Escherichia coli K-12 substr. MG1655 Polypeptide: nickel ABC transporter - membrane subunit

Gene: nikB Accession Numbers: EG12076 (EcoCyc), b3477, ECK3461

Synonyms: hydC, hydD

Regulation Summary Diagram: ?

Regulation summary diagram for nikB

Component of: nickel ABC transporter (extended summary available)

Gene Citations: [Navarro93, Becuwe, De99a, Eitinger00]

Locations: inner membrane

Map Position: [3,613,264 -> 3,614,208] (77.88 centisomes, 280°)
Length: 945 bp / 314 aa

Molecular Weight of Polypeptide: 35.248 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0011356 , CGSC:33180 , DIP:DIP-10341N , EchoBASE:EB2001 , EcoGene:EG12076 , EcoliWiki:b3477 , OU-Microarray:b3477 , PortEco:nikB , PR:PRO_000023385 , Pride:P33591 , Protein Model Portal:P33591 , RefSeq:NP_417934 , RegulonDB:EG12076 , String:511145.b3477 , UniProt:P33591

Relationship Links: InterPro:IN-FAMILY:IPR000515 , InterPro:IN-FAMILY:IPR014156 , Pfam:IN-FAMILY:PF00528 , Prosite:IN-FAMILY:PS50928

In Paralogous Gene Group: 24 (43 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for nikB

GO Terms:

Biological Process: GO:0035444 - nickel cation transmembrane transport Inferred from experiment Inferred by computational analysis [GOA01, Navarro93]
GO:0006810 - transport Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0006811 - ion transport Inferred by computational analysis [UniProtGOA11]
GO:0015675 - nickel cation transport Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0015099 - nickel cation transmembrane transporter activity Inferred from experiment Inferred by computational analysis [GOA01, Navarro93]
GO:0016151 - nickel cation binding Inferred from experiment [dePina95]
GO:0015413 - nickel-transporting ATPase activity Inferred by computational analysis [Navarro93]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Daley05]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11, Navarro93]

MultiFun Terms: cell structure membrane
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, membrane component

Essentiality data for nikB 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 - membrane subunit with features indicated

Feature Class Location Citations Comment
Transmembrane-Region 9 -> 29
UniProt: Helical;; Non-Experimental Qualifier: potential;
Sequence-Conflict 26 -> 27
[Navarro93, UniProt10a]
UniProt: (in Ref. 1; CAA51660);
Conserved-Region 98 -> 295
UniProt: ABC transmembrane type-1;
Transmembrane-Region 104 -> 124
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 137 -> 157
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 170 -> 190
UniProt: Helical;; Non-Experimental Qualifier: potential;
Sequence-Conflict 197
[Navarro93, UniProt10a]
UniProt: (in Ref. 1; CAA51660);
Transmembrane-Region 232 -> 252
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 275 -> 295
UniProt: Helical;; Non-Experimental Qualifier: potential;

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 b3477 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12076; 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

Daley05: Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G (2005). "Global topology analysis of the Escherichia coli inner membrane proteome." Science 308(5726);1321-3. PMID: 15919996

De99a: 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

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

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

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

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

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

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms 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

Zhao10a: 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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