3g5i - Revision history

OCA at 15:36, 1 November 2023

OCA — Wed, 01 Nov 2023 15:36:52 GMT

←Older revision		Revision as of 15:36, 1 November 2023
Line 1:		Line 1:

	==Crystal Structure of the E.coli RihA pyrimidine nucleosidase bound to a iminoribitol-based inhibitor==		==Crystal Structure of the E.coli RihA pyrimidine nucleosidase bound to a iminoribitol-based inhibitor==
-	<StructureSection load='3g5i' size='340' side='right'caption='[[3g5i]]' scene=''>	+	<StructureSection load='3g5i' size='340' side='right'caption='[[3g5i]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G5I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G5I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3g5i]] is a 4 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=3G5I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G5I FirstGlance]. <br>
-	</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=3g5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g5i OCA], [https://pdbe.org/3g5i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g5i RCSB], [https://www.ebi.ac.uk/pdbsum/3g5i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g5i ProSAT]</span></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]] 2.1Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DNB:(2S,3S,4R,5R)-2-(3,4-DIAMINOPHENYL)-5-(HYDROXYMETHYL)PYRROLIDINE-3,4-DIOL'>DNB</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=3g5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g5i OCA], [https://pdbe.org/3g5i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g5i RCSB], [https://www.ebi.ac.uk/pdbsum/3g5i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g5i ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/RIHA_ECOLI RIHA_ECOLI] Hydrolyzes with equal efficiency cytidine or uridine to ribose and cytosine or uracil, respectively.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 16:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3g5i ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3g5i ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BACKGROUND: Pyrimidine-preferring N-ribohydrolases (CU-NHs) are a class of Ca2+-dependent enzymes that catalyze the hydrolytic cleavage of the N-glycosidic bond in pyrimidine nucleosides. With the exception of few selected organisms, their physiological relevance in prokaryotes and eukaryotes is yet under investigation. RESULTS: Here, we report the first crystal structure of a CU-NH bound to a competitive inhibitor, the complex between the Escherichia coli enzyme RihA bound to 3, 4-diaminophenyl-iminoribitol (DAPIR) to a resolution of 2.1 A. The ligand can bind at the active site in two distinct orientations, and the stabilization of two flexible active site regions is pivotal to establish the interactions required for substrate discrimination and catalysis. CONCLUSIONS: A comparison with the product-bound RihA structure allows a rationalization of the structural rearrangements required for an enzymatic catalytic cycle, highlighting a substrate-assisted cooperative motion, and suggesting a yet overlooked role of the conserved His82 residue in modulating product release. Differences in the structural features of the active sites in the two homologous CU-NHs RihA and RihB from E. coli provide a rationale for their fine differences in substrate specificity. These new findings hint at a possible role of CU-NHs in the breakdown of modified nucleosides derived from RNA molecules.
		+
		+	Active site plasticity revealed from the structure of the enterobacterial N-ribohydrolase RihA bound to a competitive inhibitor.,Garau G, Muzzolini L, Tornaghi P, Degano M BMC Struct Biol. 2010 Jun 8;10:14. doi: 10.1186/1472-6807-10-14. PMID:20529317<ref>PMID:20529317</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 3g5i" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Degano M]]		[[Category: Degano M]]

OCA at 07:56, 9 March 2022

OCA — Wed, 09 Mar 2022 07:56:10 GMT

←Older revision		Revision as of 07:56, 9 March 2022
Line 1:		Line 1:

	==Crystal Structure of the E.coli RihA pyrimidine nucleosidase bound to a iminoribitol-based inhibitor==		==Crystal Structure of the E.coli RihA pyrimidine nucleosidase bound to a iminoribitol-based inhibitor==
-	<StructureSection load='3g5i' size='340' side='right' caption='[[3g5i]]~~, [[Resolution\|resolution]] 2.10Å~~' scene=''>	+	<StructureSection load='3g5i' size='340' side='right'caption='[[3g5i]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[3g5i]] is a 4 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=3G5I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3G5I FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G5I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G5I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DNB:(2S,3S,4R,5R)-2-(3,4-DIAMINOPHENYL)-5-(HYDROXYMETHYL)PYRROLIDINE-3,4-DIOL'>DNB</scene></td></tr>	+	</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=3g5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g5i OCA], [https://pdbe.org/3g5i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g5i RCSB], [https://www.ebi.ac.uk/pdbsum/3g5i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g5i ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yoe\|1yoe]], [[1q8f\|1q8f]]</td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ybeK ([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/Ribosylpyrimidine_nucleosidase Ribosylpyrimidine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.8 3.2.2.8] </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=3g5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g5i OCA], [~~http~~://pdbe.org/3g5i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3g5i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3g5i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3g5i ProSAT]</span></td></tr>	+
	</table>		</table>
-	== Function ==
-	[[http://www.uniprot.org/uniprot/RIHA_ECOLI RIHA_ECOLI]] Hydrolyzes with equal efficiency cytidine or uridine to ribose and cytosine or uracil, respectively.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 22:		Line 16:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3g5i ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3g5i ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Nucleoside hydrolases (NHs) are enzymes that catalyze the excision of the N-glycosidic bond in nucleosides to allow recycling of the nitrogenous bases. The fine details of the catalytic mechanism and the structural features imposing the substrate specificity of the various members of the NH family are still debated. Here we present the functional characterization of the Escherichia coli YbeK (RihA) protein as a pyrimidine nucleoside-preferring NH and its first crystal structure to 1.8 A resolution. The enzyme active site is occupied by either the alpha or beta anomer of ribose and provides the first structural description of the binding of the NH reaction product. While the amino acid residues involved in ribosyl binding are strictly conserved in pyrimidine-specific NHs, the residues involved in specific interactions with the nitrogenous bases differ considerably. Further comparison of the active site architecture of YbeK with the related NHs establishes structural determinants involved in triggering the conformational transition between the open and closed structures and suggests a mechanism for product release.
-
-	New insights into the mechanism of nucleoside hydrolases from the crystal structure of the Escherichia coli YbeK protein bound to the reaction product.,Muzzolini L, Versees W, Tornaghi P, Van Holsbeke E, Steyaert J, Degano M Biochemistry. 2006 Jan 24;45(3):773-82. PMID:16411753<ref>PMID:16411753</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3g5i" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli]]~~	+	[[Category: Large Structures]]
-	~~[[Category: Ribosylpyrimidine nucleosidase~~]]	+	[[Category: Degano M]]
-	[[Category: Degano, M]]	+	[[Category: Garau G]]
-	[[Category: Garau, G]]	+	[[Category: Muzzolini L]]
-	[[Category: Muzzolini, L]]	+	[[Category: Tornaghi P]]
-	[[Category: Tornaghi, P]]	+
-	~~[[Category: Glycosidase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 07:38, 5 December 2018

OCA — Wed, 05 Dec 2018 07:38:48 GMT

←Older revision		Revision as of 07:38, 5 December 2018
Line 16:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g5/3g5i_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g5/3g5i_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 03:03, 5 August 2016

OCA — Fri, 05 Aug 2016 03:03:44 GMT

←Older revision		Revision as of 03:03, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of the E.coli RihA pyrimidine nucleosidase bound to a iminoribitol-based inhibitor==		==Crystal Structure of the E.coli RihA pyrimidine nucleosidase bound to a iminoribitol-based inhibitor==
	<StructureSection load='3g5i' size='340' side='right' caption='[[3g5i]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3g5i' size='340' side='right' caption='[[3g5i]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3g5i]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia coli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G5I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G5I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3g5i]] is a 4 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=3G5I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G5I FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DNB:(2S,3S,4R,5R)-2-(3,4-DIAMINOPHENYL)-5-(HYDROXYMETHYL)PYRROLIDINE-3,4-DIOL'>DNB</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DNB:(2S,3S,4R,5R)-2-(3,4-DIAMINOPHENYL)-5-(HYDROXYMETHYL)PYRROLIDINE-3,4-DIOL'>DNB</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yoe\|1yoe]], [[1q8f\|1q8f]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yoe\|1yoe]], [[1q8f\|1q8f]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ybeK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~562 Escherichia coli~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ybeK ([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/Ribosylpyrimidine_nucleosidase Ribosylpyrimidine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.8 3.2.2.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribosylpyrimidine_nucleosidase Ribosylpyrimidine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.8 3.2.2.8] </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=3g5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g5i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g5i RCSB], [http://www.ebi.ac.uk/pdbsum/3g5i 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=3g5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g5i OCA], [http://pdbe.org/3g5i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g5i RCSB], [http://www.ebi.ac.uk/pdbsum/3g5i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3g5i ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3g5i ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 30:
	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 3g5i" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia coli~~]]	+	[[Category: Ecoli]]
	[[Category: Ribosylpyrimidine nucleosidase]]		[[Category: Ribosylpyrimidine nucleosidase]]
	[[Category: Degano, M]]		[[Category: Degano, M]]

OCA at 15:21, 25 December 2014

OCA — Thu, 25 Dec 2014 15:21:40 GMT

←Older revision		Revision as of 15:21, 25 December 2014
Line 9:		Line 9:
	<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=3g5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g5i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g5i RCSB], [http://www.ebi.ac.uk/pdbsum/3g5i 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=3g5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g5i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g5i RCSB], [http://www.ebi.ac.uk/pdbsum/3g5i PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RIHA_ECOLI RIHA_ECOLI]] Hydrolyzes with equal efficiency cytidine or uridine to ribose and cytosine or uracil, respectively.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 10:26, 3 December 2014

OCA — Wed, 03 Dec 2014 10:26:49 GMT

←Older revision		Revision as of 10:26, 3 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3g5i.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of the E.coli RihA pyrimidine nucleosidase bound to a iminoribitol-based inhibitor==
		+	<StructureSection load='3g5i' size='340' side='right' caption='[[3g5i]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3g5i]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G5I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G5I FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DNB:(2S,3S,4R,5R)-2-(3,4-DIAMINOPHENYL)-5-(HYDROXYMETHYL)PYRROLIDINE-3,4-DIOL'>DNB</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yoe\|1yoe]], [[1q8f\|1q8f]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ybeK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribosylpyrimidine_nucleosidase Ribosylpyrimidine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.8 3.2.2.8] </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=3g5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g5i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g5i RCSB], [http://www.ebi.ac.uk/pdbsum/3g5i PDBsum]</span></td></tr>
		+	</table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g5/3g5i_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Nucleoside hydrolases (NHs) are enzymes that catalyze the excision of the N-glycosidic bond in nucleosides to allow recycling of the nitrogenous bases. The fine details of the catalytic mechanism and the structural features imposing the substrate specificity of the various members of the NH family are still debated. Here we present the functional characterization of the Escherichia coli YbeK (RihA) protein as a pyrimidine nucleoside-preferring NH and its first crystal structure to 1.8 A resolution. The enzyme active site is occupied by either the alpha or beta anomer of ribose and provides the first structural description of the binding of the NH reaction product. While the amino acid residues involved in ribosyl binding are strictly conserved in pyrimidine-specific NHs, the residues involved in specific interactions with the nitrogenous bases differ considerably. Further comparison of the active site architecture of YbeK with the related NHs establishes structural determinants involved in triggering the conformational transition between the open and closed structures and suggests a mechanism for product release.

-	~~{{STRUCTURE_3g5i\| PDB=3g5i \| SCENE= }}~~	+	New insights into the mechanism of nucleoside hydrolases from the crystal structure of the Escherichia coli YbeK protein bound to the reaction product.,Muzzolini L, Versees W, Tornaghi P, Van Holsbeke E, Steyaert J, Degano M Biochemistry. 2006 Jan 24;45(3):773-82. PMID:16411753<ref>PMID:16411753</ref>

-	~~===Crystal Structure~~ of the E.~~coli RihA pyrimidine nucleosidase bound to a iminoribitol-based inhibitor===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16411753}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3g5i]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org~~/~~wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G5I OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016411753<~~/~~ref~~><~~ref group="xtra">PMID:015130467</ref><references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Ribosylpyrimidine nucleosidase]]		[[Category: Ribosylpyrimidine nucleosidase]]
-	[[Category: Degano, M.]]	+	[[Category: Degano, M]]
-	[[Category: Garau, G.]]	+	[[Category: Garau, G]]
-	[[Category: Muzzolini, L.]]	+	[[Category: Muzzolini, L]]
-	[[Category: Tornaghi, P.]]	+	[[Category: Tornaghi, P]]
	[[Category: Glycosidase]]		[[Category: Glycosidase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 14:46, 20 February 2013

OCA — Wed, 20 Feb 2013 14:46:46 GMT

←Older revision		Revision as of 14:46, 20 February 2013
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	[[Image:3g5i.png\|left\|200px]]		[[Image:3g5i.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3g5i", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3g5i\| PDB=3g5i \| SCENE= }}		{{STRUCTURE_3g5i\| PDB=3g5i \| SCENE= }}

	===Crystal Structure of the E.coli RihA pyrimidine nucleosidase bound to a iminoribitol-based inhibitor===		===Crystal Structure of the E.coli RihA pyrimidine nucleosidase bound to a iminoribitol-based inhibitor===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16411753}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16411753 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16411753}}		{{ABSTRACT_PUBMED_16411753}}

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	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16411753~~</ref><ref group="xtra">PMID:~~15130467~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016411753</ref><ref group="xtra">PMID:015130467</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Ribosylpyrimidine nucleosidase]]		[[Category: Ribosylpyrimidine nucleosidase]]

OCA: Protected "3g5i" [edit=sysop:move=sysop]

OCA — Mon, 14 Mar 2011 18:32:26 GMT

Protected "3g5i" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:32, 14 March 2011

OCA at 18:32, 14 March 2011

OCA — Mon, 14 Mar 2011 18:32:24 GMT

←Older revision		Revision as of 18:32, 14 March 2011
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-	~~{{Seed}}~~	+	[[Image:3g5i.png\|left\|200px]]
-	[[Image:3g5i.~~jpg~~\|left\|200px]]	+

	<!--		<!--
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	===Crystal Structure of the E.coli RihA pyrimidine nucleosidase bound to a iminoribitol-based inhibitor===		===Crystal Structure of the E.coli RihA pyrimidine nucleosidase bound to a iminoribitol-based inhibitor===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_16411753}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 16411753 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_16411753}}

	==About this Structure==		==About this Structure==
-	~~3G5I~~ is a 4 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G5I OCA].	+	[[3g5i]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G5I OCA].

	==Reference==		==Reference==
Line 26:		Line 31:
	[[Category: Glycosidase]]		[[Category: Glycosidase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 10 17:52:56 2010''

OCA at 15:52, 10 February 2010

OCA — Wed, 10 Feb 2010 15:52:57 GMT

←Older revision		Revision as of 15:52, 10 February 2010
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3g5i.jpg\|left\|200px]]

-	The ~~entry 3g5i~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3g5i", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3g5i\| PDB=3g5i \| SCENE= }}

-	~~Authors: Garau, G., Muzzolini, L., Tornaghi, P., Degano, M~~.	+	===Crystal Structure of the E.coli RihA pyrimidine nucleosidase bound to a iminoribitol-based inhibitor===

-	Description: Crystal Structure of the E.coli RihA pyrimidine nucleosidase bound to a iminoribitol-based inhibitor

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Mar 22~~ 10:24:~~00 2009~~''	+	==About this Structure==
		+	3G5I is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G5I OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:16411753</ref><ref group="xtra">PMID:15130467</ref><references group="xtra"/>
		+	[[Category: Escherichia coli]]
		+	[[Category: Ribosylpyrimidine nucleosidase]]
		+	[[Category: Degano, M.]]
		+	[[Category: Garau, G.]]
		+	[[Category: Muzzolini, L.]]
		+	[[Category: Tornaghi, P.]]
		+	[[Category: Glycosidase]]
		+	[[Category: Hydrolase]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 10 17:52:56 2010''