4jkr

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{{Large structure}}
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==Crystal Structure of E. coli RNA Polymerase in complex with ppGpp==
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{{STRUCTURE_4jkr| PDB=4jkr | SCENE= }}
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<StructureSection load='4jkr' size='340' side='right' caption='[[4jkr]], [[Resolution|resolution]] 4.20&Aring;' scene=''>
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===Crystal Structure of E. coli RNA Polymerase in complex with ppGpp===
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== Structural highlights ==
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{{ABSTRACT_PUBMED_23623685}}
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<table><tr><td colspan='2'>[[4jkr]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_bw2952 Escherichia coli bw2952], [http://en.wikipedia.org/wiki/Escherichia_coli_dh1 Escherichia coli dh1], [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12] and [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JKR FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ECDH10B_3470, O3O_23125, rpoA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1133853 Escherichia coli O104:H4 str. 2009EL-2071]), ECDH1ME8569_3846, EcDH1_4008, O3K_23925, rpoB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=536056 Escherichia coli DH1]), BWG_3647, O3O_01425, rpoC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=595496 Escherichia coli BW2952]), ECDH1ME8569_3534, EcDH1_0056, O3O_25075, rpoZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=536056 Escherichia coli DH1]), alt, b3067, JW3039, rpoD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4jkr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jkr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jkr RCSB], [http://www.ebi.ac.uk/pdbsum/4jkr PDBsum]</span></td></tr>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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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==Function==
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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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[[http://www.uniprot.org/uniprot/C9QUL2_ECOD1 C9QUL2_ECOD1]] Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits (By similarity).[HAMAP-Rule:MF_00366][SAAS:SAAS012293_004_017283] [[http://www.uniprot.org/uniprot/K0BPQ3_ECO1E K0BPQ3_ECO1E]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (By similarity).[HAMAP-Rule:MF_00059] [[http://www.uniprot.org/uniprot/C5A0S8_ECOBW C5A0S8_ECOBW]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (By similarity).[SAAS:SAAS012754_004_011999] [[http://www.uniprot.org/uniprot/C9QV90_ECOD1 C9QV90_ECOD1]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (By similarity).[HAMAP-Rule:MF_01321][RuleBase:RU000432] [[http://www.uniprot.org/uniprot/RPOD_ECOLI RPOD_ECOLI]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This is the primary sigma factor of this bacterium.
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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[[4jkr]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_bw2952 Escherichia coli bw2952], [http://en.wikipedia.org/wiki/Escherichia_coli_dh1 Escherichia coli dh1], [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12] and [http://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].
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</div>
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==Reference==
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==See Also==
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<ref group="xtra">PMID:023623685</ref><references group="xtra"/><references/>
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*[[RNA polymerase|RNA polymerase]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: DNA-directed RNA polymerase]]
[[Category: DNA-directed RNA polymerase]]
[[Category: Escherichia coli bw2952]]
[[Category: Escherichia coli bw2952]]
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[[Category: Escherichia coli k-12]]
[[Category: Escherichia coli k-12]]
[[Category: Escherichia coli o104:h4 str. 2009el-2071]]
[[Category: Escherichia coli o104:h4 str. 2009el-2071]]
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[[Category: Steitz, T A.]]
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[[Category: Steitz, T A]]
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[[Category: Wang, Y.]]
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[[Category: Wang, Y]]
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[[Category: Zuo, Y.]]
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[[Category: Zuo, Y]]
[[Category: Rna polymerase]]
[[Category: Rna polymerase]]
[[Category: Transcription]]
[[Category: Transcription]]
[[Category: Transcription regulation]]
[[Category: Transcription regulation]]
[[Category: Transferase]]
[[Category: Transferase]]

Revision as of 14:42, 21 December 2014

Crystal Structure of E. coli RNA Polymerase in complex with ppGpp

4jkr, resolution 4.20Å

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