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Escherichia coli K-12 substr. MG1655 Polypeptide: regulator of DnaA that prevents premature reinitiation of DNA replication



Gene: hda Accession Numbers: G7313 (EcoCyc), b2496, ECK2492

Synonyms: idaB, yfgE

Regulation Summary Diagram: ?

Summary:
Hda is a member of the AAA chaperone-like family of ATPases [Kato01] that is required for the inhibition of the initiation of DNA synthesis via antagonism of DnaA activity by the DNA polymerase III beta subunit (sliding clamp) [Katayama98, Kato01]. Hda and the sliding clamp stimulate ATP hydrolysis within the DnaA-ATP complex, which renders it inactive, and DNA replication activity also contributes to this downregulation [Katayama98].

Hda has been shown to interact with the beta subunit of DNA polymerase III in vitro; the interaction is mediated by a hexapeptide sequence located in the amino terminus of Hda [Kurz04]. Hda also binds to and antagonizes the activity of TrfA, an episomal factor that regulates replication of the RK2 plasmid [Kim03]. Hda counteracts the toxic effects observed upon production of a TrfA protein fragment [Kim03]. An hda mutant shows increased replication of RK2 plasmid, and overabundance of Hda causes decreased replication of RK2 [Kim03].

Reports differ on whether [Kato01] or not [Camara03] Hda is essential for viability.

Hda is localized to membranes, predominantly to the inner membrane [Kim03].

Hda has similarity to DnaA [Kato01].

Dp: "DnaA paralog" [Kim03]

Hda: "homolog of DnaA"

Gene Citations: [Zaslaver06]

Locations: cytosol, inner membrane

Map Position: [2,616,097 <- 2,616,798] (56.39 centisomes)
Length: 702 bp / 233 aa

Molecular Weight of Polypeptide: 26.633 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0008217 , DIP:DIP-48006N , EchoBASE:EB3953 , EcoGene:EG14201 , EcoliWiki:b2496 , OU-Microarray:b2496 , PortEco:hda , PR:PRO_000022867 , Protein Model Portal:P69931 , RefSeq:NP_416991 , RegulonDB:G7313 , SMR:P69931 , String:511145.b2496 , UniProt:P69931

Relationship Links: InterPro:IN-FAMILY:IPR013317 , InterPro:IN-FAMILY:IPR017788 , InterPro:IN-FAMILY:IPR020591 , InterPro:IN-FAMILY:IPR022864 , InterPro:IN-FAMILY:IPR027417 , Pfam:IN-FAMILY:PF00308 , Prints:IN-FAMILY:PR00051

In Paralogous Gene Group: 281 (4 members)

GO Terms:

Biological Process: GO:0032297 - negative regulation of DNA-dependent DNA replication initiation Inferred from experiment Inferred by computational analysis [GOA01, Kato01]
GO:0006260 - DNA replication Inferred by computational analysis [UniProtGOA11, GOA06]
GO:0008156 - negative regulation of DNA replication Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Kurz04, Keyamura11, Butland05]
GO:0042802 - identical protein binding Inferred from experiment [Rajagopala14, Kurz04]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Zhang07]
GO:0016020 - membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, Kim03]
GO:0005886 - plasma membrane Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]

MultiFun Terms: extrachromosomal plasmid related
information transfer DNA related DNA replication
regulation type of regulation posttranscriptional inhibition / activation of enzymes

Essentiality data for hda knockouts: ?

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

Sequence Features

Feature Class Location Common Name Citations Comment
Mutagenesis-Variant 6  
[Suetsugu05, Baxter12, UniProt13]
Alternate sequence: Q → A; UniProt: Severely impaired in beta clamp binding and DnaA-ATP hydrolysis, very poor growth at 30 degrees Celsius.
Protein-Binding-Region 6 -> 11 beta-binding motif
[Kurz04, Riber06, Kurz04, Kurz04]
The beta-binding motif is required for binding to the β clamp as well as for blocking TrfA toxicity.
Mutagenesis-Variant 7 -> 11  
[Kurz04, UniProt13]
Alternate sequence: LSLPL → ASAPA; UniProt: Decreased binding to beta clamp.
Mutagenesis-Variant 9  
[Suetsugu05, Baxter12, UniProt13]
Alternate sequence: L → A; UniProt: Impaired in beta clamp binding and DnaA-ATP hydrolysis, very poor growth at 30 degrees Celsius.
Alternate sequence: LP → AA; UniProt: Decreased binding to beta clamp.
Mutagenesis-Variant 56  
[Suetsugu08, UniProt11]
Alternate sequence: R → A; UniProt: Severely impaired in ADP-binding but still has clamp-binding activity in vitro, defective in DnaA-ATP hydrolysis in vivo; when associated with 102-A-A- 103.
Mutagenesis-Variant 98  
[Baxter12, UniProt13]
Alternate sequence: L → P; UniProt: No growth at 30 degrees Celsius, impaired RIDA.
Mutagenesis-Variant 102 -> 103  
[UniProt11]
Alternate sequence: DN → AA; UniProt: Impaired in ADP-binding, has clamp-binding activity in vitro.
Amino-Acid-Sites-That-Bind 132, 118, 122, 153 DnaA interaction residues
[Nakamura10]
These residues are required for Hda-ADP to interact with DnaA.
Mutagenesis-Variant 136  
[Baxter12, UniProt13]
Alternate sequence: G → D; UniProt: No growth at 30 degrees Celsius, impaired RIDA.
Mutagenesis-Variant 153  
[Suetsugu05, Baxter12, UniProt13]
Alternate sequence: R → M; UniProt: Defective in DnaA-ATP hydrolysis, binds beta clamp normally, no growth at 30 degrees Celsius.
Alternate sequence: R → A; UniProt: Defective in DnaA-ATP hydrolysis, binds beta clamp normally, no growth at 30 degrees Celsius.
Mutagenesis-Variant 157  
[Baxter12, UniProt13]
Alternate sequence: G → V; UniProt: Grows at 30 degrees Celsius, impaired RIDA.
Mutagenesis-Variant 167  
[Baxter12, UniProt13]
Alternate sequence: D → N; UniProt: Grows at 30 degrees Celsius, impaired RIDA.
Mutagenesis-Variant 196  
[Baxter12, UniProt13]
Alternate sequence: R → Q; UniProt: Grows at 30 degrees Celsius, impaired RIDA.
Mutagenesis-Variant 208 -> 210  
[Baxter12, UniProt13]
Alternate sequence: LDQ → missing; UniProt: No growth at 30 degrees Celsius, impaired RIDA.
Mutagenesis-Variant 210  
[Baxter12, UniProt13]
Alternate sequence: Q → QLDQ; UniProt: No growth at 30 degrees Celsius, impaired RIDA.
Mutagenesis-Variant 212  
[Baxter12, UniProt13]
Alternate sequence: D → N; UniProt: Grows at 30 degrees Celsius, impaired RIDA.
Mutagenesis-Variant 233  
[Baxter12, UniProt13]
Alternate sequence: L → F; UniProt: No growth at 30 degrees Celsius, impaired RIDA.


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Ingrid Keseler on Tue Feb 22, 2011:
Gene start position changed according to experimental evidence for a CTG start codon in [Suetsugu08 ].
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

Baxter12: Baxter JC, Sutton MD (2012). "Evidence for roles of the Escherichia coli Hda protein beyond regulatory inactivation of DnaA." Mol Microbiol 85(4);648-68. PMID: 22716942

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

Camara03: Camara JE, Skarstad K, Crooke E (2003). "Controlled Initiation of Chromosomal Replication in Escherichia coli Requires Functional Hda Protein." J Bacteriol 2003;185(10);3244-8. PMID: 12730188

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

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

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

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

Katayama98: Katayama T, Kubota T, Kurokawa K, Crooke E, Sekimizu K (1998). "The initiator function of DnaA protein is negatively regulated by the sliding clamp of the E. coli chromosomal replicase." Cell 1998;94(1);61-71. PMID: 9674428

Kato01: Kato J, Katayama T (2001). "Hda, a novel DnaA-related protein, regulates the replication cycle in Escherichia coli." EMBO J 2001;20(15);4253-62. PMID: 11483528

Keyamura11: Keyamura K, Katayama T (2011). "DnaA protein DNA-binding domain binds to Hda protein to promote inter-AAA+ domain interaction involved in regulatory inactivation of DnaA." J Biol Chem 286(33);29336-46. PMID: 21708944

Kim03: Kim PD, Banack T, Lerman DM, Tracy JC, Camara JE, Crooke E, Oliver D, Firshein W (2003). "Identification of a novel membrane-associated gene product that suppresses toxicity of a TrfA peptide from plasmid RK2 and its relationship to the DnaA host initiation protein." J Bacteriol 2003;185(6);1817-24. PMID: 12618445

Kurz04: Kurz M, Dalrymple B, Wijffels G, Kongsuwan K (2004). "Interaction of the sliding clamp beta-subunit and Hda, a DnaA-related protein." J Bacteriol 186(11);3508-15. PMID: 15150238

Nakamura10: Nakamura K, Katayama T (2010). "Novel essential residues of Hda for interaction with DnaA in the regulatory inactivation of DnaA: unique roles for Hda AAA Box VI and VII motifs." Mol Microbiol 76(2);302-17. PMID: 20132442

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Riber06: Riber L, Olsson JA, Jensen RB, Skovgaard O, Dasgupta S, Marinus MG, Lobner-Olesen A (2006). "Hda-mediated inactivation of the DnaA protein and dnaA gene autoregulation act in concert to ensure homeostatic maintenance of the Escherichia coli chromosome." Genes Dev 20(15);2121-34. PMID: 16882985

Suetsugu05: Su'etsugu M, Shimuta TR, Ishida T, Kawakami H, Katayama T (2005). "Protein associations in DnaA-ATP hydrolysis mediated by the Hda-replicase clamp complex." J Biol Chem 280(8);6528-36. PMID: 15611053

Suetsugu08: Su'etsugu M, Nakamura K, Keyamura K, Kudo Y, Katayama T (2008). "Hda monomerization by ADP binding promotes replicase clamp-mediated DnaA-ATP hydrolysis." J Biol Chem 283(52);36118-31. PMID: 18977760

UniProt11: 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."

Zaslaver06: Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette MG, Alon U (2006). "A comprehensive library of fluorescent transcriptional reporters for Escherichia coli." Nat Methods 3(8);623-8. PMID: 16862137

Zhang07: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111


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 Wed Nov 26, 2014, biocyc13.