6

Beta strand

601 – 605

5

Beta strand

607 – 612

6

Beta strand

614 – 617

4

Helix

619 – 622

4

Beta strand

623 – 626

4

Helix

628 – 637

10

Beta strand

640 – 644

5

Helix

652 – 655

4

Beta strand

659 – 661

3

Beta strand

670 – 675

6

Beta strand

692 – 694

3

Beta strand

697 – 701

5

Beta strand

713 – 715

3

Beta strand

717 – 722

6

Helix

734 – 736

3

Helix

738 – 743

6

Beta strand

748 – 750

3

Helix

753 – 758

6

Beta strand

766 – 770

5

Beta strand

775 – 787

13

Beta strand

792 – 796

5

Beta strand

800 – 802

3

Helix

804 – 806

3

Turn

814 – 816

3

Sequences

	Sequence		Length	Mass (Da)
	Q53176-1 [UniParc]. Last modified January 24, 2006. Version 2. Checksum: 74B35640749CC906	FASTA	831	92,637
	10 20 30 40 50 60 MTLTRRDLIK AQAAATAAAA AGLPVSALAQ PVTGGAEALR IRWSKAPCRF CGTGCGVMVG 70 80 90 100 110 120 TRDGQVVATH GDTQAEVNRG LNCVKGYFLS KIMYGEDRLT TPLLRMKDGV YHKEGEFAPV 130 140 150 160 170 180 SWDEAFDVMA AQAKRVLKEK GPKAVGMFGS GQWTIWEGYA ASKLMRAGFR SNNLDPNARH 190 200 210 220 230 240 CMASAATAFM RTFGMDEPMG CYDDFEAADA FVLWGSNMAE MHPILWSRLT DRRLSHEHVR 250 260 270 280 290 300 VAVLSTFTHR SMDLADTPII FRPGTDLAIL NYIAHHIIST GRVNRDFVDR HTNFALGATD 310 320 330 340 350 360 IGYGLRPEHQ LQLAAKGAAD AGAMTPTDFE TFAALVSEYT LEKAAEISGV EPALLEELAE 370 380 390 400 410 420 LYADPDRKVM SLWTMGFNQH VRGVWANHMV YNLHLLTGKI SEPGNSPFSL TGQPSACGTA 430 440 450 460 470 480 REVGTFAHRL PADMVVTNPE HRAHAEEIWK LPAGLLPDWV GAHAVEQDRK LHDGEINFYW 490 500 510 520 530 540 VQVNNNMQAA PNIDQETYPG YRNPENFIVV SDAYPTVTGR CADLVLPAAM WVEKEGAYGN 550 560 570 580 590 600 AERRTHFWHQ LVEAPGEARS DLWQLMEFSK RFTTDEVWPE EILSAAPAYR GKTLFEVLFA 610 620 630 640 650 660 NGSVDRFPAS DVNPDHANHE AALFGFYPQK GLFEEYAAFG RGHGHDLAPF DTYHEVRGLR 670 680 690 700 710 720 WPVVEGEETR WRYREGFDPY VKPGEGLRFY GKPDGRAVIL GVPYEPPAES PDEEFGFWLV 730 740 750 760 770 780 TGRVLEHWHS GSMTLRVPEL YKAFPGAVCF MHPEDARSRG LNRGSEVRVI SRRGEIRTRL 790 800 810 820 830 ETRGRNRMPR GVVFVPWFDA SQLINKVTLD ANDPISRQTD FKKCAVKIEA V

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Isolation of periplasmic nitrate reductase genes from Rhodobacter sphaeroides DSM 158: structural and functional differences among prokaryotic nitrate reductases." Reyes F., Roldan M.D., Klipp W., Castillo F., Moreno-Vivian C. Mol. Microbiol. 19:1307-1318(1996) [PubMed: 8730872] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Complete sequence of plasmid C of Rhodobacter sphaeroides 2.4.1." Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T., Hammon N., Israni S., Pitluck S., Richardson P., Mackenzie C., Choudhary M., Larimer F., Hauser L.J., Land M., Donohue T.J., Kaplan S. Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]	"Structural and redox plasticity in the heterodimeric periplasmic nitrate reductase." Arnoux P., Sabaty M., Alric J., Frangioni B., Guigliarelli B., Adriano J.-M., Pignol D. Nat. Struct. Biol. 10:928-934(2003) [PubMed: 14528294] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS) IN COMPLEX WITH NAPB.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

Z46806 Genomic DNA. Translation: CAA86827.1.
CP000146 Genomic DNA. Translation: ABA81591.1.

RefSeq

YP_345332.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1OGY	X-ray	3.20	A/C/E/G/I/K/M/O	30-831	[»]

ModBase

Search...

Genome annotation databases

GeneID

3711832.

GenomeReviews

Gene locus RHOS4_40230 in contig CP000146_GR.

KEGG

rsp:RSP_4116.

NMPDR

fig|272943.3.peg.66.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

Q53176.

OMA

Q53176. NAYWVQV.

Enzyme and pathway databases

BioCyc

RSPH272943:RSP_4116-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_RHOS4

Accession

Primary (citable) accession number: Q53176
Secondary accession number(s): Q3IV43

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	January 24, 2006
Last modified:	June 16, 2009
This is version 77 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)