4lk0: Difference between revisions

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 ==Crystal Structure Analysis of the E.coli holoenzyme/T7 Gp2 complex==
-<StructureSection load='4lk0' size='340' side='right' caption='[[4lk0]], [[Resolution|resolution]] 3.91&Aring;' scene=''>
+<StructureSection load='4lk0' size='340' side='right'caption='[[4lk0]], [[Resolution|resolution]] 3.91&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4lk0]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt7 Bpt7], [http://en.wikipedia.org/wiki/Ecobw Ecobw], [http://en.wikipedia.org/wiki/Ecod1 Ecod1] and [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LK0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LK0 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4lk0]] is a 14 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_phage_T7 Escherichia phage T7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LK0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LK0 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 3.9103&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rpoA, EcDH1_0418, ECDH1ME8569_3173 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=536056 ECOD1]), rpoB, EcDH1_4008, ECDH1ME8569_3846 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=536056 ECOD1]), rpoC, BWG_3647 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=595496 ECOBW]), rpoZ, EcDH1_0056, ECDH1ME8569_3534 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=536056 ECOD1]), rpoD, alt, b3067, JW3039 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), 2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10760 BPT7])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<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>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4lk0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lk0 OCA], [https://pdbe.org/4lk0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lk0 RCSB], [https://www.ebi.ac.uk/pdbsum/4lk0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lk0 ProSAT]</span></td></tr>
-<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=4lk0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lk0 OCA], [http://pdbe.org/4lk0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4lk0 RCSB], [http://www.ebi.ac.uk/pdbsum/4lk0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4lk0 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/VRPI_BPT7 VRPI_BPT7]] Bacterial RNA polymerase inhibitor, which is expressed in the late stage of lytic development, is also essential for continuous synthesis of phage DNA and functions in the packaging of the viral genome into the mature phage particle. [[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/C9QXI7_ECOD1 C9QXI7_ECOD1]] 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.
+[https://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.
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Bacteriophage T7 encodes an essential inhibitor of the Escherichia coli host RNA polymerase (RNAP), the product of gene 2 (Gp2). We determined a series of X-ray crystal structures of E. coli RNAP holoenzyme with or without Gp2. The results define the structure and location of the RNAP sigma70 subunit domain 1.1 inside the RNAP active site channel, where it must be displaced by the DNA upon formation of the open promoter complex. The structures and associated data, combined with previous results, allow for a complete delineation of the mechanism for Gp2 inhibition of E. coli RNAP. In the primary inhibition mechanism, Gp2 forms a protein-protein interaction with , preventing the normal egress of from the RNAP active site channel. Gp2 thus misappropriates a domain of the RNAP holoenzyme, , to inhibit the function of the enzyme.
-Phage T7 Gp2 inhibition of Escherichia coli RNA polymerase involves misappropriation of sigma70 domain 1.1.,Bae B, Davis E, Brown D, Campbell EA, Wigneshweraraj S, Darst SA Proc Natl Acad Sci U S A. 2013 Nov 11. PMID:24218560<ref>PMID:24218560</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4lk0" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[RNA polymerase|RNA polymerase]]
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
-*[[Sigma factor|Sigma factor]]
+*[[Sigma factor 3D structures|Sigma factor 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bpt7]]
+[[Category: Escherichia coli BW2952]]
-[[Category: DNA-directed RNA polymerase]]
+[[Category: Escherichia coli DH1]]
-[[Category: Ecobw]]
+[[Category: Escherichia coli K-12]]
-[[Category: Ecod1]]
+[[Category: Escherichia phage T7]]
-[[Category: Ecoli]]
+[[Category: Large Structures]]
-[[Category: Bae, B]]
+[[Category: Bae B]]
-[[Category: Darst, S A]]
+[[Category: Darst SA]]
-[[Category: Dna directed rna polymerase]]
-[[Category: Transferase]]