5vyt - Revision history

OCA at 14:02, 4 October 2023

OCA — Wed, 04 Oct 2023 14:02:57 GMT

←Older revision		Revision as of 14:02, 4 October 2023
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	<StructureSection load='5vyt' size='340' side='right'caption='[[5vyt]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5vyt' size='340' side='right'caption='[[5vyt]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vyt]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Brume Brume~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VYT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VYT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vyt]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Brucella_melitensis_bv._1_str._16M Brucella melitensis bv. 1 str. 16M]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VYT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VYT 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=FON:N-{[4-({[(6R)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)PHENYL]CARBONYL}-L-GLUTAMIC+ACID'>FON</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</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]] 2.2Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vyr\|5vyr]], [[5vys\|5vys]]</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=FON:N-{[4-({[(6R)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)PHENYL]CARBONYL}-L-GLUTAMIC+ACID'>FON</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BMEI1418 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224914 BRUME])~~</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=5vyt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vyt OCA], [https://pdbe.org/5vyt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vyt RCSB], [https://www.ebi.ac.uk/pdbsum/5vyt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vyt ProSAT]</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=5vyt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vyt OCA], [~~http~~://pdbe.org/5vyt PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vyt RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vyt PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vyt ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/WBKC_BRUME WBKC_BRUME] Involved in the lipopolysaccharide (LPS) O-antigen biosynthesis (PubMed:11081580). Catalyzes the transfer of a formyl group to GDP-perosamine, leading to the formation of GDP-N-formylperosamine (PubMed:11081580, PubMed:28636341). In vitro, can also function on GDP-3-deoxyperosamine, thereby providing an enzymatic method for producing a novel trideoxysugar not found in nature (PubMed:28636341).<ref>PMID:11081580</ref> <ref>PMID:28636341</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Brume~~]]	+	[[Category: Brucella melitensis bv. 1 str. 16M]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chantigian~~, D P~~]]	+	[[Category: Chantigian DP]]
-	[[Category: Holden~~, H M~~]]	+	[[Category: Holden HM]]
-	[[Category: Riegert~~, A S~~]]	+	[[Category: Riegert AS]]
-	[[Category: Thoden~~, J B]]~~	+	[[Category: Thoden JB]]
-	~~[[Category: Brucellosis]]~~	+
-	~~[[Category: Deoxysugar]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 09:43, 1 January 2020

OCA — Wed, 01 Jan 2020 09:43:15 GMT

←Older revision		Revision as of 09:43, 1 January 2020
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	==Crystal structure of the WbkC N-formyltransferase (F142A variant) from Brucella melitensis==		==Crystal structure of the WbkC N-formyltransferase (F142A variant) from Brucella melitensis==
-	<StructureSection load='5vyt' size='340' side='right' caption='[[5vyt]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5vyt' size='340' side='right'caption='[[5vyt]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vyt]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VYT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VYT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vyt]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Brume Brume]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VYT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VYT 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=FON:N-{[4-({[(6R)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)PHENYL]CARBONYL}-L-GLUTAMIC+ACID'>FON</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>		</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=FON:N-{[4-({[(6R)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)PHENYL]CARBONYL}-L-GLUTAMIC+ACID'>FON</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vyr\|5vyr]], [[5vys\|5vys]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vyr\|5vyr]], [[5vys\|5vys]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BMEI1418 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224914 BRUME])</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=5vyt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vyt OCA], [http://pdbe.org/5vyt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vyt RCSB], [http://www.ebi.ac.uk/pdbsum/5vyt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vyt ProSAT]</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=5vyt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vyt OCA], [http://pdbe.org/5vyt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vyt RCSB], [http://www.ebi.ac.uk/pdbsum/5vyt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vyt ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Brume]]
		+	[[Category: Large Structures]]
	[[Category: Chantigian, D P]]		[[Category: Chantigian, D P]]
	[[Category: Holden, H M]]		[[Category: Holden, H M]]

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

OCA — Thu, 21 Sep 2017 04:38:05 GMT

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

←Older revision

Revision as of 04:38, 21 September 2017

OCA: New page: ==Crystal structure of the WbkC N-formyltransferase (F142A variant) from Brucella melitensis== == Structural highlights ==
<table><tr><td colspan='2'>[[5vyt]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VYT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VYT 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=FON:N-{[4-({[(6R)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)PHENYL]CARBONYL}-L-GLUTAMIC+ACID'>FON</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5vyr|5vyr]], [[5vys|5vys]]</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=5vyt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vyt OCA], [http://pdbe.org/5vyt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vyt RCSB], [http://www.ebi.ac.uk/pdbsum/5vyt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vyt ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
It has become increasingly apparent within the last several years that unusual N-formylated sugars are often found on the O-antigens of such Gram negative pathogenic organisms as Francisella tularensis, Campylobacter jejuni, and Providencia alcalifaciens, among others. Indeed, in some species of Brucella, for example, the O-antigen contains 1,2-linked 4-formamido-4,6-dideoxy-alpha-d-mannosyl groups. These sugars, often referred to as N-formylperosamine, are synthesized in pathways initiating with GDP-mannose. One of the enzymes required for the production of N-formylperosamine, namely, WbkC, was first identified in 2000 and was suggested to function as an N-formyltransferase. Its biochemical activity was never experimentally verified, however. Here we describe a combined structural and functional investigation of WbkC from Brucella melitensis. Four high resolution X-ray structures of WbkC were determined in various complexes to address its active site architecture. Unexpectedly, the quaternary structure of WbkC was shown to be different from that previously observed for other sugar N-formyltransferases. Additionally, the structures revealed a second binding site for a GDP molecule distinct from that required for GDP-perosamine positioning. In keeping with this additional binding site, kinetic data with the wild type enzyme revealed complex patterns. Removal of GDP binding by mutating Phe 142 to an alanine residue resulted in an enzyme variant displaying normal Michaelis-Menten kinetics. These data suggest that this nucleotide binding pocket plays a role in enzyme regulation. Finally, by using an alternative substrate, we demonstrate that WbkC can be utilized to produce a trideoxysugar not found in nature.

Biochemical Characterization of WbkC, an N-Formyltransferase from Brucella melitensis.,Riegert AS, Chantigian DP, Thoden JB, Tipton PA, Holden HM Biochemistry. 2017 Jul 18;56(28):3657-3668. doi: 10.1021/acs.biochem.7b00494., Epub 2017 Jul 5. PMID:28636341<ref>PMID:28636341</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5vyt" style="background-color:#fffaf0;"></div>
== References ==
<references/>
TOC
</StructureSection>
[[Category: Chantigian, D P]]
[[Category: Holden, H M]]
[[Category: Riegert, A S]]
[[Category: Thoden, J B]]
[[Category: Brucellosis]]
[[Category: Deoxysugar]]
[[Category: Transferase]]