Escherichia coli K-12 substr. MG1655 Polypeptide: nickel ABC transporter - periplasmic binding protein

Gene: nikA Accession Numbers: EG12075 (EcoCyc), b3476, ECK3460

Synonyms: hydD, hydC

Regulation Summary Diagram: ?

Regulation summary diagram for nikA

Component of: nickel ABC transporter (extended summary available)

NikA is the periplasmic binding component of the nickel ABC transporter in Escherichia coli.

The crystal structure of NikA in the presence and absence of nickel has been determined to 1.95 Å and 1.85 Å respectively [Heddle03]. The structure of NikA has been determined to a resolution of 1.8 Å showing that it binds FeEDTA(H2O) with very high affinity. It also binds the nickel ion associated with a metallophore which is at least similar to EDTA [Cherrier05]. The structure in the absence of EDTA has also been resolved to 2.5 Å. Analysis of the generated electron density omit map indicates that NikA binds nickel and other metal ions chelated by a small organic molecule which is possibly butane-1,2,4-tricarboxylate (BTC) or, less likely, propane-1,2,3-tricarboxylate (tricarballylate) [Cherrier08].

Gene Citations: [Navarro93, Becuwe, De99b, Eitinger00]

Locations: inner membrane, periplasmic space

Map Position: [3,611,690 -> 3,613,264] (77.84 centisomes, 280°)
Length: 1575 bp / 524 aa

Molecular Weight of Polypeptide: 58.719 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0011354 , CGSC:18226 , DIP:DIP-10340N , EchoBASE:EB2000 , EcoGene:EG12075 , EcoliWiki:b3476 , Mint:MINT-1272849 , ModBase:P33590 , OU-Microarray:b3476 , PortEco:nikA , PR:PRO_000023384 , Pride:P33590 , Protein Model Portal:P33590 , RefSeq:NP_417933 , RegulonDB:EG12075 , SMR:P33590 , String:511145.b3476 , UniProt:P33590

Relationship Links: InterPro:IN-FAMILY:IPR000914 , InterPro:IN-FAMILY:IPR011980 , InterPro:IN-FAMILY:IPR023765 , PDB:Structure:1UIU , PDB:Structure:1UIV , PDB:Structure:1ZLQ , PDB:Structure:2NOO , PDB:Structure:3DP8 , PDB:Structure:3E3K , PDB:Structure:3MVW , PDB:Structure:3MVX , PDB:Structure:3MVY , PDB:Structure:3MVZ , PDB:Structure:3MW0 , PDB:Structure:3MZ9 , PDB:Structure:3MZB , PDB:Structure:3QIM , PDB:Structure:4DCX , PDB:Structure:4DCY , PDB:Structure:4I8C , PDB:Structure:4I9D , Pfam:IN-FAMILY:PF00496 , Prosite:IN-FAMILY:PS01040

In Paralogous Gene Group: 25 (11 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for nikA

GO Terms:

Biological Process: GO:0050919 - negative chemotaxis Inferred from experiment [dePina95]
GO:0006810 - transport Inferred by computational analysis [UniProtGOA11a]
GO:0015675 - nickel cation transport Inferred by computational analysis [GOA01a]
GO:0055085 - transmembrane transport Inferred by computational analysis [GOA01a]
Molecular Function: GO:0016151 - nickel cation binding Inferred from experiment Inferred by computational analysis [GOA01a, dePina95]
GO:0020037 - heme binding Inferred from experiment Inferred by computational analysis [GOA01a, Shepherd07]
GO:0046914 - transition metal ion binding Inferred from experiment [dePina95]
GO:0015413 - nickel-transporting ATPase activity Inferred by computational analysis
Cellular Component: GO:0030288 - outer membrane-bounded periplasmic space Inferred from experiment Inferred by computational analysis [DiazMejia09, LopezCampistrou05]
GO:0042597 - periplasmic space Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, dePina95]
GO:0043190 - ATP-binding cassette (ABC) transporter complex Inferred by computational analysis [GOA01a]

MultiFun Terms: transport Channel-type Transporters Pyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active Transporters The ATP-binding Cassette (ABC) Superfamily + ABC-type Uptake Permeases ABC superfamily, periplasmic binding component

Essentiality data for nikA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Subunit of: nickel ABC transporter

Subunit composition of nickel ABC transporter = [NikD][NikE][NikB][NikC][NikA]
         nickel ABC transporter - ATP binding subunit = NikD (extended summary available)
         nickel ABC transporter - ATP binding subunit = NikE
         nickel ABC transporter - membrane subunit = NikB
         nickel ABC transporter - membrane subunit = NikC
         nickel ABC transporter - periplasmic binding protein = NikA (summary available)

The NikABCDE ATP-dependent nickel (II) uptake system is a member of the ATP-Binding Cassette (ABC) Superfamily of transporters [Wu95]. The Nik system exhibits significant sequence similarity to the components of other ABC transporters for dipeptides or oligopeptides [Navarro93]. Based on sequence similarity, NikA is the periplasmic binding protein, NikB and NikC are the membrane components, and NikD and NikE are the ATP-binding components of the ABC transporter.

The nickel-binding properties of the protein have been studied by monitoring the quenching of intrinsic protein fluorescence [dePina95]. NikA binds one atom of nickel per molecule of protein with a Kd of less than 0.1 μM. The transporter's high specificity for nickel ion has also been demonstrated by high-performance immobilized-metal-ion affinity chromatography [dePina95].

Insertional mutation in the nik operon severely reduces nickel transport ability [Navarro93]. Nickel is an important cofactor in a variety of enzymatic reactions in prokaryotes [Eitinger00]. However, nickel at high intracellular concentrations is toxic because it can catalyze the formation of reactive forms of oxygen that can damage cellular constituents [Eitinger00]. Because of the toxicity of nickel, the synthesis of the Nik system is tightly controlled by nickel concentration. At high nickel concentrations (0.3 mM) synthesis of Nik is completely repressed by the protein NikR [Eitinger00].

Expression of NikABCDE corresponds to expression of NiFe hydrogenases for which nickel is a cofactor. Mutation and LacZ fusion experiments show that nitrate, via the activity of the NarLX two-component system, represses expression of nikABCDE considerably. NikABCDE is upregulated by FNR under anaerobic conditions [Rowe05].

Enzymatic reaction of: nickel ABC transporter

EC Number:

Transport reaction diagram for nickel ABC transporter

Sequence Features

Protein sequence of nickel ABC transporter - periplasmic binding protein with features indicated

Feature Class Location Citations Comment
Signal-Sequence 1 -> 22
Chain 23 -> 524
UniProt: Nickel-binding periplasmic protein;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b3476 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12075; confirmed by SwissProt match.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Becuwe: Becuwe P, Gratepanche S, Fourmaux MN, Van Beeumen J, Samyn B, Mercereau-Puijalon O, Touzel JP, Slomianny C, Camus D, Dive D "Characterization of iron-dependent endogenous superoxide dismutase of Plasmodium falciparum." Mol Biochem Parasitol NIL;76(1-2);125-34. PMID: 8920001

Cherrier05: Cherrier MV, Martin L, Cavazza C, Jacquamet L, Lemaire D, Gaillard J, Fontecilla-Camps JC (2005). "Crystallographic and spectroscopic evidence for high affinity binding of FeEDTA(H2O)- to the periplasmic nickel transporter NikA." J Am Chem Soc 127(28);10075-82. PMID: 16011372

Cherrier08: Cherrier MV, Cavazza C, Bochot C, Lemaire D, Fontecilla-Camps JC (2008). "Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA." Biochemistry 47(38);9937-43. PMID: 18759453

De99b: De Pina K, Desjardin V, Mandrand-Berthelot MA, Giordano G, Wu LF (1999). "Isolation and characterization of the nikR gene encoding a nickel-responsive regulator in Escherichia coli." J Bacteriol 1999;181(2);670-4. PMID: 9882686

dePina95: de Pina K, Navarro C, McWalter L, Boxer DH, Price NC, Kelly SM, Mandrand-Berthelot MA, Wu LF (1995). "Purification and characterization of the periplasmic nickel-binding protein NikA of Escherichia coli K12." Eur J Biochem 1995;227(3);857-65. PMID: 7867647

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Eitinger00: Eitinger T, Mandrand-Berthelot MA (2000). "Nickel transport systems in microorganisms." Arch Microbiol 2000;173(1);1-9. PMID: 10648098

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Heddle03: Heddle J, Scott DJ, Unzai S, Park SY, Tame JR (2003). "Crystal structures of the liganded and unliganded nickel-binding protein NikA from Escherichia coli." J Biol Chem 278(50);50322-9. PMID: 12960164

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Navarro93: Navarro C, Wu LF, Mandrand-Berthelot MA (1993). "The nik operon of Escherichia coli encodes a periplasmic binding-protein-dependent transport system for nickel." Mol Microbiol 9(6);1181-91. PMID: 7934931

Rowe05: Rowe JL, Starnes GL, Chivers PT (2005). "Complex transcriptional control links NikABCDE-dependent nickel transport with hydrogenase expression in Escherichia coli." J Bacteriol 187(18);6317-23. PMID: 16159764

Shepherd07: Shepherd M, Heath MD, Poole RK (2007). "NikA binds heme: a new role for an Escherichia coli periplasmic nickel-binding protein." Biochemistry 46(17);5030-7. PMID: 17411076

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Wu95: Wu LF, Mandrand-Berthelot MA (1995). "A family of homologous substrate-binding proteins with a broad range of substrate specificity and dissimilar biological functions." Biochimie 1995;77(9);744-50. PMID: 8789466

Other References Related to Gene Regulation

Barrios99: Barrios H, Valderrama B, Morett E (1999). "Compilation and analysis of sigma(54)-dependent promoter sequences." Nucleic Acids Res 27(22);4305-13. PMID: 10536136

Chivers00: Chivers PT, Sauer RT (2000). "Regulation of high affinity nickel uptake in bacteria. Ni2+-Dependent interaction of NikR with wild-type and mutant operator sites." J Biol Chem 2000;275(26);19735-41. PMID: 10787413

Chivers99: Chivers PT, Sauer RT (1999). "NikR is a ribbon-helix-helix DNA-binding protein." Protein Sci 1999;8(11);2494-500. PMID: 10595554

Krecisz12: Krecisz S, Jones MD, Zamble DB (2012). "Nonspecific interactions between Escherichia coli NikR and DNA are critical for nickel-activated DNA binding." Biochemistry 51(40);7873-9. PMID: 22971172

Zhao10: Zhao K, Liu M, Burgess RR (2010). "Promoter and regulon analysis of nitrogen assimilation factor, sigma54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis." Nucleic Acids Res 38(4);1273-83. PMID: 19969540

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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