3hjh

From Proteopedia

(Difference between revisions)

Current revision

A rigid N-terminal clamp restrains the motor domains of the bacterial transcription-repair coupling factor

Structural highlights

3hjh is a 1 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.95Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MFD_ECOLI Couples transcription and DNA repair by recognizing RNA polymerase (RNAP) stalled at DNA lesions. Mediates ATP-dependent release of RNAP and its truncated transcript from the DNA, and recruitment of nucleotide excision repair machinery to the damaged site. Can also dissociate RNAP that is blocked by low concentration of nucleoside triphosphates or by physical obstruction, such as bound proteins. In addition, can rescue arrested complexes by promoting forward translocation. Has ATPase activity, which is required for removal of stalled RNAP, but seems to lack helicase activity. May act through a translocase activity that rewinds upstream DNA, leading either to translocation or to release of RNAP when the enzyme active site can not continue elongation.^[1] ^[2] ^[3] ^[4] ^[5]

Evolutionary Conservation

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

Publication Abstract from PubMed

Motor proteins that translocate on nucleic acids are key players in gene expression and maintenance. While the function of these proteins is diverse, they are driven by highly conserved core motor domains. In transcription-coupled DNA repair, motor activity serves to remove RNA polymerase stalled on damaged DNA, making the lesion accessible for repair. Structural and biochemical data on the bacterial transcription-repair coupling factor Mfd suggest that this enzyme undergoes large conformational changes from a dormant state to an active state upon substrate binding. Mfd can be functionally dissected into an N-terminal part instrumental in recruiting DNA repair proteins (domains 1-3, MfdN), and a C-terminal part harboring motor activity (domains 4-7, MfdC). We show that isolated MfdC has elevated ATPase and motor activities compared to the full length protein. While MfdN has large effects on MfdC activity and thermostability in cis, these effects are not observed in trans. The structure of MfdN is independent of interactions with MfdC, implying that MfdN acts as a clamp that restrains motions of the motor domains in the dormant state. We conclude that releasing MfdN:MfdC interactions serves as a central molecular switch that upregulates Mfd functions during transcription-coupled DNA repair.

An N-terminal clamp restrains the motor domains of the bacterial transcription-repair coupling factor Mfd.,Murphy MN, Gong P, Ralto K, Manelyte L, Savery NJ, Theis K Nucleic Acids Res. 2009 Oct;37(18):6042-53. Epub 2009 Aug 21. PMID:19700770^[6]

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

References

↑ Selby CP, Sancar A. Molecular mechanism of transcription-repair coupling. Science. 1993 Apr 2;260(5104):53-8. PMID:8465200
↑ Selby CP, Sancar A. Structure and function of transcription-repair coupling factor. I. Structural domains and binding properties. J Biol Chem. 1995 Mar 3;270(9):4882-9. PMID:7876261
↑ Selby CP, Sancar A. Structure and function of transcription-repair coupling factor. II. Catalytic properties. J Biol Chem. 1995 Mar 3;270(9):4890-5. PMID:7876262
↑ Park JS, Marr MT, Roberts JW. E. coli Transcription repair coupling factor (Mfd protein) rescues arrested complexes by promoting forward translocation. Cell. 2002 Jun 14;109(6):757-67. PMID:12086674
↑ Murphy MN, Gong P, Ralto K, Manelyte L, Savery NJ, Theis K. An N-terminal clamp restrains the motor domains of the bacterial transcription-repair coupling factor Mfd. Nucleic Acids Res. 2009 Oct;37(18):6042-53. Epub 2009 Aug 21. PMID:19700770 doi:10.1093/nar/gkp680
↑ Murphy MN, Gong P, Ralto K, Manelyte L, Savery NJ, Theis K. An N-terminal clamp restrains the motor domains of the bacterial transcription-repair coupling factor Mfd. Nucleic Acids Res. 2009 Oct;37(18):6042-53. Epub 2009 Aug 21. PMID:19700770 doi:10.1093/nar/gkp680

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3hjh"

@@ Line 1: / Line 1: @@
 ==A rigid N-terminal clamp restrains the motor domains of the bacterial transcription-repair coupling factor==
-<StructureSection load='3hjh' size='340' side='right' caption='[[3hjh]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
+<StructureSection load='3hjh' size='340' side='right'caption='[[3hjh]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3hjh]] is a 1 chain structure with sequence 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=3HJH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HJH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3hjh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HJH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HJH FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene><br>
+</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><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2eyq|2eyq]], [[2b2n|2b2n]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b1114, JW1100, mfd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=3hjh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hjh OCA], [https://pdbe.org/3hjh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hjh RCSB], [https://www.ebi.ac.uk/pdbsum/3hjh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hjh ProSAT]</span></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3hjh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hjh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hjh RCSB], [http://www.ebi.ac.uk/pdbsum/3hjh PDBsum]</span></td></tr>
+</table>
-<table>
+== Function ==
+[https://www.uniprot.org/uniprot/MFD_ECOLI MFD_ECOLI] Couples transcription and DNA repair by recognizing RNA polymerase (RNAP) stalled at DNA lesions. Mediates ATP-dependent release of RNAP and its truncated transcript from the DNA, and recruitment of nucleotide excision repair machinery to the damaged site. Can also dissociate RNAP that is blocked by low concentration of nucleoside triphosphates or by physical obstruction, such as bound proteins. In addition, can rescue arrested complexes by promoting forward translocation. Has ATPase activity, which is required for removal of stalled RNAP, but seems to lack helicase activity. May act through a translocase activity that rewinds upstream DNA, leading either to translocation or to release of RNAP when the enzyme active site can not continue elongation.<ref>PMID:8465200</ref> <ref>PMID:7876261</ref> <ref>PMID:7876262</ref> <ref>PMID:12086674</ref> <ref>PMID:19700770</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hj/3hjh_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hj/3hjh_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</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/chain_selection.php?pdb_ID=2ata 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=3hjh ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3hjh" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Helicase|Helicase]]
+*[[Transcription-repair coupling factor 3D structures|Transcription-repair coupling factor 3D structures]]
-*[[Transcription-repair coupling factor|Transcription-repair coupling factor]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Escherichia coli]]
+[[Category: Escherichia coli K-12]]
-[[Category: Gong, P.]]
+[[Category: Large Structures]]
-[[Category: Manelyte, L.]]
+[[Category: Gong P]]
-[[Category: Murphy, M.]]
+[[Category: Manelyte L]]
-[[Category: Ralto, K.]]
+[[Category: Murphy M]]
-[[Category: Savery, N.]]
+[[Category: Ralto K]]
-[[Category: Theis, K.]]
+[[Category: Savery N]]
-[[Category: Atp-binding]]
+[[Category: Theis K]]
-[[Category: Dna damage]]
-[[Category: Dna repair]]
-[[Category: Dna-binding]]
-[[Category: Helicase]]
-[[Category: Hydrolase]]
-[[Category: Mfd]]
-[[Category: Mutation frequency decline]]
-[[Category: Nucleotide-binding]]
-[[Category: Transcription-coupled dna repair]]
-[[Category: Transcription-repair coupling factor]]

3hjh

From Proteopedia

Current revision

A rigid N-terminal clamp restrains the motor domains of the bacterial transcription-repair coupling factor

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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