Transcription-repair coupling factor

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[[Image:2qsr.png|left|200px|thumb|Crystal Structure of Transcription-repair coupling factor [[2qsr]]]]
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[[Image:2eyq.png|left|200px|thumb|Crystal Structure of Transcription-repair coupling factor [[2eyq]]]]
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{{STRUCTURE_2qsr| PDB=2qsr | SIZE=400| SCENE=Transcription-repair_coupling_factor/Cv/1 |right|CAPTION=Transcription-repair coupling factor Se-Met C-terminal domain[[2qsr]] }}
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{{STRUCTURE_2eyq| PDB=2eyq | SCENE=2eyq/Asymmunit/2 |CAPTION= 2eyq asymmetric unit, resolution 3.20&Aring;. <br> Click <scene name='2eyq/Biolunit/1'>here</scene> to display biological molecule.}}
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2EYQ is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EYQ OCA].
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'''Transcription-repair coupling factor (TRCF)''' enables the coupling of these processes in bacteria and humans. The TRCF has ATPase activity. The images at the left and at the right correspond to one representative TRCF, ''i.e.'' the crystal structure of TRCF C-terminus from ''Streptococcus pneumoni'' ([[2qsr]]).
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'''Transcription-repair coupling factor (TRCF)''' enables the coupling of these processes in bacteria and humans. The TRCF has ATPase activity. <scene name='2eyq/Asymmunit/2'>The crystallographic asymmetric unit of the solved structure contains 2 monomers of Mfd (residues 2-1147 of 1151 for one molecule and 5-1147 of the other), five HEPES molecules, and the sulfate ions.</scene>
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Size exclusion chromatogaphy indicates that the protein <scene name='2eyq/Biolunit/1'>exists as a monomer in solution.</scene>
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<scene name='2eyq/Figonea/2'>The monomer colored as</scene> an N→C rainbow similar to [http://www.sciencedirect.com/science?_ob=MiamiCaptionURL&_method=retrieve&_udi=B6WSN-4J79KGF-J&_image=fig1&_ba=1&_user=10&_rdoc=1&_fmt=full&_orig=search&_cdi=7051&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=a4326e4023d32f5de977da04b9a9fdf6 Figure 1A] of [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-4J79KGF-J&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=cd0b2f15037bec97859866e118038962 the article describing] the structure. {{Link Toggle FancyCartoonHighQualityView}}.
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The domains in the structure of Mfd:
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*<scene name='2eyq/Domain1a/2'>D1a</scene>
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*<scene name='2eyq/Domaind2/2'>D2 (UvrB homology module)</scene>
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*<scene name='2eyq/Domain1b/2'>D1b</scene>
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*<scene name='2eyq/Domaind3/2'>D3</scene>
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*<scene name='2eyq/Domain4/2'>D4 (RNAP Interacting Domain)</scene>
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*<scene name='2eyq/Translocation_module/3'>Translocation module (D5 and D6)</scene>
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*<scene name='2eyq/Domain7/2'>D7 (handle)</scene>
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<scene name='2eyq/Domainscoloredlabeled/1'>The domains all shown and colored</scene> similar to [http://www.sciencedirect.com/science?_ob=MiamiCaptionURL&_method=retrieve&_udi=B6WSN-4J79KGF-J&_image=fig1&_ba=1&_user=10&_rdoc=1&_fmt=full&_orig=search&_cdi=7051&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=a4326e4023d32f5de977da04b9a9fdf6 Figure 1B] and [http://www.sciencedirect.com/science?_ob=MiamiCaptionURL&_method=retrieve&_udi=B6WSN-4J79KGF-J&_image=fig2&_ba=2&_user=10&_rdoc=1&_fmt=full&_orig=search&_cdi=7051&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=b56879d585430e1112f6c5c081a1d158 Figure 2] of [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-4J79KGF-J&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=cd0b2f15037bec97859866e118038962 the article describing] the structure.
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<scene name='2eyq/Domainscolorsflabe/3'>Domains labeled and colored and displayed similar to</scene> [http://www.sciencedirect.com/science?_ob=MiamiCaptionURL&_method=retrieve&_udi=B6WSN-4J79KGF-J&_image=fig1&_ba=1&_user=10&_rdoc=1&_fmt=full&_orig=search&_cdi=7051&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=a4326e4023d32f5de977da04b9a9fdf6 Figure 1B] and [http://www.sciencedirect.com/science?_ob=MiamiCaptionURL&_method=retrieve&_udi=B6WSN-4J79KGF-J&_image=fig2&_ba=2&_user=10&_rdoc=1&_fmt=full&_orig=search&_cdi=7051&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=b56879d585430e1112f6c5c081a1d158 Figure 2] of [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-4J79KGF-J&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=cd0b2f15037bec97859866e118038962 the article describing] the structure. <scene name='2eyq/Domainscolorspacefill/1'>Unlabeled</scene>.<br>
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<nowiki>[</nowiki>Note: the following view generates a substantial surface which may take several minutes to calculate. Use the one above as an alternative unless you are willing to spend the time.<nowiki>]</nowiki> <scene name='2eyq/Domainssurflabel/1'>Domains labeled and represented much more similar to</scene> [http://www.sciencedirect.com/science?_ob=MiamiCaptionURL&_method=retrieve&_udi=B6WSN-4J79KGF-J&_image=fig1&_ba=1&_user=10&_rdoc=1&_fmt=full&_orig=search&_cdi=7051&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=a4326e4023d32f5de977da04b9a9fdf6 Figure 1B]. {{Link Toggle LabelsOff}}.
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<scene name='2eyq/Translocationmodcontext/1'>The translocation module shown in the context of the Mfd</scene> displayed as in
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[http://www.sciencedirect.com/science?_ob=MiamiCaptionURL&_method=retrieve&_udi=B6WSN-4J79KGF-J&_image=fig3&_ba=3&_user=10&_rdoc=1&_fmt=full&_orig=search&_cdi=7051&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=580f83ffa975d90b5c9d9dc0eb930d8c Figure 3A] of [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-4J79KGF-J&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=cd0b2f15037bec97859866e118038962 the article describing] the structure.
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<scene name='2eyq/Translocation_modhelciasemotif/1'>The seven ATPase/helicase motifs in the translocation domain</scene> are highlighted in red. See figure 3B.
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<scene name='2eyq/Walkera/3'>Walker A motif of Mfd</scene> displayed similar to
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[http://www.sciencedirect.com/science?_ob=MiamiCaptionURL&_method=retrieve&_udi=B6WSN-4J79KGF-J&_image=fig3&_ba=3&_user=10&_rdoc=1&_fmt=full&_orig=search&_cdi=7051&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=580f83ffa975d90b5c9d9dc0eb930d8c Figure 3B] of [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-4J79KGF-J&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=cd0b2f15037bec97859866e118038962 the article describing] the structure.
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<scene name='2eyq/Figure3c/3'>TRG motif and motif VI</scene> indicated similar to [http://www.sciencedirect.com/science?_ob=MiamiCaptionURL&_method=retrieve&_udi=B6WSN-4J79KGF-J&_image=fig3&_ba=3&_user=10&_rdoc=1&_fmt=full&_orig=search&_cdi=7051&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=580f83ffa975d90b5c9d9dc0eb930d8c Figure 3C] of [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-4J79KGF-J&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=cd0b2f15037bec97859866e118038962 the article describing] the structure.
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== 3D Structures of Transcription-repair coupling factor ==
== 3D Structures of Transcription-repair coupling factor ==
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[[2qsr]] – TRCF C terminal – ''Streptococcus pneumoni''<br />
[[2qsr]] – TRCF C terminal – ''Streptococcus pneumoni''<br />
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==Reference==
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<ref group="xtra">PMID:16469698</ref><references group="xtra"/>
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[[Category: Escherichia coli]]
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[[Category: Darst, S A.]]
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[[Category: Deaconescu, A M.]]
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[[Category: Mfd]]
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[[Category: Atp-binding]]
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[[Category: Atpase]]
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[[Category: Tudor-like domain]]
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[[Category: Tudor]]
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[[Category: Translocation Module]]
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[[Category: UvrB Homology Module]]
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[[Category: Ternary elongation complex]]
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[[Category: Transcription-repair coupling factor]]
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[[Category: DNA repair]]
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[[Category: Sf2 atpase]]
[[Category:Topic Page]]
[[Category:Topic Page]]
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<br />
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Created with the participation of [[User:Wayne Decatur|Wayne Decatur]]

Revision as of 12:55, 6 June 2012

Crystal Structure of Transcription-repair coupling factor 2eyq
Crystal Structure of Transcription-repair coupling factor 2eyq

Template:STRUCTURE 2eyq 2EYQ is a 2 chains structure of sequences from Escherichia coli. Full crystallographic information is available from OCA.

Transcription-repair coupling factor (TRCF) enables the coupling of these processes in bacteria and humans. The TRCF has ATPase activity.

Size exclusion chromatogaphy indicates that the protein

an N→C rainbow similar to Figure 1A of the article describing the structure. .

The domains in the structure of Mfd:

similar to Figure 1B and Figure 2 of the article describing the structure.

Figure 1B and Figure 2 of the article describing the structure. .
[Note: the following view generates a substantial surface which may take several minutes to calculate. Use the one above as an alternative unless you are willing to spend the time.] Figure 1B. .

displayed as in Figure 3A of the article describing the structure.

are highlighted in red. See figure 3B.

displayed similar to Figure 3B of the article describing the structure.

indicated similar to Figure 3C of the article describing the structure.

3D Structures of Transcription-repair coupling factor

Updated December 2011

2eyq, 2b2n – EcTRCF – Escherichia coli
3hjh – EcTRCF residues 1-470
3mlq – TRCF RNA polymerase interacting domain + DNA-directed RNA polymerase subunit β - Thermus thermophilus
2qsr – TRCF C terminal – Streptococcus pneumoni

Reference

  • Deaconescu AM, Chambers AL, Smith AJ, Nickels BE, Hochschild A, Savery NJ, Darst SA. Structural basis for bacterial transcription-coupled DNA repair. Cell. 2006 Feb 10;124(3):507-20. PMID:16469698 doi:10.1016/j.cell.2005.11.045


Created with the participation of Wayne Decatur

Proteopedia Page Contributors and Editors (what is this?)

Karsten Theis, Michal Harel, Alexander Berchansky, Wayne Decatur

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