1j7g - Revision history

OCA at 07:37, 7 February 2024

OCA — Wed, 07 Feb 2024 07:37:39 GMT

←Older revision		Revision as of 07:37, 7 February 2024
Line 3:		Line 3:
	<StructureSection load='1j7g' size='340' side='right'caption='[[1j7g]], [[Resolution\|resolution]] 1.64Å' scene=''>		<StructureSection load='1j7g' size='340' side='right'caption='[[1j7g]], [[Resolution\|resolution]] 1.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1j7g]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Haein Haein~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J7G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1J7G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1j7g]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae_Rd_KW20 Haemophilus influenzae Rd KW20]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J7G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J7G FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~HI0670 (~~[~~http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=71421 HAEIN])~~</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]] 1.64Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1j7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j7g OCA], [~~http~~://pdbe.org/1j7g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1j7g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1j7g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1j7g 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=1j7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j7g OCA], [https://pdbe.org/1j7g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j7g RCSB], [https://www.ebi.ac.uk/pdbsum/1j7g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j7g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DTD_HAEIN DTD_HAEIN]] Hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr). Could be a defense mechanism against a harmful effect of D-tyrosine (By similarity).	+	[https://www.uniprot.org/uniprot/DTD_HAEIN DTD_HAEIN] Hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr). Could be a defense mechanism against a harmful effect of D-tyrosine (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 19:
	</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=1j7g 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=1j7g ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	D-Tyr-tRNA(Tyr) deacylase is an editing enzyme that removes d-tyrosine and other d-amino acids from charged tRNAs, thereby preventing incorrect incorporation of d-amino acids into proteins. A model for the catalytic mechanism of this enzyme is proposed based on the crystal structure of the enzyme from Haemophilus influenzae determined at a 1.64-A resolution. Structural comparison of this dimeric enzyme with the very similar structure of the enzyme from Escherichia coli together with sequence analyses indicate that the active site is located in the dimer interface within a depression that includes an invariant threonine residue, Thr-80. The active site contains an oxyanion hole formed by the main chain nitrogen atoms of Thr-80 and Phe-79 and the side chain amide group of the invariant Gln-78. The Michaelis complex between the enzyme and D-Tyr-tRNA was modeled assuming a nucleophilic attack on the carbonyl carbon of D-Tyr by the Thr-80 O(gamma) atom and a role for the oxyanion hole in stabilizing the negatively charged tetrahedral transition states. The model is consistent with all of the available data on substrate specificity. Based on this model, we propose a substrate-assisted acylation/deacylation-catalytic mechanism in which the amino group of the D-Tyr is deprotonated and serves as the general base.
-
-	A catalytic mechanism for D-Tyr-tRNATyr deacylase based on the crystal structure of Hemophilus influenzae HI0670.,Lim K, Tempczyk A, Bonander N, Toedt J, Howard A, Eisenstein E, Herzberg O J Biol Chem. 2003 Apr 11;278(15):13496-502. Epub 2003 Feb 4. PMID:12571243<ref>PMID:12571243</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1j7g" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Haein~~]]	+	[[Category: Haemophilus influenzae Rd KW20]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Herzberg, O]]	+	[[Category: Herzberg O]]
-	[[Category: Lim, K]]	+	[[Category: Lim K]]
-	~~[[Category: S2F, Structure 2.Function Project]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hypothetical protein]]~~	+
-	~~[[Category: S2f]]~~	+
-	~~[[Category: Structural genomic]]~~	+
-	~~[[Category: Structure 2 function project~~]]	+

OCA at 07:28, 25 November 2020

OCA — Wed, 25 Nov 2020 07:28:26 GMT

←Older revision		Revision as of 07:28, 25 November 2020
Line 1:		Line 1:

	==Structure of YihZ from Haemophilus influenzae (HI0670), a D-Tyr-tRNA(Tyr) deacylase==		==Structure of YihZ from Haemophilus influenzae (HI0670), a D-Tyr-tRNA(Tyr) deacylase==
-	<StructureSection load='1j7g' size='340' side='right' caption='[[1j7g]], [[Resolution\|resolution]] 1.64Å' scene=''>	+	<StructureSection load='1j7g' size='340' side='right'caption='[[1j7g]], [[Resolution\|resolution]] 1.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1j7g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Haein Haein]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J7G OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1J7G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1j7g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Haein Haein]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J7G OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1J7G FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HI0670 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=71421 HAEIN])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HI0670 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=71421 HAEIN])</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=1j7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j7g OCA], [http://pdbe.org/1j7g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1j7g RCSB], [http://www.ebi.ac.uk/pdbsum/1j7g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1j7g ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1j7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j7g OCA], [http://pdbe.org/1j7g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1j7g RCSB], [http://www.ebi.ac.uk/pdbsum/1j7g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1j7g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</StructureSection>		</StructureSection>
	[[Category: Haein]]		[[Category: Haein]]
		+	[[Category: Large Structures]]
	[[Category: Herzberg, O]]		[[Category: Herzberg, O]]
	[[Category: Lim, K]]		[[Category: Lim, K]]

OCA at 08:37, 17 January 2018

OCA — Wed, 17 Jan 2018 08:37:26 GMT

←Older revision		Revision as of 08:37, 17 January 2018
Line 1:		Line 1:
		+
	==Structure of YihZ from Haemophilus influenzae (HI0670), a D-Tyr-tRNA(Tyr) deacylase==		==Structure of YihZ from Haemophilus influenzae (HI0670), a D-Tyr-tRNA(Tyr) deacylase==
	<StructureSection load='1j7g' size='340' side='right' caption='[[1j7g]], [[Resolution\|resolution]] 1.64Å' scene=''>		<StructureSection load='1j7g' size='340' side='right' caption='[[1j7g]], [[Resolution\|resolution]] 1.64Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1j7g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Haein Haein]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J7G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J7G FirstGlance]. <br>		<table><tr><td colspan='2'>[[1j7g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Haein Haein]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J7G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J7G FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HI0670 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=71421 HAEIN])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HI0670 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=71421 HAEIN])</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=1j7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j7g OCA], [http://pdbe.org/1j7g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1j7g RCSB], [http://www.ebi.ac.uk/pdbsum/1j7g 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=1j7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j7g OCA], [http://pdbe.org/1j7g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1j7g RCSB], [http://www.ebi.ac.uk/pdbsum/1j7g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1j7g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/j7/1j7g_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/j7/1j7g_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 00:25, 9 February 2016

OCA — Tue, 09 Feb 2016 00:25:13 GMT

←Older revision		Revision as of 00:25, 9 February 2016
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	<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=1j7g ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 16:48, 10 September 2015

OCA — Thu, 10 Sep 2015 16:48:52 GMT

←Older revision		Revision as of 16:48, 10 September 2015
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	<StructureSection load='1j7g' size='340' side='right' caption='[[1j7g]], [[Resolution\|resolution]] 1.64Å' scene=''>		<StructureSection load='1j7g' size='340' side='right' caption='[[1j7g]], [[Resolution\|resolution]] 1.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1j7g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Haemophilus_influenzae_rd_kw20 Haemophilus influenzae rd kw20~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J7G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J7G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1j7g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Haein Haein]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J7G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J7G FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HI0670 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=71421 ~~Haemophilus influenzae Rd KW20~~])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HI0670 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=71421 HAEIN])</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=1j7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j7g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1j7g RCSB], [http://www.ebi.ac.uk/pdbsum/1j7g 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=1j7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j7g OCA], [http://pdbe.org/1j7g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1j7g RCSB], [http://www.ebi.ac.uk/pdbsum/1j7g PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 26:		Line 26:
	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 1j7g" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Haemophilus influenzae rd kw20~~]]	+	[[Category: Haein]]
	[[Category: Herzberg, O]]		[[Category: Herzberg, O]]
	[[Category: Lim, K]]		[[Category: Lim, K]]

OCA at 03:11, 25 December 2014

OCA — Thu, 25 Dec 2014 03:11:40 GMT

←Older revision		Revision as of 03:11, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1j7g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae_rd_kw20 Haemophilus influenzae rd kw20]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J7G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J7G FirstGlance]. <br>		<table><tr><td colspan='2'>[[1j7g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae_rd_kw20 Haemophilus influenzae rd kw20]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J7G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J7G FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HI0670 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=71421 Haemophilus influenzae Rd KW20])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HI0670 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=71421 Haemophilus influenzae Rd KW20])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1j7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j7g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1j7g RCSB], [http://www.ebi.ac.uk/pdbsum/1j7g 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=1j7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j7g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1j7g RCSB], [http://www.ebi.ac.uk/pdbsum/1j7g PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DTD_HAEIN DTD_HAEIN]] Hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr). Could be a defense mechanism against a harmful effect of D-tyrosine (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Haemophilus influenzae rd kw20]]		[[Category: Haemophilus influenzae rd kw20]]
-	[[Category: Herzberg, O.]]	+	[[Category: Herzberg, O]]
-	[[Category: Lim, K.]]	+	[[Category: Lim, K]]
-	[[Category: S2F, Structure 2.Function Project.]]	+	[[Category: S2F, Structure 2.Function Project]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Hypothetical protein]]		[[Category: Hypothetical protein]]

OCA at 09:08, 28 September 2014

OCA — Sun, 28 Sep 2014 09:08:14 GMT

←Older revision		Revision as of 09:08, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1j7g.~~png\|left~~\|200px]]	+	==Structure of YihZ from Haemophilus influenzae (HI0670), a D-Tyr-tRNA(Tyr) deacylase==
		+	<StructureSection load='1j7g' size='340' side='right' caption='[[1j7g]], [[Resolution\|resolution]] 1.64Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1j7g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae_rd_kw20 Haemophilus influenzae rd kw20]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J7G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J7G FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HI0670 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=71421 Haemophilus influenzae Rd KW20])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1j7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j7g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1j7g RCSB], [http://www.ebi.ac.uk/pdbsum/1j7g 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/j7/1j7g_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 ==
		+	D-Tyr-tRNA(Tyr) deacylase is an editing enzyme that removes d-tyrosine and other d-amino acids from charged tRNAs, thereby preventing incorrect incorporation of d-amino acids into proteins. A model for the catalytic mechanism of this enzyme is proposed based on the crystal structure of the enzyme from Haemophilus influenzae determined at a 1.64-A resolution. Structural comparison of this dimeric enzyme with the very similar structure of the enzyme from Escherichia coli together with sequence analyses indicate that the active site is located in the dimer interface within a depression that includes an invariant threonine residue, Thr-80. The active site contains an oxyanion hole formed by the main chain nitrogen atoms of Thr-80 and Phe-79 and the side chain amide group of the invariant Gln-78. The Michaelis complex between the enzyme and D-Tyr-tRNA was modeled assuming a nucleophilic attack on the carbonyl carbon of D-Tyr by the Thr-80 O(gamma) atom and a role for the oxyanion hole in stabilizing the negatively charged tetrahedral transition states. The model is consistent with all of the available data on substrate specificity. Based on this model, we propose a substrate-assisted acylation/deacylation-catalytic mechanism in which the amino group of the D-Tyr is deprotonated and serves as the general base.

-	~~{{STRUCTURE_1j7g\| PDB=1j7g \| SCENE= }}~~	+	A catalytic mechanism for D-Tyr-tRNATyr deacylase based on the crystal structure of Hemophilus influenzae HI0670.,Lim K, Tempczyk A, Bonander N, Toedt J, Howard A, Eisenstein E, Herzberg O J Biol Chem. 2003 Apr 11;278(15):13496-502. Epub 2003 Feb 4. PMID:12571243<ref>PMID:12571243</ref>

-	~~===Structure of YihZ from Haemophilus influenzae (HI0670)~~, a ~~D-Tyr-tRNA(Tyr) deacylase===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12571243}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1j7g]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Haemophilus_influenzae_rd_kw20 Haemophilus influenzae rd kw20]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1J7G OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012571243<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Haemophilus influenzae rd kw20]]		[[Category: Haemophilus influenzae rd kw20]]
	[[Category: Herzberg, O.]]		[[Category: Herzberg, O.]]

OCA: Protected "1j7g" [edit=sysop:move=sysop]

OCA — Wed, 28 Nov 2012 14:49:13 GMT

Protected "1j7g" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:49, 28 November 2012

OCA at 14:49, 28 November 2012

OCA — Wed, 28 Nov 2012 14:49:10 GMT

←Older revision		Revision as of 14:49, 28 November 2012
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-	{{Seed}}
	[[Image:1j7g.png\|left\|200px]]		[[Image:1j7g.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1j7g", 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),
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	{{STRUCTURE_1j7g\| PDB=1j7g \| SCENE= }}		{{STRUCTURE_1j7g\| PDB=1j7g \| SCENE= }}

	===Structure of YihZ from Haemophilus influenzae (HI0670), a D-Tyr-tRNA(Tyr) deacylase===		===Structure of YihZ from Haemophilus influenzae (HI0670), a D-Tyr-tRNA(Tyr) deacylase===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12571243}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12571243 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_12571243}}		{{ABSTRACT_PUBMED_12571243}}

	==About this Structure==		==About this Structure==
-	~~1J7G~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/~~Haemophilus_influenzae~~ Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J7G OCA].	+	[[1j7g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae_rd_kw20 Haemophilus influenzae rd kw20]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J7G OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12571243~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012571243</ref><references group="xtra"/>
-	[[Category: Haemophilus influenzae]]	+	[[Category: Haemophilus influenzae rd kw20]]
	[[Category: Herzberg, O.]]		[[Category: Herzberg, O.]]
	[[Category: Lim, K.]]		[[Category: Lim, K.]]
	[[Category: S2F, Structure 2.Function Project.]]		[[Category: S2F, Structure 2.Function Project.]]
		+	[[Category: Hydrolase]]
	[[Category: Hypothetical protein]]		[[Category: Hypothetical protein]]
	[[Category: S2f]]		[[Category: S2f]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Structure 2 function project]]		[[Category: Structure 2 function project]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 04:51:59 2009''

OCA at 02:52, 17 February 2009

OCA — Tue, 17 Feb 2009 02:52:00 GMT

←Older revision		Revision as of 02:52, 17 February 2009
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	==About this Structure==		==About this Structure==
-	1J7G is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J7G OCA].	+	1J7G is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J7G OCA].

	==Reference==		==Reference==
-	A catalytic mechanism for D-Tyr-tRNATyr deacylase based on the crystal structure of Hemophilus influenzae HI0670., Lim K, Tempczyk A, Bonander N, Toedt J, Howard A, Eisenstein E, Herzberg O, J Biol Chem. 2003 Apr 11;278(15):13496-502. Epub 2003 Feb 4. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/12571243 12571243]~~	+	<ref group="xtra">PMID:12571243</ref><references group="xtra"/>
	[[Category: Haemophilus influenzae]]		[[Category: Haemophilus influenzae]]
-	[[Category: Single protein]]
	[[Category: Herzberg, O.]]		[[Category: Herzberg, O.]]
	[[Category: Lim, K.]]		[[Category: Lim, K.]]
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	[[Category: Structure 2 function project]]		[[Category: Structure 2 function project]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 1 14~~:35:~~23 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 04:51:59 2009''