2l8b

From Proteopedia

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Current revision

TraI (381-569)

Structural highlights

2l8b is a 1 chain structure with sequence from Escherichia coli K-12. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TRAI1_ECOLI 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.^[1] ^[2] ^[3] ^[4] ^[5] 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.^[6] ^[7] ^[8] ^[9] ^[10]

Publication Abstract from PubMed

TraI, the F plasmid-encoded nickase, is a 1756 amino acid protein essential for conjugative transfer of plasmid DNA from one bacterium to another. Although crystal structures of N- and C-terminal domains of F TraI have been determined, central domains of the protein are structurally unexplored. The central region (between residues 306 and 1520) is known to both bind single-stranded DNA (ssDNA) and unwind DNA through a highly processive helicase activity. Here, we show that the ssDNA binding site is located between residues 381 and 858, and we also present the high-resolution solution structure of the N-terminus of this region (residues 381-569). This fragment folds into a four-strand parallel beta sheet surrounded by alpha helices, and it resembles the structure of the N-terminus of helicases such as RecD and RecQ despite little sequence similarity. The structure supports the model that F TraI resulted from duplication of a RecD-like domain and subsequent specialization of domains into the more N-terminal ssDNA binding domain and the more C-terminal domain containing helicase motifs. In addition, we provide evidence that the nickase and ssDNA binding domains of TraI are held close together by an 80-residue linker sequence that connects the two domains. These results suggest a possible physical explanation for the apparent negative cooperativity between the nickase and ssDNA binding domain. Proteins 2012; (c) 2012 Wiley Periodicals, Inc.

Solution structure and small angle scattering analysis of TraI (381-569).,Wright NT, Raththagala M, Hemmis CW, Edwards S, Curtis JE, Krueger S, Schildbach JF Proteins. 2012 Aug;80(9):2250-61. doi: 10.1002/prot.24114. Epub 2012 Jun 18. PMID:22611034^[11]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Street LM, Harley MJ, Stern JC, Larkin C, Williams SL, Miller DL, Dohm JA, Rodgers ME, Schildbach JF. Subdomain organization and catalytic residues of the F factor TraI relaxase domain. Biochim Biophys Acta. 2003 Mar 21;1646(1-2):86-99. PMID:12637015
↑ Abdel-Monem M, Taucher-Scholz G, Klinkert MQ. Identification of Escherichia coli DNA helicase I as the traI gene product of the F sex factor. Proc Natl Acad Sci U S A. 1983 Aug;80(15):4659-63. PMID:6308637
↑ Matson SW, Nelson WC, Morton BS. Characterization of the reaction product of the oriT nicking reaction catalyzed by Escherichia coli DNA helicase I. J Bacteriol. 1993 May;175(9):2599-606. PMID:8386720
↑ Nelson WC, Howard MT, Sherman JA, Matson SW. The traY gene product and integration host factor stimulate Escherichia coli DNA helicase I-catalyzed nicking at the F plasmid oriT. J Biol Chem. 1995 Nov 24;270(47):28374-80. PMID:7499339
↑ Stern JC, Schildbach JF. DNA recognition by F factor TraI36: highly sequence-specific binding of single-stranded DNA. Biochemistry. 2001 Sep 25;40(38):11586-95. PMID:11560509
↑ Street LM, Harley MJ, Stern JC, Larkin C, Williams SL, Miller DL, Dohm JA, Rodgers ME, Schildbach JF. Subdomain organization and catalytic residues of the F factor TraI relaxase domain. Biochim Biophys Acta. 2003 Mar 21;1646(1-2):86-99. PMID:12637015
↑ Abdel-Monem M, Taucher-Scholz G, Klinkert MQ. Identification of Escherichia coli DNA helicase I as the traI gene product of the F sex factor. Proc Natl Acad Sci U S A. 1983 Aug;80(15):4659-63. PMID:6308637
↑ Matson SW, Nelson WC, Morton BS. Characterization of the reaction product of the oriT nicking reaction catalyzed by Escherichia coli DNA helicase I. J Bacteriol. 1993 May;175(9):2599-606. PMID:8386720
↑ Nelson WC, Howard MT, Sherman JA, Matson SW. The traY gene product and integration host factor stimulate Escherichia coli DNA helicase I-catalyzed nicking at the F plasmid oriT. J Biol Chem. 1995 Nov 24;270(47):28374-80. PMID:7499339
↑ Stern JC, Schildbach JF. DNA recognition by F factor TraI36: highly sequence-specific binding of single-stranded DNA. Biochemistry. 2001 Sep 25;40(38):11586-95. PMID:11560509
↑ Wright NT, Raththagala M, Hemmis CW, Edwards S, Curtis JE, Krueger S, Schildbach JF. Solution structure and small angle scattering analysis of TraI (381-569). Proteins. 2012 Aug;80(9):2250-61. doi: 10.1002/prot.24114. Epub 2012 Jun 18. PMID:22611034 doi:10.1002/prot.24114

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2l8b"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 2l8b is ON HOLD
+==TraI (381-569)==
+<StructureSection load='2l8b' size='340' side='right'caption='[[2l8b]]' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2l8b]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L8B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2L8B FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2l8b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l8b OCA], [https://pdbe.org/2l8b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2l8b RCSB], [https://www.ebi.ac.uk/pdbsum/2l8b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2l8b ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TRAI1_ECOLI TRAI1_ECOLI] 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>PMID:12637015</ref> <ref>PMID:6308637</ref> <ref>PMID:8386720</ref> <ref>PMID:7499339</ref> <ref>PMID:11560509</ref>   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>PMID:12637015</ref> <ref>PMID:6308637</ref> <ref>PMID:8386720</ref> <ref>PMID:7499339</ref> <ref>PMID:11560509</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+TraI, the F plasmid-encoded nickase, is a 1756 amino acid protein essential for conjugative transfer of plasmid DNA from one bacterium to another. Although crystal structures of N- and C-terminal domains of F TraI have been determined, central domains of the protein are structurally unexplored. The central region (between residues 306 and 1520) is known to both bind single-stranded DNA (ssDNA) and unwind DNA through a highly processive helicase activity. Here, we show that the ssDNA binding site is located between residues 381 and 858, and we also present the high-resolution solution structure of the N-terminus of this region (residues 381-569). This fragment folds into a four-strand parallel beta sheet surrounded by alpha helices, and it resembles the structure of the N-terminus of helicases such as RecD and RecQ despite little sequence similarity. The structure supports the model that F TraI resulted from duplication of a RecD-like domain and subsequent specialization of domains into the more N-terminal ssDNA binding domain and the more C-terminal domain containing helicase motifs. In addition, we provide evidence that the nickase and ssDNA binding domains of TraI are held close together by an 80-residue linker sequence that connects the two domains. These results suggest a possible physical explanation for the apparent negative cooperativity between the nickase and ssDNA binding domain. Proteins 2012; (c) 2012 Wiley Periodicals, Inc.
-Authors: Wright, N.T., Raththagala, M.U., Edwards, S., Krueger, S., Schildbach, J.F.
+Solution structure and small angle scattering analysis of TraI (381-569).,Wright NT, Raththagala M, Hemmis CW, Edwards S, Curtis JE, Krueger S, Schildbach JF Proteins. 2012 Aug;80(9):2250-61. doi: 10.1002/prot.24114. Epub 2012 Jun 18. PMID:22611034<ref>PMID:22611034</ref>
-Description: TraI (381-569)
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2l8b" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Escherichia coli K-12]]
+[[Category: Large Structures]]
+[[Category: Edwards S]]
+[[Category: Krueger S]]
+[[Category: Raththagala MU]]
+[[Category: Schildbach JF]]
+[[Category: Wright NT]]

2l8b

From Proteopedia

Current revision

TraI (381-569)

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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