4lab - Revision history

OCA at 16:15, 20 September 2023

2023-09-20T16:15:27Z

← Older revision		Revision as of 16:15, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4lab]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LAB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LAB FirstGlance]. <br>		<table><tr><td colspan='2'>[[4lab]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LAB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LAB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</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]] 2.5043Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</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=4lab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lab OCA], [https://pdbe.org/4lab PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lab RCSB], [https://www.ebi.ac.uk/pdbsum/4lab PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lab 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=4lab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lab OCA], [https://pdbe.org/4lab PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lab RCSB], [https://www.ebi.ac.uk/pdbsum/4lab PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lab ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:47, 14 December 2022

2022-12-14T10:47:47Z

← Older revision		Revision as of 10:47, 14 December 2022
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	<StructureSection load='4lab' size='340' side='right'caption='[[4lab]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='4lab' size='340' side='right'caption='[[4lab]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4lab]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LAB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4LAB FirstGlance]. <br>		<table><tr><td colspan='2'>[[4lab]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LAB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LAB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene~~></td></tr>~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b1269, JW1261, rluB, yciL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=4lab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lab OCA], [https://pdbe.org/4lab PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lab RCSB], [https://www.ebi.ac.uk/pdbsum/4lab PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lab ProSAT]</span></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/23S_rRNA_pseudouridine(2605)_synthase 23S rRNA pseudouridine(2605) synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.99.22 5.4.99.22] </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=4lab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lab OCA], [~~http~~://pdbe.org/4lab PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4lab RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4lab PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4lab ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/RLUB_ECOLI RLUB_ECOLI]] Responsible for synthesis of pseudouridine from uracil-2605 in 23S ribosomal RNA.		[https://www.uniprot.org/uniprot/RLUB_ECOLI RLUB_ECOLI] Responsible for synthesis of pseudouridine from uracil-2605 in 23S ribosomal RNA.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
	*[[Guide-independent Pseudouridine synthase\|Guide-independent Pseudouridine synthase]]		*[[Guide-independent Pseudouridine synthase\|Guide-independent Pseudouridine synthase]]
			*[[Pseudouridine synthase 3D structures\|Pseudouridine synthase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Ecoli~~]]		[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Czudnochowski, N]]		[[Category: Czudnochowski N]]
	[[Category: Finer-Moore~~, J S~~]]		[[Category: Finer-Moore JS]]
	[[Category: Stroud~~, R M]]~~		[[Category: Stroud RM]]
	~~[[Category: Alpha-beta protein]]~~
	~~[[Category: Beta sheet]]~~
	~~[[Category: E. coli ribosomal rna]]~~
	~~[[Category: Pseudouridine synthase]]~~
	~~[[Category: Rna binding protein~~]]

OCA at 12:05, 17 July 2019

2019-07-17T12:05:20Z

← Older revision		Revision as of 12:05, 17 July 2019
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	==Crystal structure of the catalytic domain of RluB==		==Crystal structure of the catalytic domain of RluB==
	<StructureSection load='4lab' size='340' side='right' caption='[[4lab]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='4lab' size='340' side='right'caption='[[4lab]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4lab]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LAB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LAB FirstGlance]. <br>		<table><tr><td colspan='2'>[[4lab]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LAB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LAB FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 4lab" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4lab" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Guide-independent Pseudouridine synthase\|Guide-independent Pseudouridine synthase]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Ecoli]]		[[Category: Ecoli]]
			[[Category: Large Structures]]
	[[Category: Czudnochowski, N]]		[[Category: Czudnochowski, N]]
	[[Category: Finer-Moore, J S]]		[[Category: Finer-Moore, J S]]

OCA at 16:56, 4 August 2016

2016-08-04T16:56:03Z

← Older revision		Revision as of 16:56, 4 August 2016
Line 1:		Line 1:

	==Crystal structure of the catalytic domain of RluB==		==Crystal structure of the catalytic domain of RluB==
	<StructureSection load='4lab' size='340' side='right' caption='[[4lab]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='4lab' size='340' side='right' caption='[[4lab]], [[Resolution\|resolution]] 2.50Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b1269, JW1261, rluB, yciL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b1269, JW1261, rluB, yciL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/23S_rRNA_pseudouridine(2605)_synthase 23S rRNA pseudouridine(2605) synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.99.22 5.4.99.22] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/23S_rRNA_pseudouridine(2605)_synthase 23S rRNA pseudouridine(2605) synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.99.22 5.4.99.22] </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=4lab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lab OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4lab RCSB], [http://www.ebi.ac.uk/pdbsum/4lab 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=4lab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lab OCA], [http://pdbe.org/4lab PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4lab RCSB], [http://www.ebi.ac.uk/pdbsum/4lab PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4lab ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 4lab" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:09, 25 December 2014

2014-12-25T11:09:15Z

← Older revision		Revision as of 11:09, 25 December 2014
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	~~{{STRUCTURE_4lab\| PDB~~=4lab \| ~~SCENE~~= }}		==Crystal structure of the catalytic domain of RluB==
	===~~Crystal~~ structure of the ~~catalytic domain of RluB~~===		<StructureSection load='4lab' size='340' side='right' caption='[[4lab]], [[Resolution\|resolution]] 2.50Å' scene=''>
	~~{{ABSTRACT_PUBMED_24214967}}~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[4lab]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LAB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LAB FirstGlance]. <br>
	==Function==		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b1269, JW1261, rluB, yciL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
			<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/23S_rRNA_pseudouridine(2605)_synthase 23S rRNA pseudouridine(2605) synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.99.22 5.4.99.22] </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=4lab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lab OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4lab RCSB], [http://www.ebi.ac.uk/pdbsum/4lab PDBsum]</span></td></tr>
			</table>
			== Function ==
	[[http://www.uniprot.org/uniprot/RLUB_ECOLI RLUB_ECOLI]] Responsible for synthesis of pseudouridine from uracil-2605 in 23S ribosomal RNA.		[[http://www.uniprot.org/uniprot/RLUB_ECOLI RLUB_ECOLI]] Responsible for synthesis of pseudouridine from uracil-2605 in 23S ribosomal RNA.
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			RluB catalyses the modification of U2605 to pseudouridine (Psi) in a stem-loop at the peptidyl transferase center of Escherichia coli 23S rRNA. The homolog RluF is specific to the adjacent nucleotide in the stem, U2604. The 1.3 A resolution crystal structure of the complex between the catalytic domain of RluB and the isolated substrate stem-loop, in which the target uridine is substituted by 5-fluorouridine (5-FU), reveals a covalent bond between the isomerized target base and tyrosine 140. The structure is compared with the catalytic domain alone determined at 2.5 A resolution. The RluB-bound stem-loop has essentially the same secondary structure as in the ribosome, with a bulge at A2602, but with 5-FU2605 flipped into the active site. We showed earlier that RluF induced a frame-shift of the RNA, moving A2602 into the stem and translating its target, U2604, into the active site. A hydrogen-bonding network stabilizes the bulge in the RluB-RNA but is not conserved in RluF and so RluF cannot stabilize the bulge. On the basis of the covalent bond between enzyme and isomerized 5-FU we propose a Michael addition mechanism for pseudouridine formation that is consistent with all experimental data.

	~~==About this Structure==~~		The mechanism of pseudouridine synthases from a covalent complex with RNA, and alternate specificity for U2605 versus U2604 between close homologs.,Czudnochowski N, Ashley GW, Santi DV, Alian A, Finer-Moore J, Stroud RM Nucleic Acids Res. 2013 Nov 7. PMID:24214967<ref>PMID:24214967</ref>
	~~[[4lab]] is~~ a ~~1 chain structure~~ with ~~sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Ecoli Ecoli]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4LAB OCA].~~

	==~~Reference~~==		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	~~<ref group="xtra">PMID:024214967</ref>~~<references ~~group="xtra"~~/><~~references~~/>		</div>
			== References ==
			<references/>
			__TOC__
			</StructureSection>
	[[Category: Ecoli]]		[[Category: Ecoli]]
	[[Category: Czudnochowski, N.]]		[[Category: Czudnochowski, N]]
	[[Category: Finer-Moore, J S.]]		[[Category: Finer-Moore, J S]]
	[[Category: Stroud, R M.]]		[[Category: Stroud, R M]]
	[[Category: Alpha-beta protein]]		[[Category: Alpha-beta protein]]
	[[Category: Beta sheet]]		[[Category: Beta sheet]]

OCA at 14:27, 3 March 2014

2014-03-03T14:27:02Z

← Older revision		Revision as of 14:27, 3 March 2014
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	==About this Structure==		==About this Structure==
	[[4lab]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LAB OCA].		[[4lab]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LAB OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:024214967</ref><references group="xtra"/><references/>		<ref group="xtra">PMID:024214967</ref><references group="xtra"/><references/>
			[[Category: Ecoli]]
	[[Category: Czudnochowski, N.]]		[[Category: Czudnochowski, N.]]
	[[Category: Finer-Moore, J S.]]		[[Category: Finer-Moore, J S.]]

OCA at 13:30, 20 November 2013

2013-11-20T13:30:02Z

← Older revision		Revision as of 13:30, 20 November 2013
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	~~'''Unreleased~~ structure~~'''~~		{{STRUCTURE_4lab\| PDB=4lab \| SCENE= }}
			===Crystal structure of the catalytic domain of RluB===
			{{ABSTRACT_PUBMED_24214967}}

	~~The entry 4lab is ON HOLD until Paper Publication~~		==Function==
			[[http://www.uniprot.org/uniprot/RLUB_ECOLI RLUB_ECOLI]] Responsible for synthesis of pseudouridine from uracil-2605 in 23S ribosomal RNA.

	~~Authors~~: ~~Czudnochowski, N., Finer-Moore, J~~.S.~~, Stroud, R~~.M.		==About this Structure==
			[[4lab]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LAB OCA].

	~~Description~~: ~~Crystal structure of the catalytic domain of RluB~~		==Reference==
			<ref group="xtra">PMID:024214967</ref><references group="xtra"/><references/>
			[[Category: Czudnochowski, N.]]
			[[Category: Finer-Moore, J S.]]
			[[Category: Stroud, R M.]]
			[[Category: Alpha-beta protein]]
			[[Category: Beta sheet]]
			[[Category: E. coli ribosomal rna]]
			[[Category: Pseudouridine synthase]]
			[[Category: Rna binding protein]]

OCA at 04:15, 1 August 2013

2013-08-01T04:15:25Z

← Older revision		Revision as of 04:15, 1 August 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Czudnochowski, N., Finer-Moore, J.S., Stroud, R.M.		Authors: Czudnochowski, N., Finer-Moore, J.S., Stroud, R.M.

	Description: Crystal structure of the catalytic domain of RluB		Description: Crystal structure of the catalytic domain of RluB

OCA: Protected "4lab" [edit=sysop:move=sysop]

2013-06-30T09:10:35Z

Protected "4lab" [edit=sysop:move=sysop]

← Older revision	Revision as of 09:10, 30 June 2013
(No difference)

OCA: New page: '''Unreleased structure''' The entry 4lab is ON HOLD Authors: Czudnochowski, N., Finer-Moore, J.S., Stroud, R.M. Description: Crystal structure of the catalytic domain of RluB

2013-06-30T09:10:33Z

New page: '''Unreleased structure''' The entry 4lab is ON HOLD Authors: Czudnochowski, N., Finer-Moore, J.S., Stroud, R.M. Description: Crystal structure of the catalytic domain of RluB

New page

'''Unreleased structure'''

The entry 4lab is ON HOLD

Authors: Czudnochowski, N., Finer-Moore, J.S., Stroud, R.M.

Description: Crystal structure of the catalytic domain of RluB