Escherichia coli K-12 substr. MG1655 Polypeptide: DpiB sensory histidine kinase

Gene: dpiB Accession Numbers: G6345 (EcoCyc), b0619, ECK0612

Synonyms: ybeP, mpdB, citA

Regulation Summary Diagram: ?

Regulation summary diagram for dpiB

Alternative forms of DpiB sensory histidine kinase: DpiB sensory histidine kinase - phosphorylated (summary available)

DpiB is the membrane associated sensor kinase component of the DpiAB two component system which regulates the expression of genes involved in anaerobic citrate fermentation in E.coli. Sequence analysis suggests that DpiB contains a periplasmic sensing domain surrounded by two transmembrane segments plus a cytoplasmic effector domain [Yamamoto09a]. The periplasmic domain of DpiB has a high affinity for citrate in vitro[Kaspar02].

Autophosphorylation of the purified cytoplasmic domain of DpiB and subsequent transfer of the phosphoryl group to the response regulator DpiA has been demonstrated in vitro [Yamamoto09a]. Autophosphorylation of DpiB is induced by DTT in vitro [Yamamoto09a].

Based on in vivo studies with fluorescence resonance energy transfer (FRET) and a bacterial two-hybrid system (BATCH), the physical interaction between DcuS and DpiB sensory histidine kinase proteins has been demonstrated [Scheu12]. Such an interaction seems to have no direct functional significance and is not involved in signal transfer between the DcuSR and DpiBA systems [Scheu12].

An amber mutation has been generated [Herring03].

Gene Citations: [Miller04a]

Locations: inner membrane

Map Position: [651,458 -> 653,116] (14.04 centisomes, 51°)
Length: 1659 bp / 552 aa

Molecular Weight of Polypeptide: 61.684 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0002129 , EchoBASE:EB3410 , EcoGene:EG13646 , EcoliWiki:b0619 , ModBase:P77510 , OU-Microarray:b0619 , PortEco:dpiB , PR:PRO_000022472 , Pride:P77510 , Protein Model Portal:P77510 , RefSeq:NP_415152 , RegulonDB:G6345 , SMR:P77510 , String:511145.b0619 , UniProt:P77510

Relationship Links: InterPro:IN-FAMILY:IPR000014 , InterPro:IN-FAMILY:IPR003594 , InterPro:IN-FAMILY:IPR003661 , InterPro:IN-FAMILY:IPR004358 , InterPro:IN-FAMILY:IPR005467 , InterPro:IN-FAMILY:IPR016120 , InterPro:IN-FAMILY:IPR029150 , InterPro:IN-FAMILY:IPR029151 , Pfam:IN-FAMILY:PF02518 , Pfam:IN-FAMILY:PF13188 , Pfam:IN-FAMILY:PF14827 , Prints:IN-FAMILY:PR00344 , Prosite:IN-FAMILY:PS50109 , Smart:IN-FAMILY:SM00091 , Smart:IN-FAMILY:SM00387

In Paralogous Gene Group: 122 (29 members)

Reactions known to consume the compound:

DpiBA Two-Component Signal Transduction System :
ATP + DpiB → ADP + DpiB sensory histidine kinase - phosphorylated

Reactions known to produce the compound:

DpiBA Two-Component Signal Transduction System :
DpiB sensory histidine kinase - phosphorylated + DpiA → DpiB + DpiA-Pasp57

Genetic Regulation Schematic: ?

Genetic regulation schematic for dpiB

GO Terms:

Biological Process: GO:0000160 - phosphorelay signal transduction system Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Yamamoto08a]
GO:0018106 - peptidyl-histidine phosphorylation Inferred from experiment [Yamamoto09a]
GO:0023014 - signal transduction by protein phosphorylation Inferred from experiment Inferred by computational analysis [GOA01, Yamamoto08a]
GO:0046777 - protein autophosphorylation Inferred from experiment [Yamamoto09a]
GO:0071310 - cellular response to organic substance Inferred from experiment [Yamamoto08a]
GO:0007165 - signal transduction Inferred by computational analysis [GOA01]
GO:0016310 - phosphorylation Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0000155 - phosphorelay sensor kinase activity Inferred from experiment Inferred by computational analysis [GOA01, Yamamoto08a]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0004673 - protein histidine kinase activity Inferred by computational analysis [GOA01a]
GO:0004871 - signal transducer activity Inferred by computational analysis [GOA01]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11]
GO:0016301 - kinase activity Inferred by computational analysis [UniProtGOA11]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0016772 - transferase activity, transferring phosphorus-containing groups Inferred by computational analysis [GOA01]
Cellular Component: GO:0005622 - intracellular Inferred by computational analysis Inferred from experiment [Yamamoto08a, UniProtGOA11, GOA01]
GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Daley05, Yamamoto09a]
GO:0005887 - integral component of plasma membrane Inferred by computational analysis [Yamamoto09a]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11, Yamamoto09a]

MultiFun Terms: cell structure membrane
information transfer protein related posttranslational modification
regulation type of regulation posttranscriptional covalent modification, demodification, maturation
regulation type of regulation transcriptional level complex regulation two component regulatory systems (external signal)

Essentiality data for dpiB 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]

Last-Curated ? 29-Nov-2010 by Mackie A , Macquarie University

Sequence Features

Protein sequence of DpiB sensory histidine kinase with features indicated

Feature Class Location Citations Comment State
Transmembrane-Region 22 -> 42
UniProt: Helical;; Non-Experimental Qualifier: potential;
Mutagenesis-Variant 138
[Kaspar02, UniProt11a]
UniProt: Reduces strongly citrate binding.
Transmembrane-Region 183 -> 203
UniProt: Helical;; Non-Experimental Qualifier: potential;
Conserved-Region 222 -> 292
UniProt: PAS;
Conserved-Region 344 -> 541
UniProt: Histidine kinase;
Phosphorylation-Modification 347
UniProt: Phosphohistidine; by autocatalysis; Non-Experimental Qualifier: by similarity.
Mutagenesis-Variant 478
[Yamamoto09a, UniProt11a]
UniProt: Loss of autophosphorylation.
Mutagenesis-Variant 517
[Yamamoto09a, UniProt11a]
UniProt: Decrease in autophosphorylation.
Sequence-Conflict 518 -> 552
[Ingmer98, UniProt10]
UniProt: (in Ref. 1; AAC28951);
Mutagenesis-Variant 529
[Yamamoto09a, UniProt11a]
UniProt: Constitutively active.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


3/2/1998 (pkarp) Merged genes G497/EG13646 and G6345/citA
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

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

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

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."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

Herring03: Herring CD, Glasner JD, Blattner FR (2003). "Gene replacement without selection: regulated suppression of amber mutations in Escherichia coli." Gene 311;153-63. PMID: 12853150

Ingmer98: Ingmer H, Miller CA, Cohen SN (1998). "Destabilized inheritance of pSC101 and other Escherichia coli plasmids by DpiA, a novel two-component system regulator." Mol Microbiol 29(1);49-59. PMID: 9701802

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

Kaspar02: Kaspar S, Bott M (2002). "The sensor kinase CitA (DpiB) of Escherichia coli functions as a high-affinity citrate receptor." Arch Microbiol 177(4);313-21. PMID: 11889485

Miller04a: Miller C, Thomsen LE, Gaggero C, Mosseri R, Ingmer H, Cohen SN (2004). "SOS response induction by beta-lactams and bacterial defense against antibiotic lethality." Science 305(5690);1629-31. PMID: 15308764

Scheu12: Scheu PD, Witan J, Rauschmeier M, Graf S, Liao YF, Ebert-Jung A, Basche T, Erker W, Unden G (2012). "CitA/CitB two-component system regulating citrate fermentation in Escherichia coli and its relation to the DcuS/DcuR system in vivo." J Bacteriol 194(3);636-45. PMID: 22101843

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 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."

Yamamoto08a: Yamamoto K, Matsumoto F, Oshima T, Fujita N, Ogasawara N, Ishihama A (2008). "Anaerobic regulation of citrate fermentation by CitAB in Escherichia coli." Biosci Biotechnol Biochem 72(11);3011-4. PMID: 18997424

Yamamoto09a: Yamamoto K, Matsumoto F, Minagawa S, Oshima T, Fujita N, Ogasawara N, Ishihama A (2009). "Characterization of CitA-CitB signal transduction activating genes involved in anaerobic citrate catabolism in Escherichia coli." Biosci Biotechnol Biochem 73(2);346-50. PMID: 19202292

Other References Related to Gene Regulation

Mandin09: Mandin P, Gottesman S (2009). "A genetic approach for finding small RNAs regulators of genes of interest identifies RybC as regulating the DpiA/DpiB two-component system." Mol Microbiol 72(3);551-65. PMID: 19426207

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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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