Reviewed, UniProtKB/Swiss-Prot P33590 (NIKA_ECOLI)

Names and origin

Protein names

Recommended name:
    Nickel-binding periplasmic protein

Gene names

Name:	nikA
Ordered Locus Names:	b3476, JW3441

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	524 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	Involved in a nickel transport system, probably represents the nickel binder.
Subcellular location	Periplasm Probable.
Sequence similarities	Belongs to the bacterial solute-binding protein 5 family.

Ontologies

Keywords
Biological process	Transport
Cellular component	Periplasm
Domain	Signal
Ligand	Nickel
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	transport Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	periplasmic space Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	nickel ion binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: IntAct transporter activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
tufA	P0A6N1	1	EBI-555182,EBI-301077

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 22

22

Chain

23 – 524

502

Nickel-binding periplasmic protein

PRO_0000031800

Secondary structure

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524

Helix Strand Turn

Details...

Beta strand

27 – 34

8

Helix

49 – 55

7

Beta strand

59 – 62

4

Beta strand

68 – 76

9

Beta strand

80 – 82

3

Beta strand

84 – 89

6

Helix

103 – 114

12

Helix

115 – 120

6

Helix

124 – 128

5

Beta strand

129 – 136

8

Beta strand

139 – 146

8

Helix

151 – 155

5

Beta strand

157 – 161

5

Helix

166 – 168

3

Beta strand

173 – 180

8

Beta strand

184 – 193

10

Turn

194 – 196

3

Beta strand

197 – 202

6

Beta strand

215 – 220

6

Helix

224 – 232

9

Beta strand

237 – 242

6

Helix

248 – 256

9

Beta strand

260 – 275

16

Turn

280 – 283

4

Helix

285 – 294

10

Helix

297 – 303

7

Beta strand

309 – 311

3

Beta strand

314 – 316

3

Helix

334 – 343

10

Beta strand

363 – 369

7

Helix

373 – 387

15

Turn

388 – 390

3

Beta strand

392 – 398

7

Helix

400 – 409

10

Beta strand

413 – 418

6

Turn

422 – 426

5

Helix

427 – 432

6

Helix

439 – 443

5

Turn

444 – 446

3

Helix

450 – 462

13

Helix

466 – 482

17

Beta strand

486 – 498

13

Helix

500 – 502

3

Helix

516 – 518

3

Sequences

	Sequence		Length	Mass (Da)
	P33590-1 [UniParc]. Last modified February 1, 1994. Version 1. Checksum: CB2E3C1CDCE42396	FASTA	524	58,719
	10 20 30 40 50 60 MLSTLRRTLF ALLACASFIV HAAAPDEITT AWPVNVGPLN PHLYTPNQMF AQSMVYEPLV 70 80 90 100 110 120 KYQADGSVIP WLAKSWTHSE DGKTWTFTLR DDVKFSNGEP FDAEAAAENF RAVLDNRQRH 130 140 150 160 170 180 AWLELANQIV DVKALSKTEL QITLKSAYYP FLQELALPRP FRFIAPSQFK NHETMNGIKA 190 200 210 220 230 240 PIGTGPWILQ ESKLNQYDVF VRNENYWGEK PAIKKITFNV IPDPTTRAVA FETGDIDLLY 250 260 270 280 290 300 GNEGLLPLDT FARFSQNPAY HTQLSQPIET VMLALNTAKA PTNELAVREA LNYAVNKKSL 310 320 330 340 350 360 IDNALYGTQQ VADTLFAPSV PYANLGLKPS QYDPQKAKAL LEKAGWTLPA GKDIREKNGQ 370 380 390 400 410 420 PLRIELSFIG TDALSKSMAE IIQADMRQIG ADVSLIGEEE SSIYARQRDG RFGMIFHRTW 430 440 450 460 470 480 GAPYDPHAFL SSMRVPSHAD FQAQQGLADK PLIDKEIGEV LATHDETQRQ ALYRDILTRL 490 500 510 520 HDEAVYLPIS YISMMVVSKP ELGNIPYAPI ATEIPFEQIK PVKP

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The nik operon of Escherichia coli encodes a periplasmic binding-protein-dependent transport system for nickel." Navarro C., Wu L.-F., Mandrand-Berthelot M.-A. Mol. Microbiol. 9:1181-1191(1993) [PubMed: 7934931] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"Analysis of the Escherichia coli genome. V. DNA sequence of the region from 76.0 to 81.5 minutes." Sofia H.J., Burland V., Daniels D.L., Plunkett G. III, Blattner F.R. Nucleic Acids Res. 22:2576-2586(1994) [PubMed: 8041620] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[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]	"Crystal structures of the liganded and unliganded nickel-binding protein NikA from Escherichia coli." Heddle J., Scott D.J., Unzai S., Park S.Y., Tame J.R. J. Biol. Chem. 278:50322-50329(2003) [PubMed: 12960164] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF 23-524.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

X73143 Genomic DNA. Translation: CAA51659.1.
U00039 Genomic DNA. Translation: AAB18451.1.
U00096 Genomic DNA. Translation: AAC76501.1.
AP009048 Genomic DNA. Translation: BAE77817.1.

PIR

S39594.

RefSeq

AP_004316.1.
NP_417933.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1UIU	X-ray	1.85	A/B	23-524	[»]
1UIV	X-ray	1.95	A/B	23-524	[»]
1ZLQ	X-ray	1.80	A/B	23-524	[»]
2NOO	X-ray	1.65	A	23-524	[»]
3DP8	X-ray	2.50	A/B/C	23-524	[»]
3E3K	X-ray	2.80	A/B/C	23-524	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:10340N.

IntAct

P33590. 1 interaction.

STRING

P33590.

Protein family/group databases

TCDB

3.A.1.5.3. ATP-binding cassette (ABC) superfamily.

Genome annotation databases

GeneID

947981.

GenomeReviews

Gene locus JW3441 in contig AP009048_GR.
Gene locus b3476 in contig U00096_GR.

KEGG

ecj:JW3441.
eco:b3476.

Organism-specific databases

EchoBASE

EB2000.

EcoGene

EG12075. nikA.

CMR

Search...

Phylogenomic databases

HOGENOM

P33590.

OMA

ELAFIGT.

Enzyme and pathway databases

BioCyc

EcoCyc:NIKA-MON.
MetaCyc:MON-8281.

Gene expression databases

Genevestigator

P33590.

Family and domain databases

InterPro

IPR011980. NikA_ABC_Ni_bd.
IPR000914. SBP_bac_5.
[Graphical view]

Pfam

PF00496. SBP_bac_5. 1 hit.
[Graphical view]

TIGRFAMs

TIGR02294. nickel_nikA. 1 hit.

PROSITE

PS01040. SBP_BACTERIAL_5. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

NIKA_ECOLI

Accession

Primary (citable) accession number: P33590
Secondary accession number(s): Q2M7D9

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1994
Last sequence update:	February 1, 1994
Last modified:	November 3, 2009
This is version 76 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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