4ff2 - Revision history

OCA at 13:21, 1 July 2026

2026-07-01T13:21:26Z

← Older revision		Revision as of 13:21, 1 July 2026
Line 10:		Line 10:
	== 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.

			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>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 4ff2" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 11:15, 1 March 2024

2024-03-01T11:15:51Z

← Older revision		Revision as of 11:15, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ff2]] 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=4FF2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FF2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ff2]] 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=4FF2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FF2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <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]] 2Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <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=4ff2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ff2 OCA], [https://pdbe.org/4ff2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ff2 RCSB], [https://www.ebi.ac.uk/pdbsum/4ff2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ff2 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=4ff2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ff2 OCA], [https://pdbe.org/4ff2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ff2 RCSB], [https://www.ebi.ac.uk/pdbsum/4ff2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ff2 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.

	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>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 4ff2" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==

OCA at 04:53, 7 October 2022

2022-10-07T04:53:20Z

← Older revision		Revision as of 04:53, 7 October 2022
Line 3:		Line 3:
	<StructureSection load='4ff2' size='340' side='right'caption='[[4ff2]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='4ff2' size='340' side='right'caption='[[4ff2]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ff2]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bpn4 Bpn4~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FF2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4FF2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ff2]] 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=4FF2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FF2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>~~</td></tr>~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ff1\|4ff1]], [[4ff3\|4ff3]], [[4ff4\|4ff4]]~~</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=4ff2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ff2 OCA], [https://pdbe.org/4ff2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ff2 RCSB], [https://www.ebi.ac.uk/pdbsum/4ff2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ff2 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=4ff2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ff2 OCA], [~~http~~://pdbe.org/4ff2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ff2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ff2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ff2 ProSAT]</span></td></tr>
	</table>		</table>
			== 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>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 20:

	==See Also==		==See Also==
	*[[RNA polymerase\|RNA polymerase]]		*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Bpn4~~]]		[[Category: Escherichia virus N4]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Basu~~, R S~~]]		[[Category: Basu RS]]
	[[Category: Murakami~~, K S]]~~		[[Category: Murakami KS]]
	~~[[Category: Rna polymerase]]~~
	~~[[Category: Transferase-dna complex~~]]

OCA at 08:17, 27 March 2019

2019-03-27T08:17:17Z

← Older revision		Revision as of 08:17, 27 March 2019
Line 1:		Line 1:

	==N4 mini-vRNAP transcription initiation complex, 2 min after soaking GTP, ATP and Mn==		==N4 mini-vRNAP transcription initiation complex, 2 min after soaking GTP, ATP and Mn==
	<StructureSection load='4ff2' size='340' side='right' caption='[[4ff2]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='4ff2' size='340' side='right'caption='[[4ff2]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ff2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpn4 Bpn4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FF2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FF2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ff2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpn4 Bpn4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FF2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FF2 FirstGlance]. <br>
Line 25:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Bpn4]]		[[Category: Bpn4]]
			[[Category: Large Structures]]
	[[Category: Basu, R S]]		[[Category: Basu, R S]]
	[[Category: Murakami, K S]]		[[Category: Murakami, K S]]
	[[Category: Rna polymerase]]		[[Category: Rna polymerase]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 10:33, 11 August 2016

2016-08-11T10:33:13Z

← Older revision		Revision as of 10:33, 11 August 2016
Line 1:		Line 1:

	==N4 mini-vRNAP transcription initiation complex, 2 min after soaking GTP, ATP and Mn==		==N4 mini-vRNAP transcription initiation complex, 2 min after soaking GTP, ATP and Mn==
	<StructureSection load='4ff2' size='340' side='right' caption='[[4ff2]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='4ff2' size='340' side='right' caption='[[4ff2]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ff2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_phage_n4 Escherichia phage n4~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FF2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FF2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ff2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpn4 Bpn4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FF2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FF2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ff1\|4ff1]], [[4ff3\|4ff3]], [[4ff4\|4ff4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ff1\|4ff1]], [[4ff3\|4ff3]], [[4ff4\|4ff4]]</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=4ff2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ff2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ff2 RCSB], [http://www.ebi.ac.uk/pdbsum/4ff2 PDBsum]</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=4ff2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ff2 OCA], [http://pdbe.org/4ff2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ff2 RCSB], [http://www.ebi.ac.uk/pdbsum/4ff2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ff2 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 4ff2" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 22:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Escherichia phage n4~~]]		[[Category: Bpn4]]
	[[Category: Basu, R S]]		[[Category: Basu, R S]]
	[[Category: Murakami, K S]]		[[Category: Murakami, K S]]
	[[Category: Rna polymerase]]		[[Category: Rna polymerase]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 11:47, 20 January 2015

2015-01-20T11:47:55Z

← Older revision		Revision as of 11:47, 20 January 2015
Line 1:		Line 1:
	[[~~Image~~:~~4ff2~~.~~png~~\|~~left~~\|~~200px~~]]		==N4 mini-vRNAP transcription initiation complex, 2 min after soaking GTP, ATP and Mn==
			<StructureSection load='4ff2' size='340' side='right' caption='[[4ff2]], [[Resolution\|resolution]] 2.00Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[4ff2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_phage_n4 Escherichia phage n4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FF2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FF2 FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ff1\|4ff1]], [[4ff3\|4ff3]], [[4ff4\|4ff4]]</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=4ff2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ff2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ff2 RCSB], [http://www.ebi.ac.uk/pdbsum/4ff2 PDBsum]</span></td></tr>
			</table>
			<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.

	~~{{STRUCTURE_4ff2\| PDB=4ff2 \| SCENE= }}~~		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>

	~~===N4 mini-vRNAP transcription initiation complex~~, ~~2 min after soaking GTP, ATP and Mn===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_23235152}}~~

	~~==About this Structure==~~
	~~[[4ff2]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_phage_n4 Escherichia phage n4]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4FF2 OCA].~~

	==See Also==		==See Also==
	*[[RNA polymerase\|RNA polymerase]]		*[[RNA polymerase\|RNA polymerase]]
			== References ==
			<references/>
			__TOC__
			</StructureSection>
	[[Category: Escherichia phage n4]]		[[Category: Escherichia phage n4]]
	[[Category: Basu, R S.]]		[[Category: Basu, R S]]
	[[Category: Murakami, K S.]]		[[Category: Murakami, K S]]
	[[Category: Rna polymerase]]		[[Category: Rna polymerase]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 12:47, 20 February 2013

2013-02-20T12:47:48Z

← Older revision		Revision as of 12:47, 20 February 2013
Line 9:		Line 9:
	==About this Structure==		==About this Structure==
	[[4ff2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_phage_n4 Escherichia phage n4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FF2 OCA].		[[4ff2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_phage_n4 Escherichia phage n4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FF2 OCA].

			==See Also==
			*[[RNA polymerase\|RNA polymerase]]
	[[Category: Escherichia phage n4]]		[[Category: Escherichia phage n4]]
	[[Category: Basu, R S.]]		[[Category: Basu, R S.]]

OCA at 11:46, 23 January 2013

2013-01-23T11:46:01Z

← Older revision		Revision as of 11:46, 23 January 2013
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	[[Image:4ff2.~~jpg~~\|left\|200px]]		[[Image:4ff2.png\|left\|200px]]

	{{STRUCTURE_4ff2\| PDB=4ff2 \| SCENE= }}		{{STRUCTURE_4ff2\| PDB=4ff2 \| SCENE= }}
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	===N4 mini-vRNAP transcription initiation complex, 2 min after soaking GTP, ATP and Mn===		===N4 mini-vRNAP transcription initiation complex, 2 min after soaking GTP, ATP and Mn===

			{{ABSTRACT_PUBMED_23235152}}

	==About this Structure==		==About this Structure==

OCA at 21:25, 12 December 2012

2012-12-12T21:25:58Z

← Older revision		Revision as of 21:25, 12 December 2012
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	~~'''Unreleased structure'''~~		[[Image:4ff2.jpg\|left\|200px]]

	~~The entry~~ 4ff2 ~~is ON HOLD~~ ~~until Paper Publication~~		{{STRUCTURE_4ff2\| PDB=4ff2 \| SCENE= }}

	~~Authors: Murakami~~, ~~K.S.~~, ~~Basu, R.S.~~		===N4 mini-vRNAP transcription initiation complex, 2 min after soaking GTP, ATP and Mn===

	~~Description~~: ~~N4 mini~~-~~vRNAP transcription initiation complex~~, ~~2 min after soaking GTP~~, ~~ATP and Mn~~
			==About this Structure==
			[[4ff2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_phage_n4 Escherichia phage n4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FF2 OCA].
			[[Category: Escherichia phage n4]]
			[[Category: Basu, R S.]]
			[[Category: Murakami, K S.]]
			[[Category: Rna polymerase]]
			[[Category: Transferase-dna complex]]

OCA at 05:18, 15 August 2012

2012-08-15T05:18:23Z

← Older revision		Revision as of 05:18, 15 August 2012
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 4ff2 is ON HOLD		The entry 4ff2 is ON HOLD until Paper Publication

	Authors: Murakami, K.S., Basu, R.S.		Authors: Murakami, K.S., Basu, R.S.

	Description: N4 mini-vRNAP transcription initiation complex, 2 min after soaking GTP, ATP and Mn		Description: N4 mini-vRNAP transcription initiation complex, 2 min after soaking GTP, ATP and Mn