3w21 - Revision history

OCA at 05:19, 3 August 2022

OCA — Wed, 03 Aug 2022 05:19:06 GMT

←Older revision		Revision as of 05:19, 3 August 2022
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	==Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase in complex with alpha-KG from Burkholderia ambifaria AMMD==		==Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase in complex with alpha-KG from Burkholderia ambifaria AMMD==
-	<StructureSection load='3w21' size='340' side='right' caption='[[3w21]], [[Resolution\|resolution]] 1.98Å' scene=''>	+	<StructureSection load='3w21' size='340' side='right'caption='[[3w21]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3w21]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Burcm Burcm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W21 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3W21 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3w21]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Burcm Burcm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W21 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W21 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</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=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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">[[3w20\|3w20]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3w20\|3w20]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Bamb_6045 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=339670 BURCM])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Bamb_6045 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=339670 BURCM])</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=3w21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w21 OCA], [~~http~~://pdbe.org/3w21 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3w21 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3w21 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3w21 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=3w21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w21 OCA], [https://pdbe.org/3w21 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w21 RCSB], [https://www.ebi.ac.uk/pdbsum/3w21 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w21 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Burcm]]		[[Category: Burcm]]
		+	[[Category: Large Structures]]
	[[Category: Hibi, M]]		[[Category: Hibi, M]]
	[[Category: Jia, M Z]]		[[Category: Jia, M Z]]

OCA at 13:01, 11 August 2016

OCA — Thu, 11 Aug 2016 13:01:17 GMT

←Older revision		Revision as of 13:01, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase in complex with alpha-KG from Burkholderia ambifaria AMMD==		==Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase in complex with alpha-KG from Burkholderia ambifaria AMMD==
	<StructureSection load='3w21' size='340' side='right' caption='[[3w21]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='3w21' size='340' side='right' caption='[[3w21]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3w21]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Burkholderia_ambifaria_ammd Burkholderia ambifaria ammd~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W21 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3W21 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3w21]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Burcm Burcm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W21 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3W21 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</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"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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">[[3w20\|3w20]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3w20\|3w20]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Bamb_6045 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=339670 ~~Burkholderia ambifaria AMMD~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Bamb_6045 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=339670 BURCM])</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=3w21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w21 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3w21 RCSB], [http://www.ebi.ac.uk/pdbsum/3w21 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=3w21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w21 OCA], [http://pdbe.org/3w21 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3w21 RCSB], [http://www.ebi.ac.uk/pdbsum/3w21 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3w21 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	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 3w21" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Burkholderia ambifaria ammd~~]]	+	[[Category: Burcm]]
	[[Category: Hibi, M]]		[[Category: Hibi, M]]
	[[Category: Jia, M Z]]		[[Category: Jia, M Z]]

OCA at 09:56, 4 January 2015

OCA — Sun, 04 Jan 2015 09:56:09 GMT

←Older revision		Revision as of 09:56, 4 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_3w21\| PDB=3w21 \| SCENE= }}~~	+	==Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase in complex with alpha-KG from Burkholderia ambifaria AMMD==
-	===Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase in complex with alpha-KG from Burkholderia ambifaria AMMD===	+	<StructureSection load='3w21' size='340' side='right' caption='[[3w21]], [[Resolution\|resolution]] 1.98Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23724013}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3w21]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_ambifaria_ammd Burkholderia ambifaria ammd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W21 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3W21 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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">[[3w20\|3w20]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Bamb_6045 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=339670 Burkholderia ambifaria AMMD])</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=3w21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w21 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3w21 RCSB], [http://www.ebi.ac.uk/pdbsum/3w21 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A novel dioxygenase from Burkholderia ambifaria AMMD (SadA) stereoselectively catalyzes the C3-hydroxylation of N-substituted branched-chain or aromatic L-amino acids, especially N-succinyl-L-leucine, coupled with the conversion of alpha-ketoglutarate to succinate and CO2. To elucidate the structural basis of the substrate specificity and stereoselective hydroxylation, we determined the crystal structures of the SadA.Zn(II) and SadA.Zn(II).alpha-KG complexes at 1.77 A and 1.98 A resolutions, respectively. SadA adopted a double-stranded beta-helix fold at the core of the structure. In addition, an HXD/EXnH motif in the active site coordinated a Zn(II) as a substitute for Fe(II). The alpha-KG molecule also coordinated Zn(II) in a bidentate manner via its 1-carboxylate and 2-oxo groups. Based on the SadA.Zn(II).alpha-KG structure and mutation analyses, we constructed substrate-binding models with N-succinyl-L-leucine and N-succinyl-L-phenylalanine, which provided new insight into the substrate specificity. The results will be useful for the rational design of SadA variants aimed at the recognition of various N-succinyl L-amino acids.

-	~~==About this~~ Structure==	+	Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase from Burkholderia ambifaria AMMD.,Qin HM, Miyakawa T, Jia MZ, Nakamura A, Ohtsuka J, Xue YL, Kawashima T, Kasahara T, Hibi M, Ogawa J, Tanokura M PLoS One. 2013 May 28;8(5):e63996. doi: 10.1371/journal.pone.0063996. Print 2013. PMID:23724013<ref>PMID:23724013</ref>
-	~~[[3w21]] is~~ a ~~2 chain structure with sequence~~ from ~~[http://en.wikipedia.org/wiki/Burkholderia_ambifaria_ammd~~ Burkholderia ambifaria ~~ammd]~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=3W21 OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:023724013</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Burkholderia ambifaria ammd]]		[[Category: Burkholderia ambifaria ammd]]
-	[[Category: Hibi, M.]]	+	[[Category: Hibi, M]]
-	[[Category: Jia, M Z.]]	+	[[Category: Jia, M Z]]
-	[[Category: Kasahara, T.]]	+	[[Category: Kasahara, T]]
-	[[Category: Kawashima, T.]]	+	[[Category: Kawashima, T]]
-	[[Category: Miyakawa, T.]]	+	[[Category: Miyakawa, T]]
-	[[Category: Nakamura, A.]]	+	[[Category: Nakamura, A]]
-	[[Category: Ogawa, J.]]	+	[[Category: Ogawa, J]]
-	[[Category: Ohtsuka, J.]]	+	[[Category: Ohtsuka, J]]
-	[[Category: Qin, H M.]]	+	[[Category: Qin, H M]]
-	[[Category: Tanokura, M.]]	+	[[Category: Tanokura, M]]
-	[[Category: Xue, Y L.]]	+	[[Category: Xue, Y L]]
	[[Category: Alpha-kg binding]]		[[Category: Alpha-kg binding]]
	[[Category: Dioxygenase]]		[[Category: Dioxygenase]]

OCA at 04:57, 18 July 2013

OCA — Thu, 18 Jul 2013 04:57:09 GMT

←Older revision		Revision as of 04:57, 18 July 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_3w21\| PDB=3w21 \| SCENE= }}
		+	===Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase in complex with alpha-KG from Burkholderia ambifaria AMMD===
		+	{{ABSTRACT_PUBMED_23724013}}

-	~~The entry~~ 3w21 is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
		+	[[3w21]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_ambifaria_ammd Burkholderia ambifaria ammd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W21 OCA].

-	~~Authors~~: ~~Qin~~, H.M.~~, Miyakawa, T.,~~ Jia, M.Z., ~~Nakamura, A~~.~~, Ohtsuka, J., Xue, Y.L.,~~ Kawashima, T.~~, Kasahara~~, T., ~~Hibi, M~~., Ogawa, J., Tanokura, M.	+	==Reference==
-		+	<ref group="xtra">PMID:023724013</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Crystal Structure of a Novel N~~-~~Substituted L-Amino Acid~~ Dioxygenase ~~in complex with alpha-KG from Burkholderia ambifaria AMMD~~	+	[[Category: Burkholderia ambifaria ammd]]
		+	[[Category: Hibi, M.]]
		+	[[Category: Jia, M Z.]]
		+	[[Category: Kasahara, T.]]
		+	[[Category: Kawashima, T.]]
		+	[[Category: Miyakawa, T.]]
		+	[[Category: Nakamura, A.]]
		+	[[Category: Ogawa, J.]]
		+	[[Category: Ohtsuka, J.]]
		+	[[Category: Qin, H M.]]
		+	[[Category: Tanokura, M.]]
		+	[[Category: Xue, Y L.]]
		+	[[Category: Alpha-kg binding]]
		+	[[Category: Dioxygenase]]
		+	[[Category: Dsbh fold]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Zn]]

OCA at 10:47, 19 December 2012

OCA — Wed, 19 Dec 2012 10:47:36 GMT

←Older revision		Revision as of 10:47, 19 December 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3w21 is ON HOLD	+	The entry 3w21 is ON HOLD until Paper Publication

-	Authors: Qin, H. M., Miyakawa, T., Jia, M. Z., Nakamura, A., Ohtsuka, J., Xue, Y. L., Kawashima, T., Kasahara, T., Hibi, M., Ogawa, J., Tanokura, M.	+	Authors: Qin, H.M., Miyakawa, T., Jia, M.Z., Nakamura, A., Ohtsuka, J., Xue, Y.L., Kawashima, T., Kasahara, T., Hibi, M., Ogawa, J., Tanokura, M.

	Description: Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase in complex with alpha-KG from Burkholderia ambifaria AMMD		Description: Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase in complex with alpha-KG from Burkholderia ambifaria AMMD

OCA: Protected "3w21" [edit=sysop:move=sysop]

OCA — Wed, 05 Dec 2012 10:17:33 GMT

Protected "3w21" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:17, 5 December 2012

OCA: New page: '''Unreleased structure''' The entry 3w21 is ON HOLD Authors: Qin, H. M., Miyakawa, T., Jia, M. Z., Nakamura, A., Ohtsuka, J., Xue, Y. L., Kawashima, T., Kasahara, T., Hibi, M., Ogawa, ...

OCA — Wed, 05 Dec 2012 10:17:32 GMT

New page: '''Unreleased structure''' The entry 3w21 is ON HOLD Authors: Qin, H. M., Miyakawa, T., Jia, M. Z., Nakamura, A., Ohtsuka, J., Xue, Y. L., Kawashima, T., Kasahara, T., Hibi, M., Ogawa, ...

New page

'''Unreleased structure'''

The entry 3w21 is ON HOLD

Authors: Qin, H. M., Miyakawa, T., Jia, M. Z., Nakamura, A., Ohtsuka, J., Xue, Y. L., Kawashima, T., Kasahara, T., Hibi, M., Ogawa, J., Tanokura, M.

Description: Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase in complex with alpha-KG from Burkholderia ambifaria AMMD