4jkr
From Proteopedia
(Difference between revisions)
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4jkr]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BW2952 Escherichia coli BW2952], [https://en.wikipedia.org/wiki/Escherichia_coli_DH1 Escherichia coli DH1], [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Escherichia_coli_O104:H4_str._2009EL-2071 Escherichia coli O104:H4 str. 2009EL-2071]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JKR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JKR FirstGlance]. <br> | <table><tr><td colspan='2'>[[4jkr]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BW2952 Escherichia coli BW2952], [https://en.wikipedia.org/wiki/Escherichia_coli_DH1 Escherichia coli DH1], [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Escherichia_coli_O104:H4_str._2009EL-2071 Escherichia coli O104:H4 str. 2009EL-2071]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JKR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JKR FirstGlance]. <br> | ||
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=G4P:GUANOSINE-5,3-TETRAPHOSPHATE'>G4P</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 4.2Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=G4P:GUANOSINE-5,3-TETRAPHOSPHATE'>G4P</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=4jkr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jkr OCA], [https://pdbe.org/4jkr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jkr RCSB], [https://www.ebi.ac.uk/pdbsum/4jkr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jkr 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=4jkr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jkr OCA], [https://pdbe.org/4jkr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jkr RCSB], [https://www.ebi.ac.uk/pdbsum/4jkr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jkr ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/A0A0E0Y7A2_ECO1C A0A0E0Y7A2_ECO1C] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01321][RuleBase:RU363031] | [https://www.uniprot.org/uniprot/A0A0E0Y7A2_ECO1C A0A0E0Y7A2_ECO1C] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01321][RuleBase:RU363031] | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | Guanosine tetraphosphate (ppGpp) is an alarmone that enables bacteria to adapt to their environment. It has been known for years that ppGpp acts directly on RNA polymerase (RNAP) to alter the rate of transcription, but its exact target site is still under debate. Here we report a crystal structure of Escherichia coli RNAP holoenzyme in complex with ppGpp at 4.5 A resolution. The structure reveals that ppGpp binds at an interface between the shelf and core modules on the outer surface of RNAP, away from the catalytic center and the nucleic acid binding path. Bound ppGpp connects these two pivotal modules that may restrain the opening of the RNAP cleft. A detailed mechanism of action of ppGpp is proposed in which ppGpp prevents the closure of the active center that is induced by the binding of NTP, which could slow down nucleotide addition cycles and destabilize the initial transcription complexes. | ||
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| - | The Mechanism of E. coli RNA Polymerase Regulation by ppGpp Is Suggested by the Structure of their Complex.,Zuo Y, Wang Y, Steitz TA Mol Cell. 2013 May 9;50(3):430-6. doi: 10.1016/j.molcel.2013.03.020. Epub 2013, Apr 25. PMID:23623685<ref>PMID:23623685</ref> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 4jkr" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]] | *[[RNA polymerase 3D structures|RNA polymerase 3D structures]] | ||
*[[Sigma factor 3D structures|Sigma factor 3D structures]] | *[[Sigma factor 3D structures|Sigma factor 3D structures]] | ||
| - | == References == | ||
| - | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
Current revision
Crystal Structure of E. coli RNA Polymerase in complex with ppGpp
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