1det - Revision history

OCA at 09:50, 20 March 2024

OCA — Wed, 20 Mar 2024 09:50:00 GMT

←Older revision		Revision as of 09:50, 20 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1det]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DET OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DET FirstGlance]. <br>		<table><tr><td colspan='2'>[[1det]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DET OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DET FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=2GP:GUANOSINE~~-~~2-MONOPHOSPHATE'>2GP</scene>~~, ~~<scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.8Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CGA:CARBOXYMETHYLATED+GLUTAMIC+ACID'>CGA</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2GP:GUANOSINE-2-MONOPHOSPHATE'>2GP</scene>, <scene name='pdbligand=CGA:CARBOXYMETHYLATED+GLUTAMIC+ACID'>CGA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Ribonuclease_T(1) Ribonuclease T(1)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.3 3.1.27.3]~~ </~~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=1det FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1det OCA], [https://pdbe.org/1det PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1det RCSB], [https://www.ebi.ac.uk/pdbsum/1det PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1det 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=1det FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1det OCA], [https://pdbe.org/1det PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1det RCSB], [https://www.ebi.ac.uk/pdbsum/1det PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1det ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/RNT1_ASPOR RNT1_ASPOR]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1det 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=1det ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The carboxymethylation of RNase T1 at the gamma-carboxyl group of Glu58 leads to a complete loss of the enzymatic activity while it retains substrate-binding ability. Accompanying the carboxymethylation, RNase T1 undergoes a remarkable thermal stabilization of 9 degrees C in the melting temperature (Tm). In order to clarify the inactivation and stabilization mechanisms of RNase T1 by carboxymethylation, the crystal structure of carboxymethylated RNase T1 (CM-RNase T1) complexed with 2'-GMP was determined at 1.8 A resolution. The structure, including 79 water molecules and two Na+, was refined to an R factor of 0.194 with 10 354 reflections > 1 sigma (F). The carboxyl group of CM-Glu58, which locates in the active site, occupies almost the same position as the phosphate group of 2'-GMP in the crystal structure of intact RNase T1.2'-GMP complex. Therefore, the phosphate group of 2'-GMP cannot locate in the active site but protrudes toward the solvent. This forces 2'-GMP to adopt an anti form, which contrasts with the syn form in the crystal of the intact RNase T1.2'-GMP complex. The inaccessibility of the phosphate group to the active site can account for the lack of the enzymatic activity in CM-RNase T1. One of the carboxyl oxygen atoms of CM-Glu58 forms two hydrogen bonds with the side-chains of Tyr38 and His40. These hydrogen bonds are considered to mainly contribute to the higher thermal stability of CM-RNase T1. Another carboxyl oxygen atoms of CM-Glu58 is situated nearby His40 and Arg77. This may provide additional electrostatic stabilization.
-
-	Crystal structure of ribonuclease T1 carboxymethylated at Glu58 in complex with 2'-GMP.,Ishikawa K, Suzuki E, Tanokura M, Takahashi K Biochemistry. 1996 Jun 25;35(25):8329-34. PMID:8679590<ref>PMID:8679590</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1det" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]		*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Aspergillus oryzae]]		[[Category: Aspergillus oryzae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ishikawa, K]]	+	[[Category: Ishikawa K]]
-	[[Category: Suzuki, E]]	+	[[Category: Suzuki E]]
-	[[Category: Takahashi, K]]	+	[[Category: Takahashi K]]
-	[[Category: Tanokura, M]]	+	[[Category: Tanokura M]]
-	~~[[Category: Endonuclease]]~~	+
-	~~[[Category: Endoribonuclease]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nuclease~~]]	+

OCA at 10:46, 14 July 2021

OCA — Wed, 14 Jul 2021 10:46:06 GMT

←Older revision		Revision as of 10:46, 14 July 2021
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	<StructureSection load='1det' size='340' side='right'caption='[[1det]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1det' size='340' side='right'caption='[[1det]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1det]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DET OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1DET FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1det]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DET OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DET FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2GP:GUANOSINE-2-MONOPHOSPHATE'>2GP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2GP:GUANOSINE-2-MONOPHOSPHATE'>2GP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CGA:CARBOXYMETHYLATED+GLUTAMIC+ACID'>CGA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CGA:CARBOXYMETHYLATED+GLUTAMIC+ACID'>CGA</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Ribonuclease_T(1) Ribonuclease T(1)], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.3 3.1.27.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribonuclease_T(1) Ribonuclease T(1)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.3 3.1.27.3] </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=1det FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1det OCA], [~~http~~://pdbe.org/1det PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1det RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1det PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1det 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=1det FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1det OCA], [https://pdbe.org/1det PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1det RCSB], [https://www.ebi.ac.uk/pdbsum/1det PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1det ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	==See Also==		==See Also==
-	*[[Ribonuclease\|Ribonuclease]]	+	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
-	*[[Temp\|Temp]]	+
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:39, 10 October 2019

OCA — Thu, 10 Oct 2019 06:39:02 GMT

←Older revision		Revision as of 06:39, 10 October 2019
Line 1:		Line 1:

	==RIBONUCLEASE T1 CARBOXYMETHYLATED AT GLU 58 IN COMPLEX WITH 2'GMP==		==RIBONUCLEASE T1 CARBOXYMETHYLATED AT GLU 58 IN COMPLEX WITH 2'GMP==
-	<StructureSection load='1det' size='340' side='right' caption='[[1det]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='1det' size='340' side='right'caption='[[1det]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1det]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DET OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DET FirstGlance]. <br>		<table><tr><td colspan='2'>[[1det]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DET OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DET FirstGlance]. <br>
Line 30:		Line 30:

	==See Also==		==See Also==
		+	*[[Ribonuclease\|Ribonuclease]]
	*[[Temp\|Temp]]		*[[Temp\|Temp]]
	== References ==		== References ==
Line 36:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Aspergillus oryzae]]		[[Category: Aspergillus oryzae]]
		+	[[Category: Large Structures]]
	[[Category: Ishikawa, K]]		[[Category: Ishikawa, K]]
	[[Category: Suzuki, E]]		[[Category: Suzuki, E]]

OCA at 08:20, 6 December 2017

OCA — Wed, 06 Dec 2017 08:20:41 GMT

←Older revision		Revision as of 08:20, 6 December 2017
Line 1:		Line 1:
		+
	==RIBONUCLEASE T1 CARBOXYMETHYLATED AT GLU 58 IN COMPLEX WITH 2'GMP==		==RIBONUCLEASE T1 CARBOXYMETHYLATED AT GLU 58 IN COMPLEX WITH 2'GMP==
	<StructureSection load='1det' size='340' side='right' caption='[[1det]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1det' size='340' side='right' caption='[[1det]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CGA:CARBOXYMETHYLATED+GLUTAMIC+ACID'>CGA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CGA:CARBOXYMETHYLATED+GLUTAMIC+ACID'>CGA</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_T(1) Ribonuclease T(1)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.3 3.1.27.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_T(1) Ribonuclease T(1)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.3 3.1.27.3] </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=1det FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1det OCA], [http://pdbe.org/1det PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1det RCSB], [http://www.ebi.ac.uk/pdbsum/1det 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=1det FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1det OCA], [http://pdbe.org/1det PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1det RCSB], [http://www.ebi.ac.uk/pdbsum/1det PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1det ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/de/1det_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/de/1det_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>
Line 29:		Line 30:

	==See Also==		==See Also==
-	*[[Ribonuclease\|Ribonuclease]]
	*[[Temp\|Temp]]		*[[Temp\|Temp]]
	== References ==		== References ==

OCA at 03:43, 8 February 2016

OCA — Mon, 08 Feb 2016 03:43:11 GMT

←Older revision		Revision as of 03:43, 8 February 2016
Line 16:		Line 16:
	<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=1det ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:32, 10 September 2015

OCA — Thu, 10 Sep 2015 07:32:27 GMT

←Older revision		Revision as of 07:32, 10 September 2015
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	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CGA:CARBOXYMETHYLATED+GLUTAMIC+ACID'>CGA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CGA:CARBOXYMETHYLATED+GLUTAMIC+ACID'>CGA</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_T(1) Ribonuclease T(1)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.3 3.1.27.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_T(1) Ribonuclease T(1)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.3 3.1.27.3] </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=1det FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1det OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1det RCSB], [http://www.ebi.ac.uk/pdbsum/1det 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=1det FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1det OCA], [http://pdbe.org/1det PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1det RCSB], [http://www.ebi.ac.uk/pdbsum/1det PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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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 1det" style="background-color:#fffaf0;"></div>

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

OCA at 04:52, 16 February 2015

OCA — Mon, 16 Feb 2015 04:52:57 GMT

←Older revision		Revision as of 04:52, 16 February 2015
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	*[[Ribonuclease\|Ribonuclease]]		*[[Ribonuclease\|Ribonuclease]]
	*[[Temp\|Temp]]		*[[Temp\|Temp]]
-	*[[User:Jaime.Prilusky/Test/tree\|User:Jaime.Prilusky/Test/tree]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 22:36, 22 December 2014

OCA — Mon, 22 Dec 2014 22:36:14 GMT

←Older revision		Revision as of 22:36, 22 December 2014
Line 29:		Line 29:
	==See Also==		==See Also==
	*[[Ribonuclease\|Ribonuclease]]		*[[Ribonuclease\|Ribonuclease]]
		+	*[[Temp\|Temp]]
		+	*[[User:Jaime.Prilusky/Test/tree\|User:Jaime.Prilusky/Test/tree]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Aspergillus oryzae]]		[[Category: Aspergillus oryzae]]
-	[[Category: Ishikawa, K.]]	+	[[Category: Ishikawa, K]]
-	[[Category: Suzuki, E.]]	+	[[Category: Suzuki, E]]
-	[[Category: Takahashi, K.]]	+	[[Category: Takahashi, K]]
-	[[Category: Tanokura, M.]]	+	[[Category: Tanokura, M]]
	[[Category: Endonuclease]]		[[Category: Endonuclease]]
	[[Category: Endoribonuclease]]		[[Category: Endoribonuclease]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Nuclease]]		[[Category: Nuclease]]

OCA at 06:23, 10 October 2014

OCA — Fri, 10 Oct 2014 06:23:30 GMT

←Older revision		Revision as of 06:23, 10 October 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1det]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DET OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DET FirstGlance]. <br>		<table><tr><td colspan='2'>[[1det]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DET OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DET FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2GP:GUANOSINE-2-MONOPHOSPHATE'>2GP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2GP:GUANOSINE-2-MONOPHOSPHATE'>2GP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CGA:CARBOXYMETHYLATED+GLUTAMIC+ACID'>CGA</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CGA:CARBOXYMETHYLATED+GLUTAMIC+ACID'>CGA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_T(1) Ribonuclease T(1)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.3 3.1.27.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_T(1) Ribonuclease T(1)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.3 3.1.27.3] </span></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=1det FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1det OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1det RCSB], [http://www.ebi.ac.uk/pdbsum/1det 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=1det FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1det OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1det RCSB], [http://www.ebi.ac.uk/pdbsum/1det PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 06:32, 4 September 2014

OCA — Thu, 04 Sep 2014 06:32:05 GMT

←Older revision		Revision as of 06:32, 4 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1det.~~png~~\|~~left~~\|200px]]	+	==RIBONUCLEASE T1 CARBOXYMETHYLATED AT GLU 58 IN COMPLEX WITH 2'GMP==
		+	<StructureSection load='1det' size='340' side='right' caption='[[1det]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1det]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DET OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DET FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2GP:GUANOSINE-2-MONOPHOSPHATE'>2GP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CGA:CARBOXYMETHYLATED+GLUTAMIC+ACID'>CGA</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_T(1) Ribonuclease T(1)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.3 3.1.27.3] </span></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=1det FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1det OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1det RCSB], [http://www.ebi.ac.uk/pdbsum/1det 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/de/1det_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 ==
		+	The carboxymethylation of RNase T1 at the gamma-carboxyl group of Glu58 leads to a complete loss of the enzymatic activity while it retains substrate-binding ability. Accompanying the carboxymethylation, RNase T1 undergoes a remarkable thermal stabilization of 9 degrees C in the melting temperature (Tm). In order to clarify the inactivation and stabilization mechanisms of RNase T1 by carboxymethylation, the crystal structure of carboxymethylated RNase T1 (CM-RNase T1) complexed with 2'-GMP was determined at 1.8 A resolution. The structure, including 79 water molecules and two Na+, was refined to an R factor of 0.194 with 10 354 reflections > 1 sigma (F). The carboxyl group of CM-Glu58, which locates in the active site, occupies almost the same position as the phosphate group of 2'-GMP in the crystal structure of intact RNase T1.2'-GMP complex. Therefore, the phosphate group of 2'-GMP cannot locate in the active site but protrudes toward the solvent. This forces 2'-GMP to adopt an anti form, which contrasts with the syn form in the crystal of the intact RNase T1.2'-GMP complex. The inaccessibility of the phosphate group to the active site can account for the lack of the enzymatic activity in CM-RNase T1. One of the carboxyl oxygen atoms of CM-Glu58 forms two hydrogen bonds with the side-chains of Tyr38 and His40. These hydrogen bonds are considered to mainly contribute to the higher thermal stability of CM-RNase T1. Another carboxyl oxygen atoms of CM-Glu58 is situated nearby His40 and Arg77. This may provide additional electrostatic stabilization.

-	~~{{STRUCTURE_1det\| PDB=1det \| SCENE= }}~~	+	Crystal structure of ribonuclease T1 carboxymethylated at Glu58 in complex with 2'-GMP.,Ishikawa K, Suzuki E, Tanokura M, Takahashi K Biochemistry. 1996 Jun 25;35(25):8329-34. PMID:8679590<ref>PMID:8679590</ref>

-	~~===RIBONUCLEASE T1 CARBOXYMETHYLATED AT GLU 58 IN COMPLEX WITH 2'GMP===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_8679590}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1det]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Aspergillus_oryzae Aspergillus oryzae]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1DET OCA].~~	+

	==See Also==		==See Also==
	*[[Ribonuclease\|Ribonuclease]]		*[[Ribonuclease\|Ribonuclease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:008679590<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Aspergillus oryzae]]		[[Category: Aspergillus oryzae]]
	[[Category: Ishikawa, K.]]		[[Category: Ishikawa, K.]]