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



Gene: ypdA Accession Numbers: G7243 (EcoCyc), b2380, ECK2376

Regulation Summary Diagram: ?

Alternative forms of YpdA sensory histidine kinase: YbdA sensory histidine kinase - his371 phosphorylated

Summary:
YpdA is the sensory kinase component of the YpdAB two-component system which senses extracellular pyruvate and induces expression of the YhjX transporter. YpdAB plays a role in the carbon control network of E. coli K-12 [Fried13].

YpdA is predicted to be an inner membrane protein with 6 trans-membrane domains [Fried13]. Phosphorylation of YbdA has not been detected in vitro, however substitution of the conserved histidine residue H371 with glutamine prevents yhjX induction in vivo [Fried13]. yhjX is not induced in a ypdABC deletion mutant. Complementation with ypdABC expressed in trans restores induction [Fried13].

A strong interaction between YpdA and the inner membrane transporters YjiY and YhjX has been detected. YpdA is capable of homo-oligomerisation [Behr14].

A mutant containing a deletion of both ypdA and ypdB does not show a significant phenotype when measured by phenotype microarray [Zhou03].

Citations: [Tchieu01]

Locations: inner membrane

Map Position: [2,496,693 -> 2,498,390] (53.81 centisomes)
Length: 1698 bp / 565 aa

Molecular Weight of Polypeptide: 62.657 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0007855 , EchoBASE:EB3900 , EcoGene:EG14148 , EcoliWiki:b2380 , ModBase:P0AA93 , OU-Microarray:b2380 , PortEco:ypdA , Pride:P0AA93 , Protein Model Portal:P0AA93 , RefSeq:NP_416881 , RegulonDB:G7243 , SMR:P0AA93 , String:511145.b2380 , UniProt:P0AA93

Relationship Links: InterPro:IN-FAMILY:IPR003018 , InterPro:IN-FAMILY:IPR003594 , InterPro:IN-FAMILY:IPR010559 , InterPro:IN-FAMILY:IPR011620 , Pfam:IN-FAMILY:PF02518 , Pfam:IN-FAMILY:PF06580 , Pfam:IN-FAMILY:PF07694 , Prosite:IN-FAMILY:PS50109 , Smart:IN-FAMILY:SM00065 , Smart:IN-FAMILY:SM00387

Reactions known to consume the compound:

YpdAB Two-Component Signal Transduction System :
YpdA[inner membrane] + ATP → YpdA-Phis371[inner membrane] + ADP

Reactions known to produce the compound:

YpdAB Two-Component Signal Transduction System :
YpdA-Phis371[inner membrane] + YpdB → YpdA[inner membrane] + YpdB-Pasp

GO Terms:

Biological Process: GO:0000160 - phosphorelay signal transduction system Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Fried13]
GO:0023014 - signal transduction by phosphorylation Inferred from experiment [Fried13]
GO:0031670 - cellular response to nutrient Inferred from experiment [Fried13]
GO:0016310 - phosphorylation Inferred by computational analysis [UniProtGOA11]
GO:0018106 - peptidyl-histidine phosphorylation Inferred by computational analysis [GOA01a, GOA01]
GO:0071555 - cell wall organization Inferred by computational analysis [GOA01]
Molecular Function: GO:0000155 - phosphorelay sensor kinase activity Inferred from experiment Inferred by computational analysis [GOA01, Fried13]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0004673 - protein histidine kinase activity Inferred by computational analysis [GOA01a, 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]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Daley05]
GO:0005887 - integral component of plasma membrane Inferred by computational analysis [Fried13]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11, GOA01]

MultiFun Terms: cell processes adaptations starvation
cell structure membrane
regulation type of regulation transcriptional level complex regulation two component regulatory systems (external signal)

Essentiality data for ypdA 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]

Credits:
Curated 20-Jan-2006 by Keseler I , SRI International
Last-Curated ? 10-Jan-2013 by Mackie A , Macquarie University


Sequence Features

Feature Class Location Citations Comment State
Transmembrane-Region 4 -> 24
[UniProt13]
UniProt: Helical; Non-Experimental Qualifier: potential.
 
Transmembrane-Region 46 -> 66
[UniProt13]
UniProt: Helical; Non-Experimental Qualifier: potential.
 
Transmembrane-Region 75 -> 95
[UniProt13]
UniProt: Helical; Non-Experimental Qualifier: potential.
 
Transmembrane-Region 108 -> 128
[UniProt13]
UniProt: Helical; Non-Experimental Qualifier: potential.
 
Transmembrane-Region 140 -> 160
[UniProt13]
UniProt: Helical; Non-Experimental Qualifier: potential.
 
Transmembrane-Region 173 -> 193
[UniProt13]
UniProt: Helical; Non-Experimental Qualifier: potential.
 
Conserved-Region 223 -> 342
[UniProt13]
UniProt: GAF.
 
Conserved-Region 343 -> 554
[UniProt13]
UniProt: Histidine kinase.
 
Mutagenesis-Variant 371
[Fried13, UniProt13]
Alternate sequence: H → Q; UniProt: Lack of activity.
 
Phosphorylation-Modification 371
[Fried13]
  Unmodified


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

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

Behr14: Behr S, Fried L, Jung K (2014). "Identification of a Novel Nutrient-Sensing Histidine Kinase/Response Regulator Network in Escherichia coli." J Bacteriol 196(11);2023-9. PMID: 24659770

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

Fried13: Fried L, Behr S, Jung K (2013). "Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli." J Bacteriol 195(4);807-15. PMID: 23222720

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.

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

Tchieu01: Tchieu JH, Norris V, Edwards JS, Saier MH (2001). "The complete phosphotransferase system in Escherichia coli." J Mol Microbiol Biotechnol 3(3);329-46. PMID: 11361063

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."

Zhou03: Zhou L, Lei XH, Bochner BR, Wanner BL (2003). "Phenotype microarray analysis of Escherichia coli K-12 mutants with deletions of all two-component systems." J Bacteriol 185(16);4956-72. PMID: 12897016


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Sun Nov 23, 2014, BIOCYC13B.