5i02 - Revision history

OCA at 08:18, 23 August 2023

OCA — Wed, 23 Aug 2023 08:18:51 GMT

←Older revision		Revision as of 08:18, 23 August 2023
Line 3:		Line 3:
	<StructureSection load='5i02' size='340' side='right'caption='[[5i02]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='5i02' size='340' side='right'caption='[[5i02]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i02]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Zymmo Zymmo~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I02 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5I02 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i02]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Zymomonas_mobilis_subsp._mobilis_ZM4_=_ATCC_31821 Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I02 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5I02 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PK2:6-AMINO-4-{2-[(CYCLOHEXYLMETHYL)AMINO]ETHYL}-2-(METHYLAMINO)-1,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE'>PK2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.25Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3eos\|3eos]], [[4kwo\|4kwo]], [[4leq\|4leq]], [[5100\|5100]], [[4puk\|4puk]], [[3ge7\|3ge7]], [[1y5x\|1y5x]], [[1y5w\|1y5w]], [[1y5v\|1y5v]], [[4fsa\|4fsa]], [[4fr6\|4fr6]], [[1p0d\|1p0d]]</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PK2:6-AMINO-4-{2-[(CYCLOHEXYLMETHYL)AMINO]ETHYL}-2-(METHYLAMINO)-1,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE'>PK2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tgt, ZMO0363 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=264203 ZYMMO])</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=5i02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i02 OCA], [https://pdbe.org/5i02 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5i02 RCSB], [https://www.ebi.ac.uk/pdbsum/5i02 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5i02 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/tRNA-guanine(34)_transglycosylase tRNA-guanine(34) transglycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.29 2.4.2.29] </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=5i02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i02 OCA], [~~http~~://pdbe.org/5i02 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5i02 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5i02 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5i02 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TGT_ZYMMO TGT_ZYMMO]] Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr). After this exchange, a cyclopentendiol moiety is attached to the 7-aminomethyl group of 7-deazaguanine, resulting in the hypermodified nucleoside queuosine (Q) (7-(((4,5-cis-dihydroxy-2-cyclopenten-1-yl)amino)methyl)-7-deazaguanosine).[HAMAP-Rule:MF_00168]	+	[https://www.uniprot.org/uniprot/TGT_ZYMMO TGT_ZYMMO] Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr). After this exchange, a cyclopentendiol moiety is attached to the 7-aminomethyl group of 7-deazaguanine, resulting in the hypermodified nucleoside queuosine (Q) (7-(((4,5-cis-dihydroxy-2-cyclopenten-1-yl)amino)methyl)-7-deazaguanosine).[HAMAP-Rule:MF_00168]

	==See Also==		==See Also==
-	*[[TRNA-guanine transglycosylase\|TRNA-guanine transglycosylase]]	+	*[[TRNA-guanine transglycosylase 3D structures\|TRNA-guanine transglycosylase 3D structures]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Zymmo~~]]	+	[[Category: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821]]
-	[[Category: Ehrmann~~, F R~~]]	+	[[Category: Ehrmann FR]]
-	[[Category: Heine, A]]	+	[[Category: Heine A]]
-	[[Category: Klebe, G]]	+	[[Category: Klebe G]]
-	[[Category: Nguyen, D]]	+	[[Category: Nguyen D]]
-	~~[[Category: Co-crystallization]]~~	+
-	~~[[Category: Shigellosis]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Transferase inhibitor~~]]	+

OCA at 08:39, 27 May 2020

OCA — Wed, 27 May 2020 08:39:01 GMT

←Older revision		Revision as of 08:39, 27 May 2020
Line 1:		Line 1:

	==tRNA guanine transglycosylase (TGT) in co-crystallized complex with 6-amino-4-{2-[(cyclohexylmethyl)amino]ethyl}-2-(methylamino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one==		==tRNA guanine transglycosylase (TGT) in co-crystallized complex with 6-amino-4-{2-[(cyclohexylmethyl)amino]ethyl}-2-(methylamino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one==
-	<StructureSection load='5i02' size='340' side='right' caption='[[5i02]], [[Resolution\|resolution]] 1.25Å' scene=''>	+	<StructureSection load='5i02' size='340' side='right'caption='[[5i02]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i02]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I02 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5I02 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i02]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Zymmo Zymmo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I02 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5I02 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PK2:6-AMINO-4-{2-[(CYCLOHEXYLMETHYL)AMINO]ETHYL}-2-(METHYLAMINO)-1,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE'>PK2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PK2:6-AMINO-4-{2-[(CYCLOHEXYLMETHYL)AMINO]ETHYL}-2-(METHYLAMINO)-1,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE'>PK2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3eos\|3eos]], [[4kwo\|4kwo]], [[4leq\|4leq]], [[5100\|5100]], [[4puk\|4puk]], [[3ge7\|3ge7]], [[1y5x\|1y5x]], [[1y5w\|1y5w]], [[1y5v\|1y5v]], [[4fsa\|4fsa]], [[4fr6\|4fr6]], [[1p0d\|1p0d]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3eos\|3eos]], [[4kwo\|4kwo]], [[4leq\|4leq]], [[5100\|5100]], [[4puk\|4puk]], [[3ge7\|3ge7]], [[1y5x\|1y5x]], [[1y5w\|1y5w]], [[1y5v\|1y5v]], [[4fsa\|4fsa]], [[4fr6\|4fr6]], [[1p0d\|1p0d]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tgt, ZMO0363 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=264203 ZYMMO])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA-guanine(34)_transglycosylase tRNA-guanine(34) transglycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.29 2.4.2.29] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA-guanine(34)_transglycosylase tRNA-guanine(34) transglycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.29 2.4.2.29] </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=5i02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i02 OCA], [http://pdbe.org/5i02 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i02 RCSB], [http://www.ebi.ac.uk/pdbsum/5i02 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i02 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=5i02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i02 OCA], [http://pdbe.org/5i02 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i02 RCSB], [http://www.ebi.ac.uk/pdbsum/5i02 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i02 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/TGT_ZYMMO TGT_ZYMMO]] Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr). After this exchange, a cyclopentendiol moiety is attached to the 7-aminomethyl group of 7-deazaguanine, resulting in the hypermodified nucleoside queuosine (Q) (7-(((4,5-cis-dihydroxy-2-cyclopenten-1-yl)amino)methyl)-7-deazaguanosine).[HAMAP-Rule:MF_00168]		[[http://www.uniprot.org/uniprot/TGT_ZYMMO TGT_ZYMMO]] Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr). After this exchange, a cyclopentendiol moiety is attached to the 7-aminomethyl group of 7-deazaguanine, resulting in the hypermodified nucleoside queuosine (Q) (7-(((4,5-cis-dihydroxy-2-cyclopenten-1-yl)amino)methyl)-7-deazaguanosine).[HAMAP-Rule:MF_00168]
		+
		+	==See Also==
		+	*[[TRNA-guanine transglycosylase\|TRNA-guanine transglycosylase]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Zymmo]]
	[[Category: Ehrmann, F R]]		[[Category: Ehrmann, F R]]
	[[Category: Heine, A]]		[[Category: Heine, A]]

OCA at 17:38, 10 March 2017

OCA — Fri, 10 Mar 2017 17:38:19 GMT

←Older revision		Revision as of 17:38, 10 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5i02 is ON HOLD until Paper Publication~~	+	==tRNA guanine transglycosylase (TGT) in co-crystallized complex with 6-amino-4-{2-[(cyclohexylmethyl)amino]ethyl}-2-(methylamino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one==
-		+	<StructureSection load='5i02' size='340' side='right' caption='[[5i02]], [[Resolution\|resolution]] 1.25Å' scene=''>
-	~~Authors: Ehrmann, F.R., Nguyen, D., Heine, A., Klebe, G.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5i02]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I02 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I02 FirstGlance]. <br>
-	~~Description:~~ tRNA guanine transglycosylase (TGT) in co-crystallized complex with 6-amino-4-{2-[(cyclohexylmethyl)amino]ethyl}-2-(methylamino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one	+	</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PK2:6-AMINO-4-{2-[(CYCLOHEXYLMETHYL)AMINO]ETHYL}-2-(METHYLAMINO)-1,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE'>PK2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3eos\|3eos]], [[4kwo\|4kwo]], [[4leq\|4leq]], [[5100\|5100]], [[4puk\|4puk]], [[3ge7\|3ge7]], [[1y5x\|1y5x]], [[1y5w\|1y5w]], [[1y5v\|1y5v]], [[4fsa\|4fsa]], [[4fr6\|4fr6]], [[1p0d\|1p0d]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA-guanine(34)_transglycosylase tRNA-guanine(34) transglycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.29 2.4.2.29] </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=5i02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i02 OCA], [http://pdbe.org/5i02 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i02 RCSB], [http://www.ebi.ac.uk/pdbsum/5i02 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i02 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TGT_ZYMMO TGT_ZYMMO]] Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr). After this exchange, a cyclopentendiol moiety is attached to the 7-aminomethyl group of 7-deazaguanine, resulting in the hypermodified nucleoside queuosine (Q) (7-(((4,5-cis-dihydroxy-2-cyclopenten-1-yl)amino)methyl)-7-deazaguanosine).[HAMAP-Rule:MF_00168]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Ehrmann, F R]]
		+	[[Category: Heine, A]]
	[[Category: Klebe, G]]		[[Category: Klebe, G]]
-	[[Category: Ehrmann, F.R]]
-	[[Category: Heine, A]]
	[[Category: Nguyen, D]]		[[Category: Nguyen, D]]
		+	[[Category: Co-crystallization]]
		+	[[Category: Shigellosis]]
		+	[[Category: Transferase]]
		+	[[Category: Transferase inhibitor]]

OCA at 01:22, 21 February 2016

OCA — Sun, 21 Feb 2016 01:22:36 GMT

←Older revision		Revision as of 01:22, 21 February 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5i02 is ON HOLD	+	The entry 5i02 is ON HOLD until Paper Publication

	Authors: Ehrmann, F.R., Nguyen, D., Heine, A., Klebe, G.		Authors: Ehrmann, F.R., Nguyen, D., Heine, A., Klebe, G.

OCA: Protected "5i02" [edit=sysop:move=sysop]

OCA — Wed, 10 Feb 2016 15:59:52 GMT

Protected "5i02" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:59, 10 February 2016

OCA: New page: '''Unreleased structure''' The entry 5i02 is ON HOLD Authors: Ehrmann, F.R., Nguyen, D., Heine, A., Klebe, G. Description: tRNA guanine transglycosylase (TGT) in co-crystallized comple...

OCA — Wed, 10 Feb 2016 15:59:51 GMT

New page: '''Unreleased structure''' The entry 5i02 is ON HOLD Authors: Ehrmann, F.R., Nguyen, D., Heine, A., Klebe, G. Description: tRNA guanine transglycosylase (TGT) in co-crystallized comple...

New page

'''Unreleased structure'''

The entry 5i02 is ON HOLD

Authors: Ehrmann, F.R., Nguyen, D., Heine, A., Klebe, G.

Description: tRNA guanine transglycosylase (TGT) in co-crystallized complex with 6-amino-4-{2-[(cyclohexylmethyl)amino]ethyl}-2-(methylamino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one
[[Category: Unreleased Structures]]
[[Category: Klebe, G]]
[[Category: Ehrmann, F.R]]
[[Category: Heine, A]]
[[Category: Nguyen, D]]