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Protein

Multifunctional conjugation protein TraI

Gene

traI

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 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. 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.
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.

Catalytic activityi

ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.
ATP + H2O = ADP + phosphate.

Cofactori

Enzyme regulationi

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.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei16O-(5'-phospho-DNA)-tyrosine intermediate; for relaxase activityCurated1
Active sitei17RelaxaseSequence analysis1
Metal bindingi146Magnesium; via pros nitrogen; catalytic1 Publication1
Metal bindingi157Magnesium; via tele nitrogen; catalytic1 Publication1
Metal bindingi159Magnesium; via tele nitrogen; catalytic1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi992 – 999ATPSequence analysis8

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase, Isomerase, Mobility protein

Keywords - Biological processi

Conjugation

Keywords - Ligandi

ATP-binding, DNA-binding, Magnesium, Metal-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Multifunctional conjugation protein TraI
Including the following 2 domains:
DNA relaxase TraI (EC:5.99.1.2)
Alternative name(s):
DNA nickase TraI
Transesterase TraI
DNA helicase I (EC:3.6.4.12)
Gene namesi
Name:traI
Ordered Locus Names:ECOK12F104
Encoded oniPlasmid F20 Publications
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Loss of conjugative DNA transfer.2 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi1Missing : Loss of ssDNA binding. 1 Publication1
Mutagenesisi3S → A: 1000-fold reduced affinity for ssDNA. 1 Publication1
Mutagenesisi16Y → F: Loss of DNA nicking ability; still binds ssDNA. 3 Publications1
Mutagenesisi17Y → F: Loss of DNA nicking ability; still binds ssDNA. 1 Publication1
Mutagenesisi23Y → F: Reduced DNA nicking ability. 1 Publication1
Mutagenesisi24Y → F: Reduced DNA nicking ability. 1 Publication1
Mutagenesisi88K → A: 10000-fold reduced affinity for ssDNA. 1 Publication1
Mutagenesisi159H → E: Loss of oriT cleavage. 1 Publication1
Mutagenesisi237R → A: 300-fold reduced affinity for ssDNA. 1 Publication1
Mutagenesisi241I → A: 1500-fold reduced affinity for ssDNA. 1 Publication1
Mutagenesisi998K → M: No helicase activity, nicks DNA, loss of DNA transfer activity. 2 Publications1
Mutagenesisi1517 – 1525Missing : 10,000-fold reduction in conjugative DNA transfer. 1 Publication9
Mutagenesisi1518 – 1525PGRKYPQP → GGRKYGQG: 100,000-fold reduction in conjugative DNA transfer. 8
Mutagenesisi1574 – 1575LQ → AA: 200-fold reduction in conjugative DNA transfer; when associated with A-1603. 1 Publication2
Mutagenesisi1603V → A: 200-fold reduction in conjugative DNA transfer; when associated with 1574-A-A-1575. 1 Publication1
Mutagenesisi1721 – 1756Missing : More than 100-fold reduction in conjugative DNA transfer. 1 PublicationAdd BLAST36

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000245041 – 1756Multifunctional conjugation protein TraIAdd BLAST1756

Proteomic databases

PRIDEiP14565.

Interactioni

Subunit structurei

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.5 Publications

Structurei

Secondary structure

11756
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 6Combined sources5
Helixi10 – 17Combined sources8
Helixi20 – 22Combined sources3
Turni24 – 26Combined sources3
Beta strandi32 – 35Combined sources4
Helixi36 – 41Combined sources6
Helixi49 – 56Combined sources8
Beta strandi61 – 63Combined sources3
Turni71 – 73Combined sources3
Beta strandi79 – 85Combined sources7
Helixi88 – 95Combined sources8
Helixi101 – 118Combined sources18
Beta strandi122 – 124Combined sources3
Beta strandi133 – 135Combined sources3
Beta strandi141 – 148Combined sources8
Beta strandi154 – 164Combined sources11
Beta strandi166 – 168Combined sources3
Beta strandi171 – 173Combined sources3
Turni179 – 181Combined sources3
Helixi185 – 190Combined sources6
Helixi193 – 210Combined sources18
Helixi220 – 222Combined sources3
Helixi231 – 234Combined sources4
Helixi236 – 244Combined sources9
Helixi251 – 260Combined sources10
Helixi270 – 282Combined sources13
Turni283 – 285Combined sources3
Helixi288 – 296Combined sources9
Helixi390 – 403Combined sources14
Helixi409 – 411Combined sources3
Helixi417 – 429Combined sources13
Helixi443 – 458Combined sources16
Beta strandi463 – 466Combined sources4
Helixi471 – 476Combined sources6
Turni479 – 481Combined sources3
Beta strandi486 – 488Combined sources3
Turni489 – 495Combined sources7
Beta strandi504 – 512Combined sources9
Helixi513 – 527Combined sources15
Beta strandi532 – 538Combined sources7
Turni539 – 541Combined sources3
Helixi544 – 552Combined sources9
Helixi1477 – 1487Combined sources11
Helixi1491 – 1493Combined sources3
Helixi1495 – 1504Combined sources10
Beta strandi1514 – 1516Combined sources3
Beta strandi1526 – 1532Combined sources7
Beta strandi1538 – 1545Combined sources8
Beta strandi1547 – 1549Combined sources3
Turni1550 – 1552Combined sources3
Beta strandi1553 – 1555Combined sources3
Beta strandi1562 – 1565Combined sources4
Beta strandi1571 – 1576Combined sources6
Beta strandi1578 – 1587Combined sources10
Helixi1588 – 1597Combined sources10
Beta strandi1601 – 1608Combined sources8
Helixi1616 – 1618Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
ProteinModelPortaliP14565.
SMRiP14565.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP14565.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 330DNA relaxaseAdd BLAST330
Regioni950 – 1500DNA helicase IAdd BLAST551
Regioni1534 – 1756Required for DNA transfer, may interact with TraMAdd BLAST223

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili1717 – 1753Sequence analysisAdd BLAST37

Domaini

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.2 Publications

Sequence similaritiesi

To TraI of plasmid IncFII R100.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

OMAiSTWETHR.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR014059. Conjug_relaxase_N.
IPR014129. Conjug_relaxase_TraI.
IPR009767. DNA_helicase_TraI.
IPR027417. P-loop_NTPase.
IPR014862. TrwC.
[Graphical view]
PfamiPF07057. TraI. 1 hit.
PF08751. TrwC. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 4 hits.
TIGRFAMsiTIGR02686. relax_trwC. 1 hit.
TIGR02760. TraI_TIGR. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative initiation. AlignAdd to basket

Isoform traI (identifier: P14565-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MMSIAQVRSA GSAGNYYTDK DNYYVLGSMG ERWAGRGAEQ LGLQGSVDKD
60 70 80 90 100
VFTRLLEGRL PDGADLSRMQ DGSNRHRPGY DLTFSAPKSV SMMAMLGGDK
110 120 130 140 150
RLIDAHNQAV DFAVRQVEAL ASTRVMTDGQ SETVLTGNLV MALFNHDTSR
160 170 180 190 200
DQEPQLHTHA VVANVTQHNG EWKTLSSDKV GKTGFIENVY ANQIAFGRLY
210 220 230 240 250
REKLKEQVEA LGYETEVVGK HGMWEMPGVP VEAFSGRSQT IREAVGEDAS
260 270 280 290 300
LKSRDVAALD TRKSKQHVDP EIKMAEWMQT LKETGFDIRA YRDAADQRAD
310 320 330 340 350
LRTLTPGPAS QDGPDVQQAV TQAIAGLSER KVQFTYTDVL ARTVGILPPE
360 370 380 390 400
NGVIERARAG IDEAISREQL IPLDREKGLF TSGIHVLDEL SVRALSRDIM
410 420 430 440 450
KQNRVTVHPE KSVPRTAGYS DAVSVLAQDR PSLAIVSGQG GAAGQRERVA
460 470 480 490 500
ELVMMAREQG REVQIIAADR RSQMNMKQDE RLSGELITGR RQLLEGMAFT
510 520 530 540 550
PGSTVIVDQG EKLSLKETLT LLDGAARHNV QVLITDSGQR TGTGSALMAM
560 570 580 590 600
KDAGVNTYRW QGGEQRPATI ISEPDRNVRY ARLAGDFAAS VKAGEESVAQ
610 620 630 640 650
VSGVREQAIL TQAIRSELKT QGVLGLPEVT MTALSPVWLD SRSRYLRDMY
660 670 680 690 700
RPGMVMEQWN PETRSHDRYV IDRVTAQSHS LTLRDAQGET QVVRISSLDS
710 720 730 740 750
SWSLFRPEKM PVADGERLRV TGKIPGLRVS GGDRLQVASV SEDAMTVVVP
760 770 780 790 800
GRAEPATLPV SDSPFTALKL ENGWVETPGH SVSDSATVFA SVTQMAMDNA
810 820 830 840 850
TLNGLARSGR DVRLYSSLDE TRTAEKLARH PSFTVVSEQI KTRAGETSLE
860 870 880 890 900
TAISHQKSAL HTPAQQAIHL ALPVVESKKL AFSMVDLLTE AKSFAAEGTG
910 920 930 940 950
FTELGGEINA QIKRGDLLYV DVAKGYGTGL LVSRASYEAE KSILRHILEG
960 970 980 990 1000
KEAVMPLMER VPGELMEKLT SGQRAATRMI LETSDRFTVV QGYAGVGKTT
1010 1020 1030 1040 1050
QFRAVMSAVN MLPESERPRV VGLGPTHRAV GEMRSAGVDA QTLASFLHDT
1060 1070 1080 1090 1100
QLQQRSGETP DFSNTLFLLD ESSMVGNTDM ARAYALIAAG GGRAVASGDT
1110 1120 1130 1140 1150
DQLQAIAPGQ PFRLQQTRSA ADVAIMKEIV RQTPELREAV YSLINRDVER
1160 1170 1180 1190 1200
ALSGLESVKP SQVPRQEGAW APEHSVTEFS HSQEAKLAEA QQKAMLKGEA
1210 1220 1230 1240 1250
FPDVPMTLYE AIVRDYTGRT PEAREQTLIV THLNEDRRVL NSMIHDVREK
1260 1270 1280 1290 1300
AGELGKEQVM VPVLNTANIR DGELRRLSTW ETHRDALVLV DNVYHRIAGI
1310 1320 1330 1340 1350
SKDDGLITLQ DAEGNTRLIS PREAVAEGVT LYTPDTIRVG TGDRMRFTKS
1360 1370 1380 1390 1400
DRERGYVANS VWTVTAVSGD SVTLSDGQQT REIRPGQEQA EQHIDLAYAI
1410 1420 1430 1440 1450
TAHGAQGASE TFAIALEGTE GNRKLMAGFE SAYVALSRMK QHVQVYTDNR
1460 1470 1480 1490 1500
QGWTDAINNA VQKGTAHDVF EPKPDREVMN AERLFSTARE LRDVAAGRAV
1510 1520 1530 1540 1550
LRQAGLAGGD SPARFIAPGR KYPQPYVALP AFDRNGKSAG IWLNPLTTDD
1560 1570 1580 1590 1600
GNGLRGFSGE GRVKGSGDAQ FVALQGSRNG ESLLADNMQD GVRIARDNPD
1610 1620 1630 1640 1650
SGVVVRIAGE GRPWNPGAIT GGRVWGDIPD NSVQPGAGNG EPVTAEVLAQ
1660 1670 1680 1690 1700
RQAEEAIRRE TERRADEIVR KMAENKPDLP DGKTEQAVRE IAGQERDRAA
1710 1720 1730 1740 1750
ITEREAALPE GVLREPQRVR EAVREIAREN LLQERLQQME RDMVRDLQKE

KTLGGD
Length:1,756
Mass (Da):192,016
Last modified:November 1, 1990 - v2
Checksum:iAA07D61DB2BFD9FA
GO
Isoform traI* (identifier: P14565-2) [UniParc]FASTAAdd to basket

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

Show »
Length:802
Mass (Da):87,882
Checksum:iED17E7673621E2EF
GO

Sequence cautioni

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

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti69 – 74MQDGSN → CRMAVT in AAA83930 (PubMed:2680768).Curated6

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0189711 – 954Missing in isoform traI*. CuratedAdd BLAST954

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
RefSeqiNP_061483.1. NC_002483.1. [P14565-1]
WP_000987005.1. NZ_CP014273.1.

Genome annotation databases

GeneIDi1263574.

Keywords - Coding sequence diversityi

Alternative initiation

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
RefSeqiNP_061483.1. NC_002483.1. [P14565-1]
WP_000987005.1. NZ_CP014273.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
ProteinModelPortaliP14565.
SMRiP14565.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiP14565.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1263574.

Phylogenomic databases

OMAiSTWETHR.

Miscellaneous databases

EvolutionaryTraceiP14565.
PROiP14565.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR014059. Conjug_relaxase_N.
IPR014129. Conjug_relaxase_TraI.
IPR009767. DNA_helicase_TraI.
IPR027417. P-loop_NTPase.
IPR014862. TrwC.
[Graphical view]
PfamiPF07057. TraI. 1 hit.
PF08751. TrwC. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 4 hits.
TIGRFAMsiTIGR02686. relax_trwC. 1 hit.
TIGR02760. TraI_TIGR. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiTRAI1_ECOLI
AccessioniPrimary (citable) accession number: P14565
Secondary accession number(s): Q51811
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: November 1, 1990
Last modified: November 30, 2016
This is version 124 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing, Multifunctional enzyme, Plasmid

Documents

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

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.