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Protein

Coupling protein TraD

Gene

traD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Conjugative DNA transfer (CDT) is the unidirectional transfer of ssDNA plasmid from a donor to a recipient cell. It is the central mechanism by which antibiotic resistance and virulence factors are propagated in bacterial populations. Couples the transferosome to a type IV secretion system. Probably forms a pore through which single-stranded plasmid DNA is transferred to the secretion system. The last 37 residues are important for determining plasmid specificity and transfer efficiency, with additional specificity conferred by the TraD-TraM pair.1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi192 – 1998ATPSequence analysis

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Conjugation

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Coupling protein TraD
Alternative name(s):
DNA transport protein TraD
Gene namesi
Name:traD
Ordered Locus Names:ECOK12F102
Encoded oniPlasmid F14 Publications
Plasmid p1658/971 Publication
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Subcellular locationi

  • Cell inner membrane 1 Publication; Multi-pass membrane protein 1 Publication

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 2727Cytoplasmic1 PublicationAdd
BLAST
Transmembranei28 – 4720HelicalCuratedAdd
BLAST
Topological domaini48 – 10457Periplasmic1 PublicationAdd
BLAST
Transmembranei105 – 13026HelicalCuratedAdd
BLAST
Topological domaini131 – 717587Cytoplasmic1 PublicationAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell inner membrane, Cell membrane, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi681 – 71737WQQEN…PGDDF → CNRKIIRTSSSRCSVVKR: 1000-fold increase in the transfer frequency of plasmids R388 and RSF1010, a 10,000-fold reduction in F plasmid transfer frequency. 1 PublicationAdd
BLAST
Mutagenesisi710 – 7178Missing : Loss of interaction with TraM, 1000-fold decrease in conjugation. 1 Publication
Mutagenesisi712 – 7121E → K: No change in conjugation efficiency. Partially rescues a TraM K-99 mutation. 1 Publication
Mutagenesisi715 – 7151D → K: 10-fold decrease in conjugation efficiency. 1 Publication
Mutagenesisi717 – 7171F → A: 5000-fold decrease in conjugation efficiency. 1 Publication
Mutagenesisi717 – 7171F → FG: 1000-fold decrease in conjugation efficiency. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 717717Coupling protein TraDPRO_0000068448Add
BLAST

Proteomic databases

PRIDEiP09130.

Interactioni

Subunit structurei

Interacts with relaxosome component TraM. May form a hexamer in the membrane.3 Publications

Protein-protein interaction databases

DIPiDIP-27652N.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3D8AX-ray2.55S/T/U/V/W/X/Y/Z708-717[»]
ProteinModelPortaliP09130.
SMRiP09130. Positions 143-577.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP09130.

Family & Domainsi

Sequence similaritiesi

Belongs to the TrwB coupling protein family.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

OMAiSVINDKK.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR027417. P-loop_NTPase.
IPR014128. T4SS_TraD.
IPR019476. T4SS_TraD_DNA-bd.
IPR022585. TraD_N.
[Graphical view]
PfamiPF12615. TraD_N. 1 hit.
PF10412. TrwB_AAD_bind. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR02759. TraD_Ftype. 1 hit.

Sequencei

Sequence statusi: Complete.

P09130-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSFNAKDMTQ GGQIASMRIR MFSQIANIML YCLFIFFWIL VGLVLWIKIS
60 70 80 90 100
WQTFVNGCIY WWCTTLEGMR DLIKSQPVYE IQYYGKTFRM NAAQVLHDKY
110 120 130 140 150
MIWCSEQLWS AFVLAAVVAL VICLITFFVV SWILGRQGKQ QSENEVTGGR
160 170 180 190 200
QLTDNPKDVA RMLKKDGKDS DIRIGDLPII RDSEIQNFCL HGTVGAGKSE
210 220 230 240 250
VIRRLANYAR QRGDMVVIYD RSGEFVKSYY DPSIDKILNP LDARCAAWDL
260 270 280 290 300
WKECLTQPDF DNTANTLIPM GTKEDPFWQG SGRTIFAEAA YLMRNDPNRS
310 320 330 340 350
YSKLVDTLLS IKIEKLRTYL RNSPAANLVE EKIEKTAISI RAVLTNYVKA
360 370 380 390 400
IRYLQGIEHN GEPFTIRDWM RGVREDQKNG WLFISSNADT HASLKPVISM
410 420 430 440 450
WLSIAIRGLL AMGENRNRRV WFFCDELPTL HKLPDLVEIL PEARKFGGCY
460 470 480 490 500
VFGIQSYAQL EDIYGEKAAA SLFDVMNTRA FFRSPSHKIA EFAAGEIGEK
510 520 530 540 550
EHLKASEQYS YGADPVRDGV STGKDMERQT LVSYSDIQSL PDLTCYVTLP
560 570 580 590 600
GPYPAVKLSL KYQTRPKVAP EFIPRDINPE MENRLSAVLA AREAEGRQMA
610 620 630 640 650
SLFEPDVPEV VSGEDVTQAE QPQQPVSPAI NDKKSDSGVN VPAGGIEQEL
660 670 680 690 700
KMKPEEEMEQ QLPPGISESG EVVDMAAYEA WQQENHPDIQ QQMQRREEVN
710
INVHRERGED VEPGDDF
Length:717
Mass (Da):81,489
Last modified:May 10, 2005 - v4
Checksum:iEA43168766F3E6F3
GO

Sequence cautioni

The sequence AAC44181.2 differs from that shown. Reason: Erroneous termination at position 718. Translated as stop.Curated
The sequence CAA30013.1 differs from that shown. Reason: Frameshift at position 19. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti19 – 6244IRMFS…CIYWW → YPHVQPDRQYHALLPVYFFL DTRWSGFMDKISWTDVVNGL FTV in AAA83928 (PubMed:2680768).CuratedAdd
BLAST
Sequence conflicti190 – 1901L → R in AAA83928 (PubMed:2680768).Curated
Sequence conflicti269 – 2702PM → RD in AAA83928 (PubMed:2680768).Curated
Sequence conflicti321 – 3255RNSPA → VIHRQ in AAA83928 (PubMed:2680768).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti396 – 3961P → L in traD39; temperature-sensitive. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M29254 Genomic DNA. Translation: AAA83928.1.
U01159 Genomic DNA. Translation: AAC44181.2. Different termination.
AJ011707 Genomic DNA. Translation: CAA09749.1.
AP001918 Genomic DNA. Translation: BAA97972.1.
AF550679 Genomic DNA. Translation: AAO49544.1.
X06915 Genomic DNA. Translation: CAA30013.1. Frameshift.
X57428 Genomic DNA. Translation: CAA40674.1.
X57431 Genomic DNA. Translation: CAA40678.1.
M54796 Genomic DNA. Translation: AAA98083.1.
PIRiJS0293. BVECAD.
RefSeqiNP_061481.1. NC_002483.1.
NP_862947.1. NC_004998.1.
WP_000009350.1. NZ_CP014273.1.
YP_009060132.1. NC_024956.1.
YP_009062862.1. NC_025014.1.
YP_009068320.1. NC_025139.1.
YP_009070586.1. NC_025175.1.

Genome annotation databases

GeneIDi1263585.
1446510.
20466888.
20468912.
20491450.
20492654.
KEGGipg:1263585.
pg:1446510.
pg:20466888.
pg:20468912.
pg:20491450.
pg:20492654.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M29254 Genomic DNA. Translation: AAA83928.1.
U01159 Genomic DNA. Translation: AAC44181.2. Different termination.
AJ011707 Genomic DNA. Translation: CAA09749.1.
AP001918 Genomic DNA. Translation: BAA97972.1.
AF550679 Genomic DNA. Translation: AAO49544.1.
X06915 Genomic DNA. Translation: CAA30013.1. Frameshift.
X57428 Genomic DNA. Translation: CAA40674.1.
X57431 Genomic DNA. Translation: CAA40678.1.
M54796 Genomic DNA. Translation: AAA98083.1.
PIRiJS0293. BVECAD.
RefSeqiNP_061481.1. NC_002483.1.
NP_862947.1. NC_004998.1.
WP_000009350.1. NZ_CP014273.1.
YP_009060132.1. NC_024956.1.
YP_009062862.1. NC_025014.1.
YP_009068320.1. NC_025139.1.
YP_009070586.1. NC_025175.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3D8AX-ray2.55S/T/U/V/W/X/Y/Z708-717[»]
ProteinModelPortaliP09130.
SMRiP09130. Positions 143-577.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-27652N.

Proteomic databases

PRIDEiP09130.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1263585.
1446510.
20466888.
20468912.
20491450.
20492654.
KEGGipg:1263585.
pg:1446510.
pg:20466888.
pg:20468912.
pg:20491450.
pg:20492654.

Phylogenomic databases

OMAiSVINDKK.

Miscellaneous databases

EvolutionaryTraceiP09130.
PROiP09130.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR027417. P-loop_NTPase.
IPR014128. T4SS_TraD.
IPR019476. T4SS_TraD_DNA-bd.
IPR022585. TraD_N.
[Graphical view]
PfamiPF12615. TraD_N. 1 hit.
PF10412. TrwB_AAD_bind. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR02759. TraD_Ftype. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Nucleotide sequence of the traD region in the Escherichia coli F sex factor."
    Jalajakumari M.B., Manning P.A.
    Gene 81:195-202(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
    Plasmid: F
  2. "Analysis of the sequence and gene products of the transfer region of the F sex factor."
    Frost L.S., Ippen-Ihler K., Skurray R.A.
    Microbiol. Rev. 58:162-210(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Plasmid: F
  3. "Comparison of proteins involved in pilus synthesis and mating pair stabilization from the related plasmids F and R100-1: insights into the mechanism of conjugation."
    Anthony K.G., Klimke W.A., Manchak J., Frost L.S.
    J. Bacteriol. 181:5149-5159(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: SEQUENCE REVISION TO 190; 269-270 AND 321-325, VARIANT LEU-396.
    Plasmid: F
  4. Krause S., Lanka E.
    Submitted (OCT-1998) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Plasmid: F
  5. "Complete nucleotide sequence of the F plasmid: its implications for organization and diversification of plasmid genomes."
    Shimizu H., Saitoh Y., Suda Y., Uehara K., Sampei G., Mizobuchi K.
    Submitted (APR-2000) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / CR63.
    Plasmid: F
  6. Zienkiewicz M., Kern-Zdanowicz I., Golebiewski M., Ceglowski P.
    Submitted (OCT-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Plasmid: p1658/97
  7. "Surface exclusion genes traS and traT of the F sex factor of Escherichia coli K-12. Determination of the nucleotide sequence and promoter and terminator activities."
    Jalajakumari M.B., Guidolin A., Buhj H.J., Manning P.A.
    J. Mol. Biol. 198:1-11(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-34.
    Strain: K12.
    Plasmid: F
  8. "Nucleotide sequence of the promoter-distal region of the tra operon of plasmid R100, including traI (DNA helicase I) and traD genes."
    Yoshioka Y., Fujita Y., Ohtsubo E.
    J. Mol. Biol. 214:39-53(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-102 AND 665-717.
    Plasmid: F
  9. "Nucleotide sequence of the traI (helicase I) gene from the sex factor F."
    Bradshaw H.D. Jr., Traxler B.A., Minkley E.G. Jr., Nester E.W., Gordon M.P.
    J. Bacteriol. 172:4127-4131(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 462-717.
    Plasmid: F
  10. "Purification and properties of the F sex factor TraD protein, an inner membrane conjugal transfer protein."
    Panicker M.M., Minkley E.G. Jr.
    J. Biol. Chem. 267:12761-12766(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
    Plasmid: F
  11. "The cytoplasmic DNA-binding protein TraM binds to the inner membrane protein TraD in vitro."
    Disque-Kochem C., Dreiseikelmann B.
    J. Bacteriol. 179:6133-6137(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH TRAM, SUBCELLULAR LOCATION.
    Plasmid: F
  12. "The carboxyl terminus of protein TraD adds specificity and efficiency to F-plasmid conjugative transfer."
    Sastre J.I., Cabezon E., de la Cruz F.
    J. Bacteriol. 180:6039-6042(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, MUTAGENESIS OF 681-TRP--PHE-717.
    Plasmid: F
  13. "Analysis of F factor TraD membrane topology by use of gene fusions and trypsin-sensitive insertions."
    Lee M.H., Kosuk N., Bailey J., Traxler B., Manoil C.
    J. Bacteriol. 181:6108-6113(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: TOPOLOGY.
    Plasmid: F
  14. "Mutations in the C-terminal region of TraM provide evidence for in vivo TraM-TraD interactions during F-plasmid conjugation."
    Lu J., Frost L.S.
    J. Bacteriol. 187:4767-4773(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH TRAM.
    Plasmid: F
  15. "Structural basis of specific TraD-TraM recognition during F plasmid-mediated bacterial conjugation."
    Lu J., Wong J.J., Edwards R.A., Manchak J., Frost L.S., Glover J.N.
    Mol. Microbiol. 70:89-99(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.55 ANGSTROMS) OF 708-717 IN COMPLEX WITH C-TERMINUS OF TRAM, MUTAGENESIS OF 710-ASP--PHE-717; GLU-712; ASP-715 AND PHE-717.
    Plasmid: F

Entry informationi

Entry nameiTRAD1_ECOLI
AccessioniPrimary (citable) accession number: P09130
Secondary accession number(s): O87742
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: May 10, 2005
Last modified: May 11, 2016
This is version 111 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Plasmid

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.