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Database: UniProt
Entry: HDA_ECOLI
LinkDB: HDA_ECOLI
Original site: 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   30-AUG-2017, entry version 106.
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.,
RA   Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N.,
RA   Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H.,
RA   Oshima T., Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S.,
RA   Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C.,
RA   Yamagata S., Horiuchi T.;
RT   "Construction of a contiguous 874-kb sequence of the Escherichia coli-
RT   K12 genome corresponding to 50.0-68.8 min on the linkage map and
RT   analysis of 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.,
RA   Mau B., 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
RT   MG1655 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
RT   DnaA-ATP hydrolysis.";
RL   J. Biol. Chem. 283:36118-36131(2008).
RN   [5]
RP   FUNCTION, AND DISRUPTION PHENOTYPE.
RC   STRAIN=K12 / C600 / 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-
RT   replicase clamp complex.";
RL   J. Biol. Chem. 280:6528-6536(2005).
RN   [7]
RP   FUNCTION IN PLASMID REPLICATION, SUBCELLULAR LOCATION, INTERACTION
RP   WITH 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
RT   suppresses toxicity of a TrfA peptide from plasmid RK2 and its
RT   relationship to the 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;
RP   LEU-98; GLY-136; ARG-153; GLY-157; ASP-167; ARG-196; 208-LEU--GLN-210;
RP   GLN-210; 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
RT   regulatory 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
CC       (dnaN). Stimulates hydrolysis of ATP-DnaA to ADP-DnaA, rendering
CC       DnaA inactive for reinitiation, a process called regulatory
CC       inhibition of DnaA or RIDA. ADP-binding activates Hda to hydrolyze
CC       DnaA-ATP; Hda monomers bind to ADP with about 200-fold greater
CC       affinity than for ATP. RIDA function can be genetically separated
CC       from viability, suggesting this protein has another function as
CC       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
CC       the RIDA complex (regulatory inactivation of DnaA) of ATP-DnaA,
CC       ADP-Hda and the DNA-loaded beta sliding clamp (dnaN). Interacts
CC       with plasmid IncP-alpha RK2-encoded protein TrfA in strain B /
CC       BL21-DE3. {ECO:0000269|PubMed:12618445,
CC       ECO:0000269|PubMed:15150238, ECO:0000269|PubMed:15611053,
CC       ECO:0000269|PubMed:18977760}.
CC   -!- INTERACTION:
CC       Self; NbExp=2; IntAct=EBI-545453, EBI-545453;
CC       P06134:ada; NbExp=3; IntAct=EBI-545453, EBI-1119501;
CC       P03004:dnaA; NbExp=2; IntAct=EBI-545453, EBI-548951;
CC       P0A988:dnaN; NbExp=8; IntAct=EBI-545453, EBI-542385;
CC   -!- SUBCELLULAR LOCATION: Cell inner membrane
CC       {ECO:0000269|PubMed:12618445}. Note=More protein is found in the
CC       inner than outer membrane fractions.
CC   -!- DISRUPTION PHENOTYPE: Essential in strain C600. Disruption in
CC       MG1655 confers cold-sensitivity with asynchronously replicating
CC       DNA, which is quickly suppressed. Increased levels of plasmid
CC       IncP-alpha RK2 in strain BL21-DE3, increased plasmid replication
CC       in vitro. {ECO:0000269|PubMed:11483528,
CC       ECO:0000269|PubMed:12618445, ECO:0000269|PubMed:22716942}.
CC   -!- MISCELLANEOUS: Starts with a CTG codon.
CC   -!- MISCELLANEOUS: There are about 50 homodimers per cell in strains
CC       C600 and K12 / MG1655.
CC   -!- SIMILARITY: Belongs to the DnaA family. HdA subfamily.
CC       {ECO:0000305}.
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   ProteinModelPortal; P69931; -.
DR   SMR; P69931; -.
DR   BioGrid; 4261436; 149.
DR   DIP; DIP-48006N; -.
DR   IntAct; P69931; 14.
DR   STRING; 316385.ECDH10B_2662; -.
DR   PaxDb; P69931; -.
DR   PRIDE; P69931; -.
DR   EnsemblBacteria; AAC75549; AAC75549; b2496.
DR   EnsemblBacteria; BAA16384; BAA16384; BAA16384.
DR   GeneID; 946977; -.
DR   KEGG; ecj:JW5397; -.
DR   KEGG; eco:b2496; -.
DR   PATRIC; fig|511145.12.peg.2592; -.
DR   EchoBASE; EB3953; -.
DR   EcoGene; EG14201; hda.
DR   eggNOG; ENOG4108KZ1; Bacteria.
DR   eggNOG; COG0593; LUCA.
DR   HOGENOM; HOG000256538; -.
DR   InParanoid; P69931; -.
DR   KO; K10763; -.
DR   PhylomeDB; P69931; -.
DR   BioCyc; EcoCyc:G7313-MONOMER; -.
DR   PRO; PR:P69931; -.
DR   Proteomes; UP000000318; Chromosome.
DR   Proteomes; UP000000625; Chromosome.
DR   GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR   GO; GO:0016020; C:membrane; IDA:EcoCyc.
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; IEA:UniProtKB-KW.
DR   GO; GO:0032297; P:negative regulation of DNA-dependent DNA replication initiation; IMP:EcoCyc.
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; Complete proteome;
KW   Direct protein sequencing; DNA replication; DNA replication inhibitor;
KW   Membrane; Nucleotide-binding; Reference proteome.
FT   CHAIN         1    233       DnaA regulatory inactivator Hda.
FT                                /FTId=PRO_0000114314.
FT   REGION        6     11       Beta clamp binding motif.
FT   MUTAGEN       6      6       Q->A: Severely impaired in beta clamp
FT                                binding and DnaA-ATP hydrolysis, very
FT                                poor growth at 30 degrees Celsius.
FT                                {ECO:0000269|PubMed:15611053,
FT                                ECO:0000269|PubMed:22716942}.
FT   MUTAGEN       7     11       LSLPL->ASAPA: Decreased binding to beta
FT                                clamp. {ECO:0000269|PubMed:15150238}.
FT   MUTAGEN       9     10       LP->AA: Decreased binding to beta clamp.
FT                                {ECO:0000269|PubMed:15150238}.
FT   MUTAGEN       9      9       L->A: Impaired in beta clamp binding and
FT                                DnaA-ATP hydrolysis, very poor growth at
FT                                30 degrees Celsius.
FT                                {ECO:0000269|PubMed:15611053,
FT                                ECO:0000269|PubMed:22716942}.
FT   MUTAGEN      56     56       R->A: Severely impaired in ADP-binding
FT                                but still has beta clamp-binding activity
FT                                in vitro, defective in DnaA-ATP
FT                                hydrolysis in vivo; when associated with
FT                                102-A-A-103.
FT                                {ECO:0000269|PubMed:18977760}.
FT   MUTAGEN      98     98       L->P: No growth at 30 degrees Celsius,
FT                                impaired RIDA.
FT                                {ECO:0000269|PubMed:22716942}.
FT   MUTAGEN     102    103       DN->AA: Impaired in ADP-binding, has beta
FT                                clamp-binding activity in vitro.
FT                                {ECO:0000269|PubMed:18977760}.
FT   MUTAGEN     136    136       G->D: No growth at 30 degrees Celsius,
FT                                impaired RIDA.
FT                                {ECO:0000269|PubMed:22716942}.
FT   MUTAGEN     153    153       R->A,M: Defective in DnaA-ATP hydrolysis,
FT                                binds beta clamp normally, no growth at
FT                                30 degrees Celsius.
FT                                {ECO:0000269|PubMed:15611053,
FT                                ECO:0000269|PubMed:22716942}.
FT   MUTAGEN     157    157       G->V: Grows at 30 degrees Celsius,
FT                                impaired RIDA.
FT                                {ECO:0000269|PubMed:22716942}.
FT   MUTAGEN     167    167       D->N: Grows at 30 degrees Celsius,
FT                                impaired RIDA.
FT                                {ECO:0000269|PubMed:22716942}.
FT   MUTAGEN     196    196       R->Q: Grows at 30 degrees Celsius,
FT                                impaired RIDA.
FT                                {ECO:0000269|PubMed:22716942}.
FT   MUTAGEN     208    210       Missing: No growth at 30 degrees Celsius,
FT                                impaired RIDA.
FT                                {ECO:0000269|PubMed:22716942}.
FT   MUTAGEN     210    210       Q->QLDQ: No growth at 30 degrees Celsius,
FT                                impaired RIDA.
FT                                {ECO:0000269|PubMed:22716942}.
FT   MUTAGEN     212    212       D->N: Grows at 30 degrees Celsius,
FT                                impaired RIDA.
FT                                {ECO:0000269|PubMed:22716942}.
FT   MUTAGEN     233    233       L->F: No growth at 30 degrees Celsius,
FT                                impaired RIDA.
FT                                {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
//
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