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Protein

DnaA regulatory inactivator Hda

Gene

hda

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Mediates the interactions of DNA replication initiator protein DnaA with DNA polymerase subunit beta sliding clamp (dnaN). Stimulates hydrolysis of ATP-DnaA to ADP-DnaA, rendering DnaA inactive for reinitiation, a process called regulatory inhibition of DnaA or RIDA. ADP-binding activates Hda to hydrolyze DnaA-ATP; Hda monomers bind to ADP with about 200-fold greater affinity than for ATP. RIDA function can be genetically separated from viability, suggesting this protein has another function as well.
Suppresses the toxic effect of overexpressing a TrfA N-terminal 163 residue fragment. Inhibits inner membrane-associated plasmid IncP-alpha RK2 replication probably by interacting with plasmid-encoded TrfA.

GO - Molecular functioni

GO - Biological processi

  • DNA replication Source: UniProtKB-HAMAP
  • negative regulation of DNA-dependent DNA replication initiation Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

DNA replication inhibitor

Keywords - Biological processi

DNA replication

Keywords - Ligandi

Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:G7313-MONOMER.
ECOL316407:JW5397-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DnaA regulatory inactivator Hda
Alternative name(s):
DnaA paralog
Short name:
Dp
Gene namesi
Name:hda
Synonyms:idaB, yfgE
Ordered Locus Names:b2496, JW5397
ORF Names:f248c
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG14201. hda.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
  • membrane Source: EcoCyc
  • plasma membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cell inner membrane, Cell membrane, Membrane

Pathology & Biotechi

Disruption phenotypei

Essential in strain C600. Disruption in MG1655 confers cold-sensitivity with asynchronously replicating DNA, which is quickly suppressed. Increased levels of plasmid IncP-alpha RK2 in strain BL21-DE3, increased plasmid replication in vitro.3 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi6Q → A: Severely impaired in beta clamp binding and DnaA-ATP hydrolysis, very poor growth at 30 degrees Celsius. 2 Publications1
Mutagenesisi7 – 11LSLPL → ASAPA: Decreased binding to beta clamp. 1 Publication5
Mutagenesisi9 – 10LP → AA: Decreased binding to beta clamp. 1 Publication2
Mutagenesisi9L → A: Impaired in beta clamp binding and DnaA-ATP hydrolysis, very poor growth at 30 degrees Celsius. 2 Publications1
Mutagenesisi56R → A: Severely impaired in ADP-binding but still has beta clamp-binding activity in vitro, defective in DnaA-ATP hydrolysis in vivo; when associated with 102-A-A-103. 1 Publication1
Mutagenesisi98L → P: No growth at 30 degrees Celsius, impaired RIDA. 1 Publication1
Mutagenesisi102 – 103DN → AA: Impaired in ADP-binding, has beta clamp-binding activity in vitro. 1 Publication2
Mutagenesisi136G → D: No growth at 30 degrees Celsius, impaired RIDA. 1 Publication1
Mutagenesisi153R → A or M: Defective in DnaA-ATP hydrolysis, binds beta clamp normally, no growth at 30 degrees Celsius. 2 Publications1
Mutagenesisi157G → V: Grows at 30 degrees Celsius, impaired RIDA. 1 Publication1
Mutagenesisi167D → N: Grows at 30 degrees Celsius, impaired RIDA. 1 Publication1
Mutagenesisi196R → Q: Grows at 30 degrees Celsius, impaired RIDA. 1 Publication1
Mutagenesisi208 – 210Missing : No growth at 30 degrees Celsius, impaired RIDA. 1 Publication3
Mutagenesisi210Q → QLDQ: No growth at 30 degrees Celsius, impaired RIDA. 1 Publication1
Mutagenesisi212D → N: Grows at 30 degrees Celsius, impaired RIDA. 1 Publication1
Mutagenesisi233L → F: No growth at 30 degrees Celsius, impaired RIDA. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001143141 – 233DnaA regulatory inactivator HdaAdd BLAST233

Proteomic databases

PaxDbiP69931.
PRIDEiP69931.

Interactioni

Subunit structurei

The active form seems to be an ADP-bound monomer; apo-Hda forms homo-multimers that do not hydrolzye DnaA-bound ATP. Forms the RIDA complex (regulatory inactivation of DnaA) of ATP-DnaA, ADP-Hda and the DNA-loaded beta sliding clamp (dnaN). Interacts with plasmid IncP-alpha RK2-encoded protein TrfA in strain B / BL21-DE3.4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
itself2EBI-545453,EBI-545453
adaP061343EBI-545453,EBI-1119501
dnaAP030042EBI-545453,EBI-548951
dnaNP0A9888EBI-545453,EBI-542385

Protein-protein interaction databases

BioGridi4261436. 149 interactors.
DIPiDIP-48006N.
IntActiP69931. 14 interactors.
STRINGi511145.b2496.

Structurei

3D structure databases

ProteinModelPortaliP69931.
SMRiP69931.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni6 – 11Beta clamp binding motif6

Sequence similaritiesi

Belongs to the DnaA family. HdA subfamily.Curated

Phylogenomic databases

eggNOGiENOG4108KZ1. Bacteria.
COG0593. LUCA.
HOGENOMiHOG000256538.
InParanoidiP69931.
KOiK10763.
PhylomeDBiP69931.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_01158. Hda. 1 hit.
InterProiIPR020591. Chromosome_initiator_DnaA-like.
IPR013317. DnaA.
IPR017788. Hda.
IPR022864. Hda_Enterobact.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF00308. Bac_DnaA. 1 hit.
[Graphical view]
PRINTSiPR00051. DNAA.
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR03420. DnaA_homol_Hda. 1 hit.

Sequencei

Sequence statusi: Complete.

P69931-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNTPAQLSLP LYLPDDETFA SFWPGDNSSL LAALQNVLRQ EHSGYIYLWA
60 70 80 90 100
REGAGRSHLL HAACAELSQR GDAVGYVPLD KRTWFVPEVL DGMEHLSLVC
110 120 130 140 150
IDNIECIAGD ELWEMAIFDL YNRILESGKT RLLITGDRPP RQLNLGLPDL
160 170 180 190 200
ASRLDWGQIY KLQPLSDEDK LQALQLRARL RGFELPEDVG RFLLKRLDRE
210 220 230
MRTLFMTLDQ LDRASITAQR KLTIPFVKEI LKL
Length:233
Mass (Da):26,633
Last modified:November 24, 2009 - v2
Checksum:iD25C7CDF31DAF7DC
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC75549.2.
AP009048 Genomic DNA. Translation: BAA16384.1.
PIRiG65025.
RefSeqiNP_416991.2. NC_000913.3.

Genome annotation databases

EnsemblBacteriaiAAC75549; AAC75549; b2496.
BAA16384; BAA16384; BAA16384.
GeneIDi946977.
KEGGiecj:JW5397.
eco:b2496.
PATRICi32120379. VBIEscCol129921_2592.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC75549.2.
AP009048 Genomic DNA. Translation: BAA16384.1.
PIRiG65025.
RefSeqiNP_416991.2. NC_000913.3.

3D structure databases

ProteinModelPortaliP69931.
SMRiP69931.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261436. 149 interactors.
DIPiDIP-48006N.
IntActiP69931. 14 interactors.
STRINGi511145.b2496.

Proteomic databases

PaxDbiP69931.
PRIDEiP69931.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75549; AAC75549; b2496.
BAA16384; BAA16384; BAA16384.
GeneIDi946977.
KEGGiecj:JW5397.
eco:b2496.
PATRICi32120379. VBIEscCol129921_2592.

Organism-specific databases

EchoBASEiEB3953.
EcoGeneiEG14201. hda.

Phylogenomic databases

eggNOGiENOG4108KZ1. Bacteria.
COG0593. LUCA.
HOGENOMiHOG000256538.
InParanoidiP69931.
KOiK10763.
PhylomeDBiP69931.

Enzyme and pathway databases

BioCyciEcoCyc:G7313-MONOMER.
ECOL316407:JW5397-MONOMER.

Miscellaneous databases

PROiP69931.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_01158. Hda. 1 hit.
InterProiIPR020591. Chromosome_initiator_DnaA-like.
IPR013317. DnaA.
IPR017788. Hda.
IPR022864. Hda_Enterobact.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF00308. Bac_DnaA. 1 hit.
[Graphical view]
PRINTSiPR00051. DNAA.
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR03420. DnaA_homol_Hda. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiHDA_ECOLI
AccessioniPrimary (citable) accession number: P69931
Secondary accession number(s): P76570, P76979
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 4, 2005
Last sequence update: November 24, 2009
Last modified: November 2, 2016
This is version 98 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Starts with a CTG codon.
There are about 50 homodimers per cell in strains C600 and K12 / MG1655.

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.