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P14565 (TRAI1_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 110. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Multifunctional conjugation protein TraI

Including the following 2 domains:

  1. DNA relaxase TraI
    EC=5.99.1.2
    Alternative name(s):
    DNA nickase TraI
    Transesterase TraI
  2. DNA helicase I
    EC=3.6.4.12
Gene names
Name:traI
Ordered Locus Names:ECOK12F104
Encoded onPlasmid F Ref.1 Ref.2 Ref.3 Ref.4 Ref.5 Ref.6 Ref.7 Ref.8 Ref.9 Ref.10 Ref.11 Ref.12 Ref.13 Ref.14 Ref.15 Ref.16 Ref.17 Ref.18 Ref.19 Ref.20
OrganismEscherichia coli (strain K12)
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length1756 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Part of the relaxosome, which facilitates a site- and strand-specific cut in the origin of transfer by TraI, at the nic site. Relaxosome formation requires binding of IHF and TraY to the oriT region, which then faciliates binding of TraI relaxase. TraI forms a covalent 5'-phosphotyrosine intermediate linkage to the ssDNA. The transesterified T-strand moves from the donor cell to the recipient cell in a 5'to 3' direction, with the DNA helicase activity of TraI unwinding the DNA. DNA transfer occurs via the conjugative pore (transferosome) an intercellular junction mediated by a type IV secretion system, with TraD providing the means to link the relaxosome to the conjugative pore. The relaxase completes DNA transfer by reversing the covalent phosphotyrosine linkage and releasing the T-strand. Ref.6 Ref.8 Ref.9 Ref.10 Ref.12

TraI has also been identified as DNA helicase I. DNA. helicase I is a potent, highly processive DNA-dependent ATPase, able to unwind about 1.1 kb dsDNA per second in a 5' to 3' manner. Ref.6 Ref.8 Ref.9 Ref.10 Ref.12

Catalytic activity

ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.

ATP + H2O = ADP + phosphate.

Cofactor

Mg2+.

Enzyme regulation

Nicking activity (relaxase) is inhibited by bisphosphonates such as the non-competitive inhibitor imidobisphosphate (PNP), etidronic acid (ETIDRO) and clodronic acid (CLODRO). The latter 2 are competitive inhibitors, and are already used clinically to treat bone loss (marketed as Didronel and Bonefos). All 3 compounds also inhibit conjugation and kill F plasmid-containing cells. They are specific to dual tyrosine relaxases such as those found in F and related R conjugative plasmids. Ref.19

Subunit structure

Monomer. Part of the relaxosome, a complex composed of plasmid-encodes TraI, TraM, TraY and host-encoded IHF bound to the F plasmid origin of transfer (oriT). Directly contacts coupling protein TraD. Seems to directly contact TraM via its C-terminus. Ref.6 Ref.15 Ref.16

Subcellular location

Cytoplasm Probable.

Domain

Has 4 domains; the relaxase domain (residues 1-330), an unknown domain (residues 330-990), the helicase domain (residues 990-1450) and the C-terminal domain (1450-1756) which is required for conjugative DNA transfer, possibly via interaction with TraM. Ref.13 Ref.14

Disruption phenotype

Loss of conjugative DNA transfer. Ref.13 Ref.20

Sequence similarities

To TraI of plasmid IncFII R100.

Sequence caution

The sequence AAA83930.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Ontologies

Alternative products

This entry describes 2 isoforms produced by alternative initiation. [Align] [Select]
Isoform traI (identifier: P14565-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform traI* (identifier: P14565-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-954: Missing.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 17561756Multifunctional conjugation protein TraI
PRO_0000024504

Regions

Nucleotide binding992 – 9998ATP Potential
Region1 – 330330DNA relaxase
Region950 – 1500551DNA helicase I
Region1534 – 1756223Required for DNA transfer, may interact with TraM
Coiled coil1717 – 175337 Potential

Sites

Active site161O-(5'-phospho-DNA)-tyrosine intermediate; for relaxase activity Probable
Active site171Relaxase Potential
Metal binding1461Magnesium; via pros nitrogen; catalytic
Metal binding1571Magnesium; via tele nitrogen; catalytic
Metal binding1591Magnesium; via tele nitrogen; catalytic

Natural variations

Alternative sequence1 – 954954Missing in isoform traI*.
VSP_018971

Experimental info

Mutagenesis11Missing: Loss of ssDNA binding. Ref.18
Mutagenesis31S → A: 1000-fold reduced affinity for ssDNA. Ref.18
Mutagenesis161Y → F: Loss of DNA nicking ability; still binds ssDNA. Ref.6 Ref.12 Ref.18
Mutagenesis171Y → F: Loss of DNA nicking ability; still binds ssDNA. Ref.6
Mutagenesis231Y → F: Reduced DNA nicking ability. Ref.6
Mutagenesis241Y → F: Reduced DNA nicking ability. Ref.6
Mutagenesis881K → A: 10000-fold reduced affinity for ssDNA. Ref.18
Mutagenesis1591H → E: Loss of oriT cleavage. Ref.19
Mutagenesis2371R → A: 300-fold reduced affinity for ssDNA. Ref.18
Mutagenesis2411I → A: 1500-fold reduced affinity for ssDNA. Ref.18
Mutagenesis9981K → M: No helicase activity, nicks DNA, loss of DNA transfer activity. Ref.13 Ref.14
Mutagenesis1517 – 15259Missing: 10,000-fold reduction in conjugative DNA transfer. Ref.20
Mutagenesis1518 – 15258PGRKYPQP → GGRKYGQG: 100,000-fold reduction in conjugative DNA transfer.
Mutagenesis1574 – 15752LQ → AA: 200-fold reduction in conjugative DNA transfer; when associated with A-1603.
Mutagenesis16031V → A: 200-fold reduction in conjugative DNA transfer; when associated with 1574-A-A-1575. Ref.20
Mutagenesis1721 – 175636Missing: More than 100-fold reduction in conjugative DNA transfer. Ref.20
Sequence conflict69 – 746MQDGSN → CRMAVT in AAA83930. Ref.4

Secondary structure

........................................................................................................... 1756
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform traI [UniParc].

Last modified November 1, 1990. Version 2.
Checksum: AA07D61DB2BFD9FA

FASTA1,756192,016
        10         20         30         40         50         60 
MMSIAQVRSA GSAGNYYTDK DNYYVLGSMG ERWAGRGAEQ LGLQGSVDKD VFTRLLEGRL 

        70         80         90        100        110        120 
PDGADLSRMQ DGSNRHRPGY DLTFSAPKSV SMMAMLGGDK RLIDAHNQAV DFAVRQVEAL 

       130        140        150        160        170        180 
ASTRVMTDGQ SETVLTGNLV MALFNHDTSR DQEPQLHTHA VVANVTQHNG EWKTLSSDKV 

       190        200        210        220        230        240 
GKTGFIENVY ANQIAFGRLY REKLKEQVEA LGYETEVVGK HGMWEMPGVP VEAFSGRSQT 

       250        260        270        280        290        300 
IREAVGEDAS LKSRDVAALD TRKSKQHVDP EIKMAEWMQT LKETGFDIRA YRDAADQRAD 

       310        320        330        340        350        360 
LRTLTPGPAS QDGPDVQQAV TQAIAGLSER KVQFTYTDVL ARTVGILPPE NGVIERARAG 

       370        380        390        400        410        420 
IDEAISREQL IPLDREKGLF TSGIHVLDEL SVRALSRDIM KQNRVTVHPE KSVPRTAGYS 

       430        440        450        460        470        480 
DAVSVLAQDR PSLAIVSGQG GAAGQRERVA ELVMMAREQG REVQIIAADR RSQMNMKQDE 

       490        500        510        520        530        540 
RLSGELITGR RQLLEGMAFT PGSTVIVDQG EKLSLKETLT LLDGAARHNV QVLITDSGQR 

       550        560        570        580        590        600 
TGTGSALMAM KDAGVNTYRW QGGEQRPATI ISEPDRNVRY ARLAGDFAAS VKAGEESVAQ 

       610        620        630        640        650        660 
VSGVREQAIL TQAIRSELKT QGVLGLPEVT MTALSPVWLD SRSRYLRDMY RPGMVMEQWN 

       670        680        690        700        710        720 
PETRSHDRYV IDRVTAQSHS LTLRDAQGET QVVRISSLDS SWSLFRPEKM PVADGERLRV 

       730        740        750        760        770        780 
TGKIPGLRVS GGDRLQVASV SEDAMTVVVP GRAEPATLPV SDSPFTALKL ENGWVETPGH 

       790        800        810        820        830        840 
SVSDSATVFA SVTQMAMDNA TLNGLARSGR DVRLYSSLDE TRTAEKLARH PSFTVVSEQI 

       850        860        870        880        890        900 
KTRAGETSLE TAISHQKSAL HTPAQQAIHL ALPVVESKKL AFSMVDLLTE AKSFAAEGTG 

       910        920        930        940        950        960 
FTELGGEINA QIKRGDLLYV DVAKGYGTGL LVSRASYEAE KSILRHILEG KEAVMPLMER 

       970        980        990       1000       1010       1020 
VPGELMEKLT SGQRAATRMI LETSDRFTVV QGYAGVGKTT QFRAVMSAVN MLPESERPRV 

      1030       1040       1050       1060       1070       1080 
VGLGPTHRAV GEMRSAGVDA QTLASFLHDT QLQQRSGETP DFSNTLFLLD ESSMVGNTDM 

      1090       1100       1110       1120       1130       1140 
ARAYALIAAG GGRAVASGDT DQLQAIAPGQ PFRLQQTRSA ADVAIMKEIV RQTPELREAV 

      1150       1160       1170       1180       1190       1200 
YSLINRDVER ALSGLESVKP SQVPRQEGAW APEHSVTEFS HSQEAKLAEA QQKAMLKGEA 

      1210       1220       1230       1240       1250       1260 
FPDVPMTLYE AIVRDYTGRT PEAREQTLIV THLNEDRRVL NSMIHDVREK AGELGKEQVM 

      1270       1280       1290       1300       1310       1320 
VPVLNTANIR DGELRRLSTW ETHRDALVLV DNVYHRIAGI SKDDGLITLQ DAEGNTRLIS 

      1330       1340       1350       1360       1370       1380 
PREAVAEGVT LYTPDTIRVG TGDRMRFTKS DRERGYVANS VWTVTAVSGD SVTLSDGQQT 

      1390       1400       1410       1420       1430       1440 
REIRPGQEQA EQHIDLAYAI TAHGAQGASE TFAIALEGTE GNRKLMAGFE SAYVALSRMK 

      1450       1460       1470       1480       1490       1500 
QHVQVYTDNR QGWTDAINNA VQKGTAHDVF EPKPDREVMN AERLFSTARE LRDVAAGRAV 

      1510       1520       1530       1540       1550       1560 
LRQAGLAGGD SPARFIAPGR KYPQPYVALP AFDRNGKSAG IWLNPLTTDD GNGLRGFSGE 

      1570       1580       1590       1600       1610       1620 
GRVKGSGDAQ FVALQGSRNG ESLLADNMQD GVRIARDNPD SGVVVRIAGE GRPWNPGAIT 

      1630       1640       1650       1660       1670       1680 
GGRVWGDIPD NSVQPGAGNG EPVTAEVLAQ RQAEEAIRRE TERRADEIVR KMAENKPDLP 

      1690       1700       1710       1720       1730       1740 
DGKTEQAVRE IAGQERDRAA ITEREAALPE GVLREPQRVR EAVREIAREN LLQERLQQME 

      1750 
RDMVRDLQKE KTLGGD 

« Hide

Isoform traI* [UniParc].

Checksum: ED17E7673621E2EF
Show »

FASTA80287,882

References

« Hide 'large scale' references
[1]"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], PARTIAL PROTEIN SEQUENCE.
[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].
[3]"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.
[4]"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] OF 1-150.
Strain: K12.
[5]"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 1-72.
[6]"Subdomain organization and catalytic residues of the F factor TraI relaxase domain."
Street L.M., Harley M.J., Stern J.C., Larkin C., Williams S.L., Miller D.L., Dohm J.A., Rodgers M.E., Schildbach J.F.
Biochim. Biophys. Acta 1646:86-99(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 1-5, FUNCTION IN SS-DNA DIGESTION, SUBUNIT, CHARACTERIZATION OF RELAXASE CATALYTIC RESIDUES, MUTAGENESIS OF TYR-16; TYR-17; TYR-23 AND TYR-24.
[7]"Regulation of the expression of the traM gene of the F sex factor of Escherichia coli."
Penfold S.S., Simon J., Frost L.S.
Mol. Microbiol. 20:549-558(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 955-1756.
[8]"Identification of Escherichia coli DNA helicase I as the traI gene product of the F sex factor."
Abdel-Monem M., Taucher-Scholz G., Klinkert M.Q.
Proc. Natl. Acad. Sci. U.S.A. 80:4659-4663(1983) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION AS DNA HELICASE I.
[9]"Characterization of the reaction product of the oriT nicking reaction catalyzed by Escherichia coli DNA helicase I."
Matson S.W., Nelson W.C., Morton B.S.
J. Bacteriol. 175:2599-2606(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN COVALENT BINDING TO SS-DNA.
[10]"The traY gene product and integration host factor stimulate Escherichia coli DNA helicase I-catalyzed nicking at the F plasmid oriT."
Nelson W.C., Howard M.T., Sherman J.A., Matson S.W.
J. Biol. Chem. 270:28374-28380(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN F PLASMID NICKING.
[11]"Stepwise assembly of a relaxosome at the F plasmid origin of transfer."
Howard M.T., Nelson W.C., Matson S.W.
J. Biol. Chem. 270:28381-28386(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION OF RELAXOSOME ASSEMBLY ORDER.
[12]"DNA recognition by F factor TraI36: highly sequence-specific binding of single-stranded DNA."
Stern J.C., Schildbach J.F.
Biochemistry 40:11586-11595(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN SS-DNA-BINDING, CHARACTERIZATION OF DNA SEQUENCE SPECIFICITY, MUTAGENESIS OF TYR-16.
[13]"F plasmid conjugative DNA transfer: the TraI helicase activity is essential for DNA strand transfer."
Matson S.W., Sampson J.K., Byrd D.R.
J. Biol. Chem. 276:2372-2379(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: DOMAINS, DISRUPTION PHENOTYPE, MUTAGENESIS OF LYS-998.
[14]"The F-plasmid TraI protein contains three functional domains required for conjugative DNA strand transfer."
Matson S.W., Ragonese H.
J. Bacteriol. 187:697-706(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION OF THE C-TERMINUS, DOMAINS, MUTAGENESIS OF LYS-998.
[15]"DNA unwinding by Escherichia coli DNA helicase I (TraI) provides evidence for a processive monomeric molecular motor."
Sikora B., Eoff R.L., Matson S.W., Raney K.D.
J. Biol. Chem. 281:36110-36116(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION OF HELICASE ACTIVITY, SUBUNIT.
[16]"The F plasmid-encoded TraM protein stimulates relaxosome-mediated cleavage at oriT through an interaction with TraI."
Ragonese H., Haisch D., Villareal E., Choi J.H., Matson S.W.
Mol. Microbiol. 63:1173-1184(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH TRAM; TRAY AND IHF, SUBUNIT.
[17]"Structural insights into single-stranded DNA binding and cleavage by F factor TraI."
Datta S., Larkin C., Schildbach J.F.
Structure 11:1369-1379(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 1-330 IN COMPLEX WITH MAGNESIUM.
[18]"Inter- and intramolecular determinants of the specificity of single-stranded DNA binding and cleavage by the F factor relaxase."
Larkin C., Datta S., Harley M.J., Anderson B.J., Ebie A., Hargreaves V., Schildbach J.F.
Structure 13:1533-1544(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.72 ANGSTROMS) OF 1-330 BOUND TO SS-DNA AND MAGNESIUM, CHARACTERIZATION OF RELAXASE CATALYTIC RESIDUE, MUTAGENESIS OF MET-1; SER-3; TYR-16; LYS-88; ARG-237 AND ILE-241.
[19]"Disrupting antibiotic resistance propagation by inhibiting the conjugative DNA relaxase."
Lujan S.A., Guogas L.M., Ragonese H., Matson S.W., Redinbo M.R.
Proc. Natl. Acad. Sci. U.S.A. 104:12282-12287(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.42 ANGSTROMS) OF 1-300 IN COMPLEX WITH SS-DNA WITH AND WITHOUT INHIBITOR, ENZYME REGULATION, MUTAGENESIS OF HIS-159.
[20]"A novel fold in the TraI relaxase-helicase c-terminal domain is essential for conjugative DNA transfer."
Guogas L.M., Kennedy S.A., Lee J.H., Redinbo M.R.
J. Mol. Biol. 386:554-568(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 1476-1628, DNA-BINDING BY C-TERMINUS, MUTAGENESIS OF 1517-ALA--GLY-1525; 1574-LEU-GLN-1575; VAL-1603 AND 1721-GLU--ASP-1756, DISRUPTION PHENOTYPE.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M54796 Genomic DNA. Translation: AAA98085.1.
M54796 Genomic DNA. Translation: AAA98086.1.
U01159 Genomic DNA. Translation: AAC44186.1.
AP001918 Genomic DNA. Translation: BAA97974.1.
M29254 Genomic DNA. Translation: AAA83930.1. Different initiation.
X57430 Genomic DNA. Translation: CAA40677.1.
U01159 Genomic DNA. Translation: AAC44187.1.
RefSeqNP_061483.1. NC_002483.1. [P14565-1]

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1P4DX-ray2.60A/B/C1-330[»]
2A0IX-ray2.72A1-330[»]
2L8BNMR-A381-569[»]
2Q7TX-ray2.42A/B1-300[»]
2Q7UX-ray3.00A/B1-300[»]
3FLDX-ray2.40A/B1476-1628[»]
ProteinModelPortalP14565.
SMRP14565. Positions 1-306, 962-1033, 1398-1448, 1476-1628.
ModBaseSearch...
MobiDBSearch...

Proteomic databases

PRIDEP14565.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID1263574.

Phylogenomic databases

OMAETHRDAL.

Gene expression databases

GenevestigatorP14565.

Family and domain databases

Gene3D3.40.50.300. 1 hit.
InterProIPR014059. Conjug_relaxase_N.
IPR014129. Conjug_relaxase_TraI.
IPR009767. DNA_helicase_TraI.
IPR027417. P-loop_NTPase.
IPR014862. TrwC.
[Graphical view]
PfamPF07057. TraI. 1 hit.
PF08751. TrwC. 1 hit.
[Graphical view]
SUPFAMSSF52540. SSF52540. 4 hits.
TIGRFAMsTIGR02686. relax_trwC. 1 hit.
TIGR02760. TraI_TIGR. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP14565.
PROP14565.

Entry information

Entry nameTRAI1_ECOLI
AccessionPrimary (citable) accession number: P14565
Secondary accession number(s): Q51811
Entry history
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: November 1, 1990
Last modified: May 14, 2014
This is version 110 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references