HDA_ECOLI
ID HDA_ECOLI Reviewed; 233 AA.
AC P69931; P76570; P76979;
DT 04-JAN-2005, integrated into UniProtKB/Swiss-Prot.
DT 24-NOV-2009, sequence version 2.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=DnaA regulatory inactivator Hda;
DE AltName: Full=DnaA paralog;
DE Short=Dp;
GN Name=hda; Synonyms=idaB, yfgE; OrderedLocusNames=b2496, JW5397;
GN ORFNames=f248c;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9205837; DOI=10.1093/dnares/4.2.91;
RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K.,
RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S.,
RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H.,
RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12
RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of
RT its sequence features.";
RL DNA Res. 4:91-113(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP PROTEIN SEQUENCE OF 1-5, IDENTIFICATION OF START CODON, ADP-BINDING,
RP SUBUNIT, IDENTIFICATION IN RIDA COMPLEX, AND MUTAGENESIS OF ARG-56 AND
RP 102-ASP-ASN-103.
RX PubMed=18977760; DOI=10.1074/jbc.m803158200;
RA Su'etsugu M., Nakamura K., Keyamura K., Kudo Y., Katayama T.;
RT "Hda monomerization by ADP binding promotes replicase clamp-mediated DnaA-
RT ATP hydrolysis.";
RL J. Biol. Chem. 283:36118-36131(2008).
RN [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / C600 / CR34 / ATCC 23724 / DSM 3925 / LMG 3041 / NCIB 10222;
RX PubMed=11483528; DOI=10.1093/emboj/20.15.4253;
RA Kato J., Katayama T.;
RT "Hda, a novel DnaA-related protein, regulates the replication cycle in
RT Escherichia coli.";
RL EMBO J. 20:4253-4262(2001).
RN [6]
RP SUBUNIT, PROTEIN CONCENTRATION, AND MUTAGENESIS OF GLN-6; LEU-9 AND
RP ARG-153.
RX PubMed=15611053; DOI=10.1074/jbc.m412060200;
RA Su'etsugu M., Shimuta T.R., Ishida T., Kawakami H., Katayama T.;
RT "Protein associations in DnaA-ATP hydrolysis mediated by the Hda-replicase
RT clamp complex.";
RL J. Biol. Chem. 280:6528-6536(2005).
RN [7]
RP FUNCTION IN PLASMID REPLICATION, SUBCELLULAR LOCATION, INTERACTION WITH
RP TRFA, AND DISRUPTION PHENOTYPE.
RC STRAIN=B / BL21-DE3;
RX PubMed=12618445; DOI=10.1128/jb.185.6.1817-1824.2003;
RA Kim P.D., Banack T., Lerman D.M., Tracy J.C., Camara J.E., Crooke E.,
RA Oliver D., Firshein W.;
RT "Identification of a novel membrane-associated gene product that suppresses
RT toxicity of a TrfA peptide from plasmid RK2 and its relationship to the
RT DnaA host initiation protein.";
RL J. Bacteriol. 185:1817-1824(2003).
RN [8]
RP INTERACTION WITH BETA SLIDING CLAMP (DNAN), AND MUTAGENESIS OF
RP 7-LEU--LEU-11 AND 9-LEU-PRO-10.
RX PubMed=15150238; DOI=10.1128/jb.186.11.3508-3515.2004;
RA Kurz M., Dalrymple B., Wijffels G., Kongsuwan K.;
RT "Interaction of the sliding clamp beta-subunit and Hda, a DnaA-related
RT protein.";
RL J. Bacteriol. 186:3508-3515(2004).
RN [9]
RP FUNCTION IN RIDA.
RX PubMed=12730188; DOI=10.1128/jb.185.10.3244-3248.2003;
RA Camara J.E., Skarstad K., Crooke E.;
RT "Controlled initiation of chromosomal replication in Escherichia coli
RT requires functional Hda protein.";
RL J. Bacteriol. 185:3244-3248(2003).
RN [10]
RP FUNCTION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF GLN-6; LEU-9; LEU-98;
RP GLY-136; ARG-153; GLY-157; ASP-167; ARG-196; 208-LEU--GLN-210; GLN-210;
RP ASP-212 AND LEU-233.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=22716942; DOI=10.1111/j.1365-2958.2012.08129.x;
RA Baxter J.C., Sutton M.D.;
RT "Evidence for roles of the Escherichia coli Hda protein beyond regulatory
RT inactivation of DnaA.";
RL Mol. Microbiol. 85:648-668(2012).
CC -!- FUNCTION: Mediates the interactions of DNA replication initiator
CC protein DnaA with DNA polymerase subunit beta sliding clamp (dnaN).
CC Stimulates hydrolysis of ATP-DnaA to ADP-DnaA, rendering DnaA inactive
CC for reinitiation, a process called regulatory inhibition of DnaA or
CC RIDA. ADP-binding activates Hda to hydrolyze DnaA-ATP; Hda monomers
CC bind to ADP with about 200-fold greater affinity than for ATP. RIDA
CC function can be genetically separated from viability, suggesting this
CC protein has another function as well.
CC -!- FUNCTION: Suppresses the toxic effect of overexpressing a TrfA N-
CC terminal 163 residue fragment. Inhibits inner membrane-associated
CC plasmid IncP-alpha RK2 replication probably by interacting with
CC plasmid-encoded TrfA.
CC -!- SUBUNIT: The active form seems to be an ADP-bound monomer; apo-Hda
CC forms homo-multimers that do not hydrolzye DnaA-bound ATP. Forms the
CC RIDA complex (regulatory inactivation of DnaA) of ATP-DnaA, ADP-Hda and
CC the DNA-loaded beta sliding clamp (dnaN). Interacts with plasmid IncP-
CC alpha RK2-encoded protein TrfA in strain B / BL21-DE3.
CC {ECO:0000269|PubMed:12618445, ECO:0000269|PubMed:15150238,
CC ECO:0000269|PubMed:15611053, ECO:0000269|PubMed:18977760}.
CC -!- INTERACTION:
CC P69931; P06134: ada; NbExp=3; IntAct=EBI-545453, EBI-1119501;
CC P69931; P03004: dnaA; NbExp=2; IntAct=EBI-545453, EBI-548951;
CC P69931; P0A988: dnaN; NbExp=9; IntAct=EBI-545453, EBI-542385;
CC P69931; P69931: hda; NbExp=2; IntAct=EBI-545453, EBI-545453;
CC -!- SUBCELLULAR LOCATION: Cell inner membrane
CC {ECO:0000269|PubMed:12618445}. Note=More protein is found in the inner
CC than outer membrane fractions.
CC -!- DISRUPTION PHENOTYPE: Essential in strain C600. Disruption in MG1655
CC confers cold-sensitivity with asynchronously replicating DNA, which is
CC quickly suppressed. Increased levels of plasmid IncP-alpha RK2 in
CC strain BL21-DE3, increased plasmid replication in vitro.
CC {ECO:0000269|PubMed:11483528, ECO:0000269|PubMed:12618445,
CC ECO:0000269|PubMed:22716942}.
CC -!- MISCELLANEOUS: Starts with a CTG codon.
CC -!- MISCELLANEOUS: There are about 50 homodimers per cell in strains C600
CC and K12 / MG1655.
CC -!- SIMILARITY: Belongs to the DnaA family. HdA subfamily. {ECO:0000305}.
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DR EMBL; U00096; AAC75549.2; -; Genomic_DNA.
DR EMBL; AP009048; BAA16384.1; -; Genomic_DNA.
DR PIR; G65025; G65025.
DR RefSeq; NP_416991.2; NC_000913.3.
DR RefSeq; WP_001307333.1; NZ_JACEFS010000004.1.
DR AlphaFoldDB; P69931; -.
DR SMR; P69931; -.
DR BioGRID; 4261436; 151.
DR BioGRID; 851316; 5.
DR ComplexPortal; CPX-1945; Regulatory inactivation of dnaA (RIDA) complex.
DR ComplexPortal; CPX-1954; hda-beta clamp complex.
DR DIP; DIP-48006N; -.
DR IntAct; P69931; 14.
DR STRING; 511145.b2496; -.
DR jPOST; P69931; -.
DR PaxDb; P69931; -.
DR PRIDE; P69931; -.
DR EnsemblBacteria; AAC75549; AAC75549; b2496.
DR EnsemblBacteria; BAA16384; BAA16384; BAA16384.
DR GeneID; 66673639; -.
DR GeneID; 946977; -.
DR KEGG; ecj:JW5397; -.
DR KEGG; eco:b2496; -.
DR PATRIC; fig|511145.12.peg.2592; -.
DR EchoBASE; EB3953; -.
DR eggNOG; COG0593; Bacteria.
DR InParanoid; P69931; -.
DR OMA; DWGQIYR; -.
DR PhylomeDB; P69931; -.
DR BioCyc; EcoCyc:G7313-MON; -.
DR PRO; PR:P69931; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:1990085; C:Hda-beta clamp complex; IPI:ComplexPortal.
DR GO; GO:0016020; C:membrane; IDA:EcoCyc.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:1990078; C:replication inhibiting complex; IPI:ComplexPortal.
DR GO; GO:0043531; F:ADP binding; IDA:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0006260; P:DNA replication; IBA:GO_Central.
DR GO; GO:0006270; P:DNA replication initiation; IBA:GO_Central.
DR GO; GO:0032297; P:negative regulation of DNA-templated DNA replication initiation; IMP:EcoCyc.
DR GO; GO:0030174; P:regulation of DNA-templated DNA replication initiation; IC:ComplexPortal.
DR Gene3D; 3.40.50.300; -; 1.
DR HAMAP; MF_01158; Hda; 1.
DR InterPro; IPR020591; Chromosome_initiator_DnaA-like.
DR InterPro; IPR013317; DnaA.
DR InterPro; IPR017788; Hda.
DR InterPro; IPR022864; Hda_Enterobact.
DR InterPro; IPR027417; P-loop_NTPase.
DR Pfam; PF00308; Bac_DnaA; 1.
DR PRINTS; PR00051; DNAA.
DR SUPFAM; SSF52540; SSF52540; 1.
DR TIGRFAMs; TIGR03420; DnaA_homol_Hda; 1.
PE 1: Evidence at protein level;
KW Cell inner membrane; Cell membrane; Direct protein sequencing;
KW DNA replication; DNA replication inhibitor; Membrane; Nucleotide-binding;
KW Reference proteome.
FT CHAIN 1..233
FT /note="DnaA regulatory inactivator Hda"
FT /id="PRO_0000114314"
FT REGION 6..11
FT /note="Beta clamp binding motif"
FT MUTAGEN 6
FT /note="Q->A: Severely impaired in beta clamp binding and
FT DnaA-ATP hydrolysis, very poor growth at 30 degrees
FT Celsius."
FT /evidence="ECO:0000269|PubMed:15611053,
FT ECO:0000269|PubMed:22716942"
FT MUTAGEN 7..11
FT /note="LSLPL->ASAPA: Decreased binding to beta clamp."
FT /evidence="ECO:0000269|PubMed:15150238"
FT MUTAGEN 9..10
FT /note="LP->AA: Decreased binding to beta clamp."
FT /evidence="ECO:0000269|PubMed:15150238"
FT MUTAGEN 9
FT /note="L->A: Impaired in beta clamp binding and DnaA-ATP
FT hydrolysis, very poor growth at 30 degrees Celsius."
FT /evidence="ECO:0000269|PubMed:15611053,
FT ECO:0000269|PubMed:22716942"
FT MUTAGEN 56
FT /note="R->A: Severely impaired in ADP-binding but still has
FT beta clamp-binding activity in vitro, defective in DnaA-ATP
FT hydrolysis in vivo; when associated with 102-A-A-103."
FT /evidence="ECO:0000269|PubMed:18977760"
FT MUTAGEN 98
FT /note="L->P: No growth at 30 degrees Celsius, impaired
FT RIDA."
FT /evidence="ECO:0000269|PubMed:22716942"
FT MUTAGEN 102..103
FT /note="DN->AA: Impaired in ADP-binding, has beta clamp-
FT binding activity in vitro."
FT /evidence="ECO:0000269|PubMed:18977760"
FT MUTAGEN 136
FT /note="G->D: No growth at 30 degrees Celsius, impaired
FT RIDA."
FT /evidence="ECO:0000269|PubMed:22716942"
FT MUTAGEN 153
FT /note="R->A,M: Defective in DnaA-ATP hydrolysis, binds beta
FT clamp normally, no growth at 30 degrees Celsius."
FT /evidence="ECO:0000269|PubMed:15611053,
FT ECO:0000269|PubMed:22716942"
FT MUTAGEN 157
FT /note="G->V: Grows at 30 degrees Celsius, impaired RIDA."
FT /evidence="ECO:0000269|PubMed:22716942"
FT MUTAGEN 167
FT /note="D->N: Grows at 30 degrees Celsius, impaired RIDA."
FT /evidence="ECO:0000269|PubMed:22716942"
FT MUTAGEN 196
FT /note="R->Q: Grows at 30 degrees Celsius, impaired RIDA."
FT /evidence="ECO:0000269|PubMed:22716942"
FT MUTAGEN 208..210
FT /note="Missing: No growth at 30 degrees Celsius, impaired
FT RIDA."
FT /evidence="ECO:0000269|PubMed:22716942"
FT MUTAGEN 210
FT /note="Q->QLDQ: No growth at 30 degrees Celsius, impaired
FT RIDA."
FT /evidence="ECO:0000269|PubMed:22716942"
FT MUTAGEN 212
FT /note="D->N: Grows at 30 degrees Celsius, impaired RIDA."
FT /evidence="ECO:0000269|PubMed:22716942"
FT MUTAGEN 233
FT /note="L->F: No growth at 30 degrees Celsius, impaired
FT RIDA."
FT /evidence="ECO:0000269|PubMed:22716942"
SQ SEQUENCE 233 AA; 26633 MW; D25C7CDF31DAF7DC CRC64;
MNTPAQLSLP LYLPDDETFA SFWPGDNSSL LAALQNVLRQ EHSGYIYLWA REGAGRSHLL
HAACAELSQR GDAVGYVPLD KRTWFVPEVL DGMEHLSLVC IDNIECIAGD ELWEMAIFDL
YNRILESGKT RLLITGDRPP RQLNLGLPDL ASRLDWGQIY KLQPLSDEDK LQALQLRARL
RGFELPEDVG RFLLKRLDRE MRTLFMTLDQ LDRASITAQR KLTIPFVKEI LKL
