4ff1
From Proteopedia
(Difference between revisions)
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4ff1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_N4 Escherichia virus N4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FF1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FF1 FirstGlance]. <br> | <table><tr><td colspan='2'>[[4ff1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_N4 Escherichia virus N4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FF1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FF1 FirstGlance]. <br> | ||
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.47Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=4ff1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ff1 OCA], [https://pdbe.org/4ff1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ff1 RCSB], [https://www.ebi.ac.uk/pdbsum/4ff1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ff1 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=4ff1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ff1 OCA], [https://pdbe.org/4ff1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ff1 RCSB], [https://www.ebi.ac.uk/pdbsum/4ff1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ff1 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/RPOLV_BPN4 RPOLV_BPN4] DNA-dependent RNA polymerase, which is injected into the host upon infection and transcribes the phage early genes from promoters that have a 5-bp stem-3 nt loop hairpin structure.<ref>PMID:18362338</ref> <ref>PMID:19061645</ref> | [https://www.uniprot.org/uniprot/RPOLV_BPN4 RPOLV_BPN4] DNA-dependent RNA polymerase, which is injected into the host upon infection and transcribes the phage early genes from promoters that have a 5-bp stem-3 nt loop hairpin structure.<ref>PMID:18362338</ref> <ref>PMID:19061645</ref> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | The challenge for structural biology is to understand atomic-level macromolecular motions during enzymatic reaction (1-3). X-ray crystallography can reveal high-resolution structures; however, one perceived limitation is that it reveals only static views. Here we use time-dependent soak-trigger-freeze X-ray crystallography, namely, soaking nucleotide and divalent metal into the bacteriophage RNA polymerase (RNAP)-promoter DNA complex crystals to trigger the nucleotidyl transfer reaction and freezing crystals at different time points, to capture real-time intermediates in the pathway of transcription. In each crystal structure, different intensities and shapes of electron density maps corresponding to the nucleotide and metal were revealed at the RNAP active site that allow watching the nucleotide and metal bindings and the phosphodiester bond formation in a time perspective. Our study provides temporal order of substrate assembly and metal co-factor binding at the active site of enzyme that completes our understanding of the two-metal-ion mechanism (4-6) and fidelity mechanism in single-subunit RNAPs. The nucleotide binding metal (MeB) is coordinated at the active site prior to the catalytic metal (MeA). MeA coordination is only temporal, established just before and dissociated immediately after phosphodiester bond formation. We captured these elusive intermediates exploiting the slow enzymatic reaction in crystallo. These results demonstrate that the simple time-dependent soak-trigger-freeze X-ray crystallography offers a direct means for monitoring enzymatic reactions. | ||
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| - | Watching the bacteriophage N4 RNA polymerase transcription by time-dependent soak-trigger-freeze X-ray crystallography.,Basu RS, Murakami KS J Biol Chem. 2012 Dec 12. PMID:23235152<ref>PMID:23235152</ref> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 4ff1" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
Current revision
N4 mini-vRNAP transcription initiation complex, 1 min after soaking GTP, ATP and Mn
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