oriTDB

The information of the oriT region

oriTDB accession number	100001
Name	oriT_RP4
Sequence Completeness	intact
oriT length	99 nt
oriT sequence	GAATAAGGGACAGTGAAGAAGGAACACCCGCTCGCGGGTGGGCCTACTTCACCTATCCTG CCCGGCTGACGCCGTTGGATACACCAAGGAAAGTCTACA
IR (inverted repeat)	[13-31] [34-52] nt (GTGAAGAAGGAACACCCGC..GCGGGTGGGCCTACTTCAC)
Location of nic site	[60-61] nt
Conserved sequence flanking the nic site	TATCCTG\|C
Note	minimal oriT sequence
	L:13-31;R:34-52;D:60-61

Visualization of oriT structure (The oriT was characterized experimentally)

1...5....10....15....20....25....30....35....40....45....50....55....60

1

GAATAAGGGACAGTGAAGAAGGAACACCCGCTCGCGGGTGGGCCTACTTCACCTATCCTG

61

CCCGGCTGACGCCGTTGGATACACCAAGGAAAGTCTACA

Reference

[1] Pansegrau W et al (1988) The origin of conjugative IncP plasmid transfer: interaction with plasmid-encoded products and the nucleotide sequence at the relaxation site. Biochim Biophys Acta. 951(2-3):365-74. [PMID:2850014]

[2] Pansegrau W et al (1993) Relaxase (TraI) of IncP alpha plasmid RP4 catalyzes a site-specific cleaving-joining reaction of single-stranded DNA. Proc Natl Acad Sci U S A. 90(7):2925-9. [PMID:8385350]

[3] Pansegrau W et al (1990) In vitro assembly of relaxosomes at the transfer origin of plasmid RP4. Proc Natl Acad Sci U S A. 87(17):6555-9. [PMID:2168553]

[4] Cook DM et al (1992) The oriT region of the Agrobacterium tumefaciens Ti plasmid pTiC58 shares DNA sequence identity with the transfer origins of RSF1010 and RK2/RP4 and with T-region borders. J Bacteriol. 174(19):6238-46. [PMID:1400174]

[5] Fürste JP et al (1989) Conjugative transfer of promiscuous IncP plasmids: interaction of plasmid-encoded products with the transfer origin. Proc Natl Acad Sci U S A. 86(6):1771-5. [PMID:2538813]

[6] Dam B et al (2009) Conjugative Type 4 secretion system of a novel large plasmid from the chemoautotroph Tetrathiobacter kashmirensis and construction of shuttle vectors for Alcaligenaceae. Appl Environ Microbiol. 75(13):4362-73. [PMID:19411426]

I. Information of Relaxase

ID	1
Name	TraI_RP4
GenBank accession number	CAA38336
Family	MOB_P
Length	732 aa
UniProt ID	Q00191
PDB ID	_
Pfam	Relaxase [PF03432.13], Evalue: 7.90E-67, Aligned region: 12..252
Note	relaxase; to recognize the conserved nick region sequence
Protein sequence [Download]	MIAKHVPMRSIKKSDFAELVKYITDEQGKTERLGHVRVTNCEANTLPAVMAEVMATQHGN TRSEADKTYHLLVSFRAGEKPDAETLRAIEDRICAGLGFAEHQRVSAVHHDTDNLHIHIA INKIHPTRNTIHEPYRAYRALADLCATLERDYGLERDNHETRQRVSENRANDMERHAGVE SLVGWIKRECLPELQAAQSWEDLHRVLRENGLKLRERGNGFIFEAGDGTTVKASTVSRDL SKPKLEARFGAFTPAEGGEAPRRREYRAKPLKTRIDTTELYARYQSERQEMGAVRKGELD TLRRRRDRLIEAAMRSNRLRRAAIKLLGEGRIAKRLMYAQAHKALRADLDKINREYRQGR QAVQERTQRRAWADWLKAEAMKGDDKALAALRAREGRSDLKGNTIQGSGEAKPGHAAVTD NITKKGTIIYRVGSSAVRDDGDRLQVSREATTDGLDAALRLAMERFGDRITVNGTAEFKE RIAQAAAAGRLAITFDDAALERRRQELLTKEQAHEQPERNDGRRDRGGDGGIRPAAARTT LNATGGDGDRRDARAVSAGGTVALRKPNVGRIGRKPPPQSQNRLRALSQLGVVRIAGGAE MLLPRDVPGHVEQQGAEPAHALRRGVSGPGRGLKPEQIAAAEKYVAEREQKRLNGFDIPK HARYTDYVGALSYAGTRNVEDQALALLRKENDEILVLPVDKATVQRMKRLAIGDPVTVTP RGSLKTTRGRSR

Reference

[1] Pansegrau W et al (1988) The origin of conjugative IncP plasmid transfer: interaction with plasmid-encoded products and the nucleotide sequence at the relaxation site. Biochim Biophys Acta. 951(2-3):365-74. [PMID:2850014]

[2] Pansegrau W et al (1993) Relaxase (TraI) of IncP alpha plasmid RP4 catalyzes a site-specific cleaving-joining reaction of single-stranded DNA. Proc Natl Acad Sci U S A. 90(7):2925-9. [PMID:8385350]

[3] Grahn AM et al (2000) Components of the RP4 Conjugative Transfer Apparatus Form an Envelope Structure Bridging Inner and Outer Membranes of Donor Cells: Implications for Related Macromolecule Transport Systems. J Bacteriol. 182(6):1564-74. [PMID:10692361]

[4] Pansegrau W et al (1990) In vitro assembly of relaxosomes at the transfer origin of plasmid RP4. Proc Natl Acad Sci U S A. 87(17):6555-9. [PMID:2168553]

II. Auxiliary DNA-binding protein(s) of the relaxosome

#	ID	Name	GenBank	Length	Note
1	1	TraJ_RP4	CAA38338	123 aa	to specifically bind to the nick site-proximal arm of the 19-bp inverted repeat sequence
2	2	TraH_RP4	CAA38335	119 aa	The role of TraH is to stabilize the initialcomplex of form I oriT DNA, TraJ, and TraI by specific protein-protein interactions
3	3	TraK_RP4	CAA38339	134 aa	TraK oriT binding protein

Information of T4CP

ID	1
Name	TraG_RP4
SecReT4 accesion number	_
GenBank accession number	CAA38334
Family	VirD4/TraG
Length	635
UniProt ID	Q00185
PDB ID	_
Pfam	T4SS-DNA_transf [PF02534.13], Evalue: 2.20E-174, Aligned region: 120..624 TraG-D_C [PF12696.6], Evalue: 2.70E-31, Aligned region: 443..568 TrwB_AAD_bind [PF10412.8], Evalue: 1.80E-23, Aligned region: 175..575
Note	conjugal transfer coupling protein TraG
Protein sequence [Download]	MKNRNNAVGPQIRAKKPKASKTVPILAGLSLGAGLQTATQYFAHSFQYQAGLGWNINHVY TPWSILQWAGKWYGQYPDDFMRAASMGMVVSTVGLLGTAVTQMVKANTGKANDYLHGSAR WADKKDIQAAGLLPRPRTVVELVSGKHPPTSSGVYVGGWQDKDGKFHYLRHNGPEHVLTY APTRSGKGVGLVVPTLLSWAHSAVITDLKGELWALTAGWRKKHARNKVVRFEPASAQGSA CWNPLDEIRLGTEYEVGDVQNLATLIVDPDGKGLESHWQKTSQALLVGVILHALYKAKNE GTPATLPSVDGMLADPNRDVGELWMEMTTYGHVDGQNHPAVGSAARDMMDRPEEESGSVL STAKSYLALYRDPVVARNVSKSDFRIKQLMHHDDPVSLFIVTQPNDKARLRPLVRVMVNM IVRLLADKMDFENGRPVAHYKHRLLMMLDEFPSLGKLEILQESLAFVAGYGIKCYLICQD INQLKSRETGYGHDESITSNCHVQNAYPPNRVETAEHLSKLTGTTTIVKEQITTSGRRTS ALLGNVSRTFQEVQRPLLTPDECLRMPGPKKSADGSIEEAGDMVVYVAGYPAIYGKQPLY FKDPIFQARAAVPAPKVSDKLIQTATVEEGEGITI

Reference

[1] Grahn AM et al (2000) Conjugative Type 4 secretion system of a novel large plasmid from the chemoautotroph Tetrathiobacter kashmirensis and construction of shuttle vectors for Alcaligenaceae. J Bacteriol. 182(6):1564-74. [PMID:10692361]

[2] Cabezón E et al (1994) Conjugative Type 4 secretion system of a novel large plasmid from the chemoautotroph Tetrathiobacter kashmirensis and construction of shuttle vectors for Alcaligenaceae. J Bacteriol. 176(14):4455-8. [PMID:8021231]

[3] Hamilton CM et al (2000) Conjugative Type 4 secretion system of a novel large plasmid from the chemoautotroph Tetrathiobacter kashmirensis and construction of shuttle vectors for Alcaligenaceae. J Bacteriol. 182(6):1541-8. [PMID:10692358]

[4] Gomis-Rüth FX et al (2004) Conjugative Type 4 secretion system of a novel large plasmid from the chemoautotroph Tetrathiobacter kashmirensis and construction of shuttle vectors for Alcaligenaceae. Curr Pharm Des. 10(13):1551-65. [PMID:15134575]

Information of plasmid

ID	1
Plasmid name	RP4
GenBank accession number	X14165.1
Incompatibility group	IncP1
Genome size	60099 bp
Coordinate of oriT [Strand]	_
Drug resistance	resistance to carbenicillin, kanamycin, ampicillin and tetracycline
Heavy-metal resistance	_
Virulence factor	_
Xenobiotic degradation	degradation of biphenyl and 4-chlorobiphenyl
Host bacterium [NCBI Taxonomy ID]	Pseudomonas aeruginosa S8 [287]

Reference

[1] Saunders JR et al (1972) Properties of RP4, an R factor which originated in Pseudomonas aeruginosa S8.. J Bacteriol. 112(2):690-6. [PMID:4628745]

[2] Datta N et al (1971) Properties of an R factor from Pseudomonas aeruginosa. J Bacteriol. 108(3):1244-9. [PMID:4945193]

[3] Toussaint A et al (2003) The biphenyl- and 4-chlorobiphenyl-catabolic transposon Tn4371, a member of a new family of genomic islands related to IncP and Ti plasmids. Appl Environ Microbiol. 69(8):4837-45. [PMID:12902278]

[4] Springael D et al (1993) Identification of a catabolic transposon, Tn4371, carrying biphenyl and 4-chlorobiphenyl degradation genes in ＿i>Alcaligenes eutrophus A5. J Bacteriol. 175(6):1674-81. [PMID:8383664]