Periplasmic nitrate reductase precursor - Escherichia coli (strain K12)

Preferred order of sections

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) [Reference 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. HAMAP-Rule MF_01630
Catalytic activity	Nitrite + acceptor = nitrate + reduced acceptor. HAMAP-Rule 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	Exported by the Tat system. The position of the signal peptide cleavage has been experimentally proven. HAMAP-Rule 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 Reference proteome
Gene Ontology (GO)
Biological_process	Mo-molybdopterin cofactor biosynthetic process Inferred from electronic annotation. Source: HAMAP anaerobic respiration Inferred from genetic interaction PubMed 11844760. Source: EcoliWiki electron transport chain Inferred from electronic annotation. Source: UniProtKB-KW nitrate assimilation Inferred from electronic annotation. Source: HAMAP
Cellular_component	outer membrane-bounded periplasmic space Inferred from direct assay Ref.6. Source: EcoCyc
Molecular_function	4 iron, 4 sulfur cluster binding Inferred from direct assay PubMed 17130127. Source: EcoCyc electron carrier activity Inferred from electronic annotation. Source: HAMAP iron ion binding Inferred from electronic annotation. Source: HAMAP molybdenum ion binding Inferred from direct assay PubMed 17130127. Source: EcoCyc nitrate reductase activity Inferred from direct assay PubMed 8830238. Source: EcoCyc oxidoreductase activity, acting on NAD(P)H Inferred from Biological aspect of Ancestor. Source: RefGenome
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
napD	P0A9I5	3	EBI-554952,EBI-554985

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-Rule 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

.

828

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P33937 [UniParc].

Last modified November 1, 1997. Version 3.
Checksum: CE2D7AB000FEAFCA
Show »

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

« Hide

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] [Europe PMC] [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] [Europe PMC] [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. Horiuchi T. DNA Res. 3:379-392(1996) [PubMed] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 37-43, SUBCELLULAR LOCATION.
[7]	"Export pathway selectivity of Escherichia coli twin arginine translocation signal peptides." Tullman-Ercek D., DeLisa M.P., Kawarasaki Y., Iranpour P., Ribnicky B., Palmer T., Georgiou G. J. Biol. Chem. 282:8309-8316(2007) [PubMed] [Europe PMC] [Abstract] Cited for: EXPORT VIA THE TAT-SYSTEM.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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

PIR

D64990.

RefSeq

NP_416710.1. NC_000913.2.
YP_490444.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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

ProteinModelPortal

P33937.

SMR

P33937. Positions 1-35, 37-827.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10304N.

IntAct

P33937. 12 interactions.

MINT

MINT-1243254.

STRING

511145.b2206.

Proteomic databases

PaxDb

P33937.

PRIDE

P33937.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC75266; AAC75266; b2206.
BAA15989; BAA15989; BAA15989.

GeneID

12933227.
947093.

KEGG

ecj:Y75_p2167.
eco:b2206.

PATRIC

32119771. VBIEscCol129921_2295.

Organism-specific databases

EchoBASE

EB1994.

EcoGene

EG12067. napA.

Phylogenomic databases

eggNOG

COG0243.

HOGENOM

HOG000031441.

KO

K02567.

OMA

HWIKAAR.

ProtClustDB

PRK13532.

Enzyme and pathway databases

BioCyc

EcoCyc:NAPA-MONOMER.
ECOL316407:JW2194-MONOMER.
MetaCyc:NAPA-MONOMER.

Gene expression databases

Genevestigator

P33937.

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_Fe4S4_dom.
IPR006655. Mopterin_OxRdtase_prok_CS.
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

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...

Other

EvolutionaryTrace

P33937.

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:	May 1, 2013
This is version 131 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents