3sgl - Revision history

OCA at 12:56, 14 March 2024

OCA — Thu, 14 Mar 2024 12:56:09 GMT

←Older revision		Revision as of 12:56, 14 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/MNMC_YERPE MNMC_YERPE] Catalyzes the last two steps in the biosynthesis of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position (U34) in tRNA. Catalyzes the FAD-dependent demodification of cmnm(5)s(2)U34 to nm(5)s(2)U34, followed by the transfer of a methyl group from S-adenosyl-L-methionine to nm(5)s(2)U34, to form mnm(5)s(2)U34 (By similarity).		[https://www.uniprot.org/uniprot/MNMC_YERPE MNMC_YERPE] Catalyzes the last two steps in the biosynthesis of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position (U34) in tRNA. Catalyzes the FAD-dependent demodification of cmnm(5)s(2)U34 to nm(5)s(2)U34, followed by the transfer of a methyl group from S-adenosyl-L-methionine to nm(5)s(2)U34, to form mnm(5)s(2)U34 (By similarity).
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	BACKGROUND: Methylaminomethyl modification of uridine or 2-thiouridine (mnm5U34 or mnm5s2U34) at the wobble position of tRNAs specific for glutamate, lysine and arginine are observed in Escherichia coli and allow for specific recognition of codons ending in A or G. In the biosynthetic pathway responsible for this post-transcriptional modification, the bifunctional enzyme MnmC catalyzes the conversion of its hypermodified substrate carboxymethylaminomethyl uridine (cmnm5U34) to mnm5U34. MnmC catalyzes the flavin adenine dinucleotide (FAD)-dependent oxidative cleavage of carboxymethyl group from cmnm5U34 via an imine intermediate to generate aminomethyl uridine (nm5U34), which is subsequently methylated by S-adenosyl-L-methionine (SAM) to yield methylaminomethyl uridine (mnm5U34). RESULTS: The X-ray crystal structures of SAM/FAD-bound bifunctional MnmC from Escherichia coli and Yersinia pestis, and FAD-bound bifunctional MnmC from Yersinia pestis were determined and the catalytic functions verified in an in vitro assay. CONCLUSION: The crystal structures of MnmC from two Gram negative bacteria reveal the overall architecture of the enzyme and the relative disposition of the two independent catalytic domains: a Rossmann-fold domain containing the SAM binding site and an FAD containing domain structurally homologous to glycine oxidase from Bacillus subtilis. The structures of MnmC also reveal the detailed atomic interactions at the interdomain interface and provide spatial restraints relevant to the overall catalytic mechanism.
-
-	Structural basis for hypermodification of the wobble uridine in tRNA by bifunctional enzyme MnmC.,Kim J, Almo SC BMC Struct Biol. 2013 Apr 24;13:5. doi: 10.1186/1472-6807-13-5. PMID:23617613<ref>PMID:23617613</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3sgl" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:15, 6 December 2023

OCA — Wed, 06 Dec 2023 08:15:26 GMT

←Older revision		Revision as of 08:15, 6 December 2023
Line 3:		Line 3:
	<StructureSection load='3sgl' size='340' side='right'caption='[[3sgl]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='3sgl' size='340' side='right'caption='[[3sgl]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3sgl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus~~ pestis~~" (lehmann and neumann 1896) migula 1900~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SGL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SGL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3sgl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SGL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SGL 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=FAD:FLAVIN~~-~~ADENINE+DINUCLEOTIDE'>FAD</scene>~~, ~~<scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.7Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/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=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td><~~td class~~=~~"sblockDat"><div style~~=~~'overflow~~: ~~auto; max-height: 3em;~~'>~~[[3pvc\|3pvc]], [[3ps9\|3ps9]]~~</~~div~~><~~/td></tr>~~	+
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">mnmC, YPO2756, y1590, YP_2407 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900])~~</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=3sgl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sgl OCA], [https://pdbe.org/3sgl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sgl RCSB], [https://www.ebi.ac.uk/pdbsum/3sgl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sgl 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=3sgl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sgl OCA], [https://pdbe.org/3sgl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sgl RCSB], [https://www.ebi.ac.uk/pdbsum/3sgl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sgl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/MNMC_YERPE MNMC_YERPE]] Catalyzes the last two steps in the biosynthesis of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position (U34) in tRNA. Catalyzes the FAD-dependent demodification of cmnm(5)s(2)U34 to nm(5)s(2)U34, followed by the transfer of a methyl group from S-adenosyl-L-methionine to nm(5)s(2)U34, to form mnm(5)s(2)U34 (By similarity).	+	[https://www.uniprot.org/uniprot/MNMC_YERPE MNMC_YERPE] Catalyzes the last two steps in the biosynthesis of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position (U34) in tRNA. Catalyzes the FAD-dependent demodification of cmnm(5)s(2)U34 to nm(5)s(2)U34, followed by the transfer of a methyl group from S-adenosyl-L-methionine to nm(5)s(2)U34, to form mnm(5)s(2)U34 (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Almo, S C~~]]	+	[[Category: Yersinia pestis]]
-	[[Category: ~~Kim, J~~]]	+	[[Category: Almo SC]]
-	[[Category: ~~Structural genomic]]~~	+	[[Category: Kim J]]
-	~~[[Category: Fad binding sam binding]]~~	+
-	~~[[Category: Methyltransferase]]~~	+
-	~~[[Category: Nysgrc]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: PSI, Protein structure initiative]]~~	+
-	~~[[Category: Psi-biology]]~~	+
-	~~[[Category: Rossmann fold]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:55, 29 June 2022

OCA — Wed, 29 Jun 2022 07:55:19 GMT

←Older revision		Revision as of 07:55, 29 June 2022
Line 1:		Line 1:

	==The crystal structure of MnmC from Yersinia pestis bound with FAD and SAM==		==The crystal structure of MnmC from Yersinia pestis bound with FAD and SAM==
-	<StructureSection load='3sgl' size='340' side='right' caption='[[3sgl]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='3sgl' size='340' side='right'caption='[[3sgl]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3sgl]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus pestis" (lehmann and neumann 1896) migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SGL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3SGL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3sgl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus pestis" (lehmann and neumann 1896) migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SGL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SGL 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=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</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=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3pvc\|3pvc]], [[3ps9\|3ps9]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3pvc\|3pvc]], [[3ps9\|3ps9]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mnmC, YPO2756, y1590, YP_2407 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mnmC, YPO2756, y1590, YP_2407 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900])</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=3sgl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sgl OCA], [~~http~~://pdbe.org/3sgl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3sgl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3sgl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3sgl 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=3sgl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sgl OCA], [https://pdbe.org/3sgl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sgl RCSB], [https://www.ebi.ac.uk/pdbsum/3sgl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sgl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/MNMC_YERPE MNMC_YERPE]] Catalyzes the last two steps in the biosynthesis of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position (U34) in tRNA. Catalyzes the FAD-dependent demodification of cmnm(5)s(2)U34 to nm(5)s(2)U34, followed by the transfer of a methyl group from S-adenosyl-L-methionine to nm(5)s(2)U34, to form mnm(5)s(2)U34 (By similarity).	+	[[https://www.uniprot.org/uniprot/MNMC_YERPE MNMC_YERPE]] Catalyzes the last two steps in the biosynthesis of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position (U34) in tRNA. Catalyzes the FAD-dependent demodification of cmnm(5)s(2)U34 to nm(5)s(2)U34, followed by the transfer of a methyl group from S-adenosyl-L-methionine to nm(5)s(2)U34, to form mnm(5)s(2)U34 (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Almo, S C]]		[[Category: Almo, S C]]
	[[Category: Kim, J]]		[[Category: Kim, J]]

OCA at 04:52, 5 August 2016

OCA — Fri, 05 Aug 2016 04:52:27 GMT

←Older revision		Revision as of 04:52, 5 August 2016
Line 1:		Line 1:
		+
	==The crystal structure of MnmC from Yersinia pestis bound with FAD and SAM==		==The crystal structure of MnmC from Yersinia pestis bound with FAD and SAM==
	<StructureSection load='3sgl' size='340' side='right' caption='[[3sgl]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='3sgl' size='340' side='right' caption='[[3sgl]], [[Resolution\|resolution]] 2.70Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3pvc\|3pvc]], [[3ps9\|3ps9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3pvc\|3pvc]], [[3ps9\|3ps9]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mnmC, YPO2756, y1590, YP_2407 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mnmC, YPO2756, y1590, YP_2407 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900])</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=3sgl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sgl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3sgl RCSB], [http://www.ebi.ac.uk/pdbsum/3sgl 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=3sgl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sgl OCA], [http://pdbe.org/3sgl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3sgl RCSB], [http://www.ebi.ac.uk/pdbsum/3sgl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3sgl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	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 3sgl" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:55, 25 December 2014

OCA — Thu, 25 Dec 2014 15:55:29 GMT

←Older revision		Revision as of 15:55, 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=3sgl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sgl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3sgl RCSB], [http://www.ebi.ac.uk/pdbsum/3sgl 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=3sgl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sgl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3sgl RCSB], [http://www.ebi.ac.uk/pdbsum/3sgl PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MNMC_YERPE MNMC_YERPE]] Catalyzes the last two steps in the biosynthesis of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position (U34) in tRNA. Catalyzes the FAD-dependent demodification of cmnm(5)s(2)U34 to nm(5)s(2)U34, followed by the transfer of a methyl group from S-adenosyl-L-methionine to nm(5)s(2)U34, to form mnm(5)s(2)U34 (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 18:37, 21 December 2014

OCA — Sun, 21 Dec 2014 18:37:44 GMT

←Older revision		Revision as of 18:37, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3sgl\| PDB=3sgl \| SCENE= }}~~	+	==The crystal structure of MnmC from Yersinia pestis bound with FAD and SAM==
-	===The crystal structure of MnmC from Yersinia pestis bound with FAD and SAM===	+	<StructureSection load='3sgl' size='340' side='right' caption='[[3sgl]], [[Resolution\|resolution]] 2.70Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23617613}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3sgl]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus pestis" (lehmann and neumann 1896) migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SGL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SGL 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=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3pvc\|3pvc]], [[3ps9\|3ps9]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mnmC, YPO2756, y1590, YP_2407 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900])</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=3sgl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sgl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3sgl RCSB], [http://www.ebi.ac.uk/pdbsum/3sgl PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BACKGROUND: Methylaminomethyl modification of uridine or 2-thiouridine (mnm5U34 or mnm5s2U34) at the wobble position of tRNAs specific for glutamate, lysine and arginine are observed in Escherichia coli and allow for specific recognition of codons ending in A or G. In the biosynthetic pathway responsible for this post-transcriptional modification, the bifunctional enzyme MnmC catalyzes the conversion of its hypermodified substrate carboxymethylaminomethyl uridine (cmnm5U34) to mnm5U34. MnmC catalyzes the flavin adenine dinucleotide (FAD)-dependent oxidative cleavage of carboxymethyl group from cmnm5U34 via an imine intermediate to generate aminomethyl uridine (nm5U34), which is subsequently methylated by S-adenosyl-L-methionine (SAM) to yield methylaminomethyl uridine (mnm5U34). RESULTS: The X-ray crystal structures of SAM/FAD-bound bifunctional MnmC from Escherichia coli and Yersinia pestis, and FAD-bound bifunctional MnmC from Yersinia pestis were determined and the catalytic functions verified in an in vitro assay. CONCLUSION: The crystal structures of MnmC from two Gram negative bacteria reveal the overall architecture of the enzyme and the relative disposition of the two independent catalytic domains: a Rossmann-fold domain containing the SAM binding site and an FAD containing domain structurally homologous to glycine oxidase from Bacillus subtilis. The structures of MnmC also reveal the detailed atomic interactions at the interdomain interface and provide spatial restraints relevant to the overall catalytic mechanism.

-	~~==Function==~~	+	Structural basis for hypermodification of the wobble uridine in tRNA by bifunctional enzyme MnmC.,Kim J, Almo SC BMC Struct Biol. 2013 Apr 24;13:5. doi: 10.1186/1472-6807-13-5. PMID:23617613<ref>PMID:23617613</ref>
-	~~[[http://www.uniprot.org/uniprot/MNMC_YERPE MNMC_YERPE]] Catalyzes the last two steps in the biosynthesis~~ of ~~5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at~~ the wobble ~~position (U34)~~ in tRNA. ~~Catalyzes the FAD-dependent demodification of cmnm(~~5~~)s(2)U34 to nm(5)s(2)U34, followed by the transfer of a methyl group from S~~-~~adenosyl~~-L-~~methionine to nm(~~5~~)s(2)U34, to form mnm(5)s(2)U34 (By similarity)~~.	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3sgl]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus pestis" (lehmann and neumann 1896) migula 1900]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3SGL OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:023617613</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
-	[[Category: Almo, S C.]]	+	</StructureSection>
-	[[Category: Kim, J.]]	+	[[Category: Almo, S C]]
-	[[Category: ~~NYSGRC, New York~~ Structural ~~Genomics Research Consortium.~~]]	+	[[Category: Kim, J]]
		+	[[Category: Structural genomic]]
	[[Category: Fad binding sam binding]]		[[Category: Fad binding sam binding]]
	[[Category: Methyltransferase]]		[[Category: Methyltransferase]]
-	[[Category: New york structural genomics research consortium]]
	[[Category: Nysgrc]]		[[Category: Nysgrc]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-	[[Category: Protein structure initiative]]	+	[[Category: PSI, Protein structure initiative]]
	[[Category: Psi-biology]]		[[Category: Psi-biology]]
	[[Category: Rossmann fold]]		[[Category: Rossmann fold]]
-	[[Category: Structural genomic]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 08:55, 25 December 2013

OCA — Wed, 25 Dec 2013 08:55:46 GMT

←Older revision		Revision as of 08:55, 25 December 2013
Line 1:		Line 1:
-	[[Image:3sgl.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3sgl", 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_3sgl\| PDB=3sgl \| SCENE= }}		{{STRUCTURE_3sgl\| PDB=3sgl \| SCENE= }}
-
	===The crystal structure of MnmC from Yersinia pestis bound with FAD and SAM===		===The crystal structure of MnmC from Yersinia pestis bound with FAD and SAM===
		+	{{ABSTRACT_PUBMED_23617613}}

		+	==Function==
		+	[[http://www.uniprot.org/uniprot/MNMC_YERPE MNMC_YERPE]] Catalyzes the last two steps in the biosynthesis of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position (U34) in tRNA. Catalyzes the FAD-dependent demodification of cmnm(5)s(2)U34 to nm(5)s(2)U34, followed by the transfer of a methyl group from S-adenosyl-L-methionine to nm(5)s(2)U34, to form mnm(5)s(2)U34 (By similarity).

	==About this Structure==		==About this Structure==
-	[[3sgl]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Yersinia_pestis Yersinia~~ pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SGL OCA].	+	[[3sgl]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus pestis" (lehmann and neumann 1896) migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SGL OCA].
-	~~[[Category~~: ~~Yersinia pestis]]~~	+
		+	==Reference==
		+	<ref group="xtra">PMID:023617613</ref><references group="xtra"/><references/>
	[[Category: Almo, S C.]]		[[Category: Almo, S C.]]
	[[Category: Kim, J.]]		[[Category: Kim, J.]]

OCA at 10:59, 16 November 2011

OCA — Wed, 16 Nov 2011 10:59:12 GMT

←Older revision		Revision as of 10:59, 16 November 2011
Line 1:		Line 1:
-	[[Image:3sgl.~~jpg~~\|left\|200px]]	+	[[Image:3sgl.png\|left\|200px]]

	<!--		<!--

OCA at 19:04, 6 July 2011

OCA — Wed, 06 Jul 2011 19:04:18 GMT

←Older revision		Revision as of 19:04, 6 July 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3sgl.jpg\|left\|200px]]

-	The ~~entry 3sgl~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3sgl", 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_3sgl\| PDB=3sgl \| SCENE= }}

-	~~Authors: Kim, J., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)~~	+	===The crystal structure of MnmC from Yersinia pestis bound with FAD and SAM===

-	~~Description: The crystal~~ structure ~~of MnmC~~ from Yersinia pestis ~~bound with FAD and SAM~~	+
		+	==About this Structure==
		+	[[3sgl]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SGL OCA].
		+	[[Category: Yersinia pestis]]
		+	[[Category: Almo, S C.]]
		+	[[Category: Kim, J.]]
		+	[[Category: NYSGRC, New York Structural Genomics Research Consortium.]]
		+	[[Category: Fad binding sam binding]]
		+	[[Category: Methyltransferase]]
		+	[[Category: New york structural genomics research consortium]]
		+	[[Category: Nysgrc]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Protein structure initiative]]
		+	[[Category: Psi-biology]]
		+	[[Category: Rossmann fold]]
		+	[[Category: Structural genomic]]
		+	[[Category: Transferase]]

OCA at 05:44, 29 June 2011

OCA — Wed, 29 Jun 2011 05:44:50 GMT

←Older revision		Revision as of 05:44, 29 June 2011
Line 3:		Line 3:
	The entry 3sgl is ON HOLD		The entry 3sgl is ON HOLD

-	Authors: Kim, J., Almo,S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)	+	Authors: Kim, J., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

	Description: The crystal structure of MnmC from Yersinia pestis bound with FAD and SAM		Description: The crystal structure of MnmC from Yersinia pestis bound with FAD and SAM