Q56350 (NAPA_PARPN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Periplasmic nitrate reductase
EC=1.7.99.4

Gene names

Name:

napA

Organism

Paracoccus pantotrophus (Thiosphaera pantotropha)

Taxonomic identifier

82367 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Alphaproteobacteria › Rhodobacterales › Rhodobacteraceae › Paracoccus

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-Rule MF_01630
Catalytic activity	Nitrite + acceptor = nitrate + reduced acceptor. HAMAP-Rule MF_01630
Cofactor	Binds 1 4Fe-4S cluster By similarity. HAMAP-Rule MF_01630 Binds 1 molybdenum ion per subunit. Binds 2 molybdopterin guanine dinucleotide (MGD) groups per subunit.
Subunit structure	Interacts with NapB By similarity. HAMAP-Rule MF_01630
Subcellular location	Periplasm HAMAP-Rule 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-Rule MF_01630
Sequence similarities	Belongs to the prokaryotic molybdopterin-containing oxidoreductase family. NasA/NapA/NarB subfamily. Contains 1 4Fe-4S Mo/W bis-MGD-type domain.

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	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
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: InterPro 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 – 31	31	Tat-type signal Potential
	Chain	32 – 831	800	Periplasmic nitrate reductase HAMAP-Rule MF_01630		PRO_0000019172
Regions
	Domain	41 – 97	57	4Fe-4S Mo/W bis-MGD-type
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	128	1	T → D AA sequence Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Q56350 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: ED78963BD2DA2144	FASTA	831	92,618
	10 20 30 40 50 60 MTISRRDLLK AQAAGIAAMA ANIPLSSQAP AVPGGVESLQ ITWSKAPCRF CGTGCGVMVG 70 80 90 100 110 120 VKEGRVVATH GDLLAEVNRG LNCVKGYFLS KIMYGADRLT QPLLRKKDGV YAKDGEFTPV 130 140 150 160 170 180 SWEEAFDTMA AQAKRVLRDK GPTALGMFGS GQWTIFEGYA ATKLMRAGFR SNNLDPNARH 190 200 210 220 230 240 CMASAAYAFM RTFGMDEPMG CYDDFEAADA FVLWGSNMAE MHPILWTRVA DRRLGHPHVK 250 260 270 280 290 300 VAVLSTFTHR SSDLADIPIV FKPGTDLAIL NYIANHIIQT GRVNRDFVDR HTTFVAGATG 310 320 330 340 350 360 IGYGLRDDDP REMAARTAED PAATTPSTFE EFAELVSEYT LDKVSELSGV EPAFLEQLAE 370 380 390 400 410 420 LYADPDRKVM SLWTMGFNQH VRGVWANQMV YNLHLLTGKI SEPGNSPFSL TGQASACGTA 430 440 450 460 470 480 RQVGTFRHRL PSDMTVTNPE RRQDAEEIWR IPHGVIPEQP GLHAVAQDRA LHDGTLNFYW 490 500 510 520 530 540 IQVNNNLQAS PNNDGEAWPG YRNPDNFIVV SDAYPTVTAL AADLILPAAM WVEKEGAYGN 550 560 570 580 590 600 AERRTHVWHQ LVEAPGEARS DLWQMMEFST RFTTDEVWPE EILAANPNYR GQSLFDVLFR 610 620 630 640 650 660 NGSVDRFDLS ELNPVTPTAE SNAFGFYVQK GLFEEYAPFG RGHGHDLAPY DTYHEVRGLR 670 680 690 700 710 720 WPVVDGKETL WRYREGLDPY VEPGAGVQFY GNPDGKARII AVPYEPPAEP PDEEYNIWLV 730 740 750 760 770 780 TGRVLEHWHS GSMTMRVPEL YRAFPGARCF MNPEDARDMG FNQGAEVRIV SRRGEIRSRV 790 800 810 820 830 ETRGRNRMPR GVVFVPWFDA SQLINKVTLD ATDPISKQTD FKKCAVKILP V

References

[1]	"The napEDABC gene cluster encoding the periplasmic nitrate reductase system of Thiosphaera pantotropha." Berks B.C., Richardson D.J., Reilly A., Willis A.C., Ferguson S.J. Biochem. J. 309:983-992(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE. Strain: ATCC 35512 / DSM 2944 / LMD 82.5 / NCCB 82005.
[2]	"Purification and characterization of the periplasmic nitrate reductase from Thiosphaera pantotropha." Berks B.C., Richardson D.J., Robinson C., Reilly A., Aplin R.T., Ferguson S.J. Eur. J. Biochem. 220:117-124(1994) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION. Strain: M-6.
[3]	"Characterization of the paramagnetic iron-containing redox centres of Thiosphaera pantotropha periplasmic nitrate reductase." Breton J., Berks B.C., Reilly A., Thomson A.J., Ferguson S.J., Richardson D.J. FEBS Lett. 345:76-80(1994) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION, PROTEIN SEQUENCE OF 642-655 AND 699-715. Strain: M-6.

Cross-references

Sequence databases
EMBL GenBank DDBJ	Z36773 Genomic DNA. Translation: CAA85346.1.
PIR	S50163.
3D structure databases
ProteinModelPortal	Q56350.
SMR	Q56350. Positions 41-828.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Family and domain databases
Gene3D	2.40.40.20. 1 hit.
HAMAP	MF_01630. Nitrate_reduct.
InterPro	IPR009010. Asp_de-COase-like_dom. IPR006657. MoPterin_dinucl-bd_dom. IPR006656. Mopterin_OxRdtase. IPR006963. Mopterin_OxRdtase_4Fe-4S_dom. IPR027467. MopterinOxRdtase_cofactor_BS. IPR010051. Periplasm_NO3_reductase_lsu. IPR006311. TAT_signal. IPR019546. TAT_signal_bac_arc. [Graphical view]
Pfam	PF04879. Molybdop_Fe4S4. 1 hit. PF00384. Molybdopterin. 1 hit. PF01568. Molydop_binding. 1 hit. [Graphical view]
SMART	SM00926. Molybdop_Fe4S4. 1 hit. [Graphical view]
SUPFAM	SSF50692. Asp_decarb_fold. 1 hit.
TIGRFAMs	TIGR01706. NAPA. 1 hit. TIGR01409. TAT_signal_seq. 1 hit.
PROSITE	PS51669. 4FE4S_MOW_BIS_MGD. 1 hit. 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_PARPN

Accession

Primary (citable) accession number: Q56350

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1996
Last modified:	May 29, 2013
This is version 85 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program