1owf: Difference between revisions

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<StructureSection load='1owf' size='340' side='right'caption='[[1owf]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
<StructureSection load='1owf' size='340' side='right'caption='[[1owf]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1owf]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OWF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OWF FirstGlance]. <br>
<table><tr><td colspan='2'>[[1owf]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OWF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OWF FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ihf|1ihf]], [[1ouz|1ouz]], [[1owg|1owg]]</div></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95&#8491;</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=1owf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1owf OCA], [https://pdbe.org/1owf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1owf RCSB], [https://www.ebi.ac.uk/pdbsum/1owf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1owf ProSAT]</span></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=1owf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1owf OCA], [https://pdbe.org/1owf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1owf RCSB], [https://www.ebi.ac.uk/pdbsum/1owf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1owf ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/IHFA_ECOLI IHFA_ECOLI]] One of the 2 subunits of integration host factor (IHF), a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control.<ref>PMID:7499339</ref> <ref>PMID:17238924</ref>  Plays a crucial role in the lysogenic life cycle of bacteriophage lambda, as it is required not only in the recombination reaction, which inserts lambda DNA into the E.coli chromosome, but also for the synthesis of int and cI repressor, two phage proteins necessary for DNA insertion and repression, respectively. The synthesis of int and cI proteins is regulated indirectly by IHF via translational control of the lambda cII protein.<ref>PMID:7499339</ref> <ref>PMID:17238924</ref>  Has an essential role in conjugative DNA transfer (CDT), 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.<ref>PMID:7499339</ref> <ref>PMID:17238924</ref>  [[https://www.uniprot.org/uniprot/IHFB_ECOLI IHFB_ECOLI]] One of the 2 subunits of integration host factor (IHF), a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control.<ref>PMID:7499339</ref> <ref>PMID:17238924</ref>  Plays a crucial role in the lysogenic life cycle of bacteriophage lambda, as it is required not only in the recombination reaction, which inserts lambda DNA into the E.coli chromosome, but also for the synthesis of int and cI repressor, two phage proteins necessary for DNA insertion and repression, respectively. The synthesis of int and cI proteins is regulated indirectly by IHF via translational control of the lambda cII protein.<ref>PMID:7499339</ref> <ref>PMID:17238924</ref>  Has an essential role in conjugative DNA transfer (CDT), 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.<ref>PMID:7499339</ref> <ref>PMID:17238924</ref>
[https://www.uniprot.org/uniprot/IHFA_ECOLI IHFA_ECOLI] One of the 2 subunits of integration host factor (IHF), a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control.<ref>PMID:7499339</ref> <ref>PMID:17238924</ref>  Plays a crucial role in the lysogenic life cycle of bacteriophage lambda, as it is required not only in the recombination reaction, which inserts lambda DNA into the E.coli chromosome, but also for the synthesis of int and cI repressor, two phage proteins necessary for DNA insertion and repression, respectively. The synthesis of int and cI proteins is regulated indirectly by IHF via translational control of the lambda cII protein.<ref>PMID:7499339</ref> <ref>PMID:17238924</ref>  Has an essential role in conjugative DNA transfer (CDT), 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.<ref>PMID:7499339</ref> <ref>PMID:17238924</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1owf ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1owf ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Integration host factor (IHF) is a DNA-bending protein that recognizes its cognate sites through indirect readout. Previous studies have shown that binding of wild-type (WT)-IHF is disrupted by a T to A mutation at the center position of a conserved TTR motif in its binding site, and that substitution of betaGlu44 with Ala prevented IHF from discriminating between A and T at this position. We have determined the crystal structures and relative binding affinities for all combinations of WT-IHF and IHF-betaGlu44Ala bound to the WT and mutant DNAs. Comparison of these structures reveals that DNA twist plays a major role in DNA recognition by IHF, and that this geometric parameter is dependent on the dinucleotide step and not on the bound IHF variant.
Integration host factor: putting a twist on protein-DNA recognition.,Lynch TW, Read EK, Mattis AN, Gardner JF, Rice PA J Mol Biol. 2003 Jul 11;330(3):493-502. PMID:12842466<ref>PMID:12842466</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1owf" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus coli migula 1895]]
[[Category: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Gardner, J F]]
[[Category: Gardner JF]]
[[Category: Lynch, T W]]
[[Category: Lynch TW]]
[[Category: Mattis, A N]]
[[Category: Mattis AN]]
[[Category: Read, E K]]
[[Category: Read EK]]
[[Category: Rice, P A]]
[[Category: Rice PA]]
[[Category: Dna bending]]
[[Category: Ihf]]
[[Category: Indirect readout]]
[[Category: Minor groove]]
[[Category: Protein-dna recognition]]
[[Category: Transcription-dna complex]]

Latest revision as of 11:03, 14 February 2024

Crystal structure of a mutant IHF (BetaE44A) complexed with the native H' SiteCrystal structure of a mutant IHF (BetaE44A) complexed with the native H' Site

Structural highlights

1owf is a 5 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.95Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

IHFA_ECOLI One of the 2 subunits of integration host factor (IHF), a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control.[1] [2] Plays a crucial role in the lysogenic life cycle of bacteriophage lambda, as it is required not only in the recombination reaction, which inserts lambda DNA into the E.coli chromosome, but also for the synthesis of int and cI repressor, two phage proteins necessary for DNA insertion and repression, respectively. The synthesis of int and cI proteins is regulated indirectly by IHF via translational control of the lambda cII protein.[3] [4] Has an essential role in conjugative DNA transfer (CDT), 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.[5] [6]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

  1. ↑ 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
  2. ↑ Ragonese H, Haisch D, Villareal E, Choi JH, Matson SW. The F plasmid-encoded TraM protein stimulates relaxosome-mediated cleavage at oriT through an interaction with TraI. Mol Microbiol. 2007 Feb;63(4):1173-84. PMID:17238924 doi:http://dx.doi.org/10.1111/j.1365-2958.2006.05576.x
  3. ↑ 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
  4. ↑ Ragonese H, Haisch D, Villareal E, Choi JH, Matson SW. The F plasmid-encoded TraM protein stimulates relaxosome-mediated cleavage at oriT through an interaction with TraI. Mol Microbiol. 2007 Feb;63(4):1173-84. PMID:17238924 doi:http://dx.doi.org/10.1111/j.1365-2958.2006.05576.x
  5. ↑ 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
  6. ↑ Ragonese H, Haisch D, Villareal E, Choi JH, Matson SW. The F plasmid-encoded TraM protein stimulates relaxosome-mediated cleavage at oriT through an interaction with TraI. Mol Microbiol. 2007 Feb;63(4):1173-84. PMID:17238924 doi:http://dx.doi.org/10.1111/j.1365-2958.2006.05576.x

1owf, resolution 1.95Å

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