1xpu

From Proteopedia

(Difference between revisions)

Revision as of 07:56, 15 May 2024

Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic 5a-(3-formylphenylsulfanyl)-dihydrobicyclomycin (FPDB)

Structural highlights

1xpu is a 12 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 3.05Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RHO_ECOLI Facilitates transcription termination by a mechanism that involves rho binding to the nascent RNA, activation of rho's RNA-dependent ATPase activity, and release of the mRNA from the DNA template. RNA-dependent NTPAse which utilizes all four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01884]

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

Rho is a hexameric RNA/DNA helicase/translocase that terminates transcription of select genes in bacteria. The naturally occurring antibiotic, bicyclomycin (BCM), acts as a noncompetitive inhibitor of ATP turnover to disrupt this process. We have determined three independent X-ray crystal structures of Rho complexed with BCM and two semisynthetic derivatives, 5a-(3-formylphenylsulfanyl)-dihydrobicyclomycin (FPDB) and 5a-formylbicyclomycin (FB) to 3.15, 3.05, and 3.15 A resolution, respectively. The structures show that BCM and its derivatives are nonnucleotide inhibitors that interact with Rho at a pocket adjacent to the ATP and RNA binding sites in the C-terminal half of the protein. BCM association prevents ATP turnover by an unexpected mechanism, occluding the binding of the nucleophilic water molecule required for ATP hydrolysis. Our data explain why only certain elements of BCM have been amenable to modification and serve as a template for the design of new inhibitors.

Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin.,Skordalakes E, Brogan AP, Park BS, Kohn H, Berger JM Structure. 2005 Jan;13(1):99-109. PMID:15642265^[1]

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

References

↑ Skordalakes E, Brogan AP, Park BS, Kohn H, Berger JM. Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin. Structure. 2005 Jan;13(1):99-109. PMID:15642265 doi:10.1016/j.str.2004.10.013

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/1xpu"

@@ Line 3: / Line 3: @@
 <StructureSection load='1xpu' size='340' side='right'caption='[[1xpu]], [[Resolution|resolution]] 3.05&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1xpu]] is a 12 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=1XPU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XPU FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1xpu]] is a 12 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=1XPU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XPU FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=FPD:5A-(3-FORMYLPHENYLSULFANYL)-DIHYDROBICYCLOMYCIN'>FPD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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]] 3.05&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1xpo|1xpo]], [[1xpr|1xpr]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=FPD:5A-(3-FORMYLPHENYLSULFANYL)-DIHYDROBICYCLOMYCIN'>FPD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=1xpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xpu OCA], [https://pdbe.org/1xpu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xpu RCSB], [https://www.ebi.ac.uk/pdbsum/1xpu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xpu ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/MEMA_METCA MEMA_METCA]] Responsible for the initial oxygenation of methane to methanol in methanotrophs. It also catalyzes the monohydroxylation of a variety of unactivated alkenes, alicyclic, aromatic and heterocyclic compounds.
+[https://www.uniprot.org/uniprot/RHO_ECOLI RHO_ECOLI] Facilitates transcription termination by a mechanism that involves rho binding to the nascent RNA, activation of rho's RNA-dependent ATPase activity, and release of the mRNA from the DNA template. RNA-dependent NTPAse which utilizes all four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01884]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 36: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Berger, J M]]
+[[Category: Berger JM]]
-[[Category: Brogan, A P]]
+[[Category: Brogan AP]]
-[[Category: Kohn, H]]
+[[Category: Kohn H]]
-[[Category: Park, B S]]
+[[Category: Park BS]]
-[[Category: Skordalakes, E]]
+[[Category: Skordalakes E]]
-[[Category: Atpgamma]]
-[[Category: Rho transcription termination factor]]
-[[Category: Transcription-rna complex]]

1xpu

From Proteopedia

Revision as of 07:56, 15 May 2024

Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic 5a-(3-formylphenylsulfanyl)-dihydrobicyclomycin (FPDB)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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