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Protein

Antitoxin phd

Gene

phd

Organism
Enterobacteria phage P1 (Bacteriophage P1)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Antitoxin component of a toxin-antitoxin (TA) module. A labile antitoxin that binds to cognate doc toxin and neutralizes its ability to phosphorylate host EF-Tu. Does not reverse phosphorylation. Bacteriophage P1 lysogenizes bacteria as a low-copy number plasmid; phd and doc proteins function in unison to stabilize plasmid number by inducing a lethal response to P1 plasmid prophage loss.
Binds to its own promoter repressing its expression; toxin doc acts as a corepressor or derepressor depending on the ratio, repressing or inducing expression.

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Names & Taxonomyi

Protein namesi
Recommended name:
Antitoxin phd
Alternative name(s):
Addiction protein pdh
Prevent host death protein
Gene namesi
Name:phd
OrganismiEnterobacteria phage P1 (Bacteriophage P1)
Taxonomic identifieri10678 [NCBI]
Taxonomic lineageiVirusesdsDNA viruses, no RNA stageCaudoviralesMyoviridaePunalikevirus
Virus hostiEnterobacteriaceae [TaxID: 543]
Proteomesi
  • UP000008091 Componenti: Genome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi44 – 441F → A: Significantly decreases repressor activity, binds DNA less well, inhibits doc normally. 1 Publication
Mutagenesisi47 – 471Y → A: Decreases repressor activity, binds DNA less well, inhibits doc normally. 1 Publication
Mutagenesisi48 – 481K → M: Decreases repressor activity, binds DNA less well, inhibits doc normally. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 7373Antitoxin phdPRO_0000165279Add
BLAST

Post-translational modificationi

Degraded by the ClpXP protease.

Interactioni

Subunit structurei

Homodimer. Interacts with cognate toxin doc, the exact ratio of doc:phd varies from 1:1 to 1:3. Interaction with doc prevents both kinase activity and dephosphorylation of EF-Tu.4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
docQ062594EBI-2908787,EBI-2908816

Protein-protein interaction databases

IntActiQ06253. 1 interaction.

Structurei

Secondary structure

1
73
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 54Combined sources
Helixi6 – 116Combined sources
Helixi13 – 219Combined sources
Beta strandi26 – 294Combined sources
Beta strandi31 – 333Combined sources
Beta strandi36 – 405Combined sources
Helixi41 – 499Combined sources
Turni50 – 534Combined sources
Helixi55 – 628Combined sources
Helixi64 – 707Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3DD7X-ray1.70B/D51-73[»]
3HRYX-ray2.25A/B/C1-73[»]
3HS2X-ray2.20A/B/C/D/E/F/G/H1-58[»]
3K33X-ray2.40B/C/D1-73[»]
3KH2X-ray2.71E/F/G/H1-73[»]
4ZLXX-ray2.31A/B1-45[»]
4ZM0X-ray3.17A/B/C/D1-73[»]
4ZM2X-ray3.88A/B/C/D1-73[»]
DisProtiDP00288.
ProteinModelPortaliQ06253.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ06253.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni50 – 7324Sufficient for antitoxin activity, its presence prevents formation of a doc-EF-Tu complexAdd
BLAST

Sequence similaritiesi

Belongs to the phD/YefM antitoxin family.Curated

Phylogenomic databases

KOiK19165.

Family and domain databases

Gene3Di3.40.1620.10. 1 hit.
InterProiIPR006442. Antitoxin_Phd/YefM.
[Graphical view]
PfamiPF02604. PhdYeFM_antitox. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01552. phd_fam. 1 hit.

Sequencei

Sequence statusi: Complete.

Q06253-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQSINFRTAR GNLSEVLNNV EAGEEVEITR RGREPAVIVS KATFEAYKKA
60 70
ALDAEFASLF DTLDSTNKEL VNR
Length:73
Mass (Da):8,133
Last modified:February 1, 1995 - v1
Checksum:i5FDB9D3565440050
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M95666 Unassigned DNA. Translation: AAA16932.1.
AF234172 Genomic DNA. Translation: AAQ14074.1.
PIRiS40015.
RefSeqiYP_006570.1. NC_005856.1.

Genome annotation databases

GeneIDi2777473.
KEGGivg:2777473.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M95666 Unassigned DNA. Translation: AAA16932.1.
AF234172 Genomic DNA. Translation: AAQ14074.1.
PIRiS40015.
RefSeqiYP_006570.1. NC_005856.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3DD7X-ray1.70B/D51-73[»]
3HRYX-ray2.25A/B/C1-73[»]
3HS2X-ray2.20A/B/C/D/E/F/G/H1-58[»]
3K33X-ray2.40B/C/D1-73[»]
3KH2X-ray2.71E/F/G/H1-73[»]
4ZLXX-ray2.31A/B1-45[»]
4ZM0X-ray3.17A/B/C/D1-73[»]
4ZM2X-ray3.88A/B/C/D1-73[»]
DisProtiDP00288.
ProteinModelPortaliQ06253.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ06253. 1 interaction.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi2777473.
KEGGivg:2777473.

Phylogenomic databases

KOiK19165.

Miscellaneous databases

EvolutionaryTraceiQ06253.

Family and domain databases

Gene3Di3.40.1620.10. 1 hit.
InterProiIPR006442. Antitoxin_Phd/YefM.
[Graphical view]
PfamiPF02604. PhdYeFM_antitox. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01552. phd_fam. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Plasmid addiction genes of bacteriophage P1: doc, which causes cell death on curing of prophage, and phd, which prevents host death when prophage is retained."
    Lehnherr H., Maguin E., Jafri S., Yarmolinsky M.B.
    J. Mol. Biol. 233:414-428(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "Addiction protein Phd of plasmid prophage P1 is a substrate of the ClpXP serine protease of Escherichia coli."
    Lehnherr H., Yarmolinsky M.B.
    Proc. Natl. Acad. Sci. U.S.A. 92:3274-3277(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: CLEAVAGE BY THE CLPXP PROTEASE.
  4. "Corepression of the P1 addiction operon by Phd and Doc."
    Magnuson R., Yarmolinsky M.B.
    J. Bacteriol. 180:6342-6351(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A TRANSCRIPTION REGULATOR, DNA-BINDING, SUBUNIT.
  5. "Bacterial addiction module toxin Doc inhibits translation elongation through its association with the 30S ribosomal subunit."
    Liu M., Zhang Y., Inouye M., Woychik N.A.
    Proc. Natl. Acad. Sci. U.S.A. 105:5885-5890(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS AN ANTITOXIN, SUBUNIT.
  6. "The Fic protein Doc uses an inverted substrate to phosphorylate and inactivate EF-Tu."
    Castro-Roa D., Garcia-Pino A., De Gieter S., van Nuland N.A., Loris R., Zenkin N.
    Nat. Chem. Biol. 9:811-817(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS ANTITOXIN, DOMAIN.
  7. "Doc of prophage P1 is inhibited by its antitoxin partner Phd through fold complementation."
    Garcia-Pino A., Christensen-Dalsgaard M., Wyns L., Yarmolinsky M., Magnuson R.D., Gerdes K., Loris R.
    J. Biol. Chem. 283:30821-30827(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 51-73 IN COMPLEX WITH TOXIN DOC.
  8. "Allostery and intrinsic disorder mediate transcription regulation by conditional cooperativity."
    Garcia-Pino A., Balasubramanian S., Wyns L., Gazit E., De Greve H., Magnuson R.D., Charlier D., van Nuland N.A., Loris R.
    Cell 142:101-111(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS), MODE OF TRANSCRIPTION REGULATION, MUTAGENESIS OF PHE-44; TYR-47 AND LYS-48.
  9. "Crystal structures of Phd-Doc, HigA, and YeeU establish multiple evolutionary links between microbial growth-regulating toxin-antitoxin systems."
    Arbing M.A., Handelman S.K., Kuzin A.P., Verdon G., Wang C., Su M., Rothenbacher F.P., Abashidze M., Liu M., Hurley J.M., Xiao R., Acton T., Inouye M., Montelione G.T., Woychik N.A., Hunt J.F.
    Structure 18:996-1010(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.71 ANGSTROMS), SUBUNIT.

Entry informationi

Entry nameiPHD_BPP1
AccessioniPrimary (citable) accession number: Q06253
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: June 8, 2016
This is version 81 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

The concentration of phd in P1 lysogens is far greater than that of the toxin it antagonizes. Such an excess may assure the well-being of carriers of the addicting plasmid.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.