6daq - Revision history

OCA at 09:44, 2 April 2025

2025-04-02T09:44:43Z

← Older revision		Revision as of 09:44, 2 April 2025
Line 3:		Line 3:
	<StructureSection load='6daq' size='340' side='right'caption='[[6daq]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='6daq' size='340' side='right'caption='[[6daq]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6daq]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Dsm_7251 Dsm 7251~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DAQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DAQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[6daq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_vanbaalenii Mycolicibacterium vanbaalenii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DAQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DAQ FirstGlance]. <br>
	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non~~-~~Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=9KP:'>9KP</scene>, <scene name='pdbligand=KPI:(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC+ACID'>KPI</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]] 2Å</td></tr>
	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phdJ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=110539 DSM 7251])~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9KP:(E)-N~6~-[(2E)-1-carboxy-3-(2-carboxyphenyl)prop-2-en-1-ylidene]-L-lysine'>9KP</scene>, <scene name='pdbligand=KPI:(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC+ACID'>KPI</scene></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=6daq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6daq OCA], [~~http~~://pdbe.org/6daq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6daq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6daq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6daq 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=6daq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6daq OCA], [https://pdbe.org/6daq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6daq RCSB], [https://www.ebi.ac.uk/pdbsum/6daq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6daq ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/Q6H2K0_MYCVN Q6H2K0_MYCVN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Dsm 7251]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~LeVieux, J A~~]]		[[Category: Mycolicibacterium vanbaalenii]]
	[[Category: ~~Medellin, B P~~]]		[[Category: LeVieux JA]]
	[[Category: ~~Whitman, C P~~]]		[[Category: Medellin BP]]
	[[Category: ~~Zhang, Y J~~]]		[[Category: Whitman CP]]
	[[Category: ~~Aldolase]]~~		[[Category: Zhang YJ]]
	~~[[Category: Lyase~~]]

OCA at 10:58, 1 January 2020

2020-01-01T10:58:03Z

← Older revision		Revision as of 10:58, 1 January 2020
Line 3:		Line 3:
	<StructureSection load='6daq' size='340' side='right'caption='[[6daq]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='6daq' size='340' side='right'caption='[[6daq]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6daq]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DAQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DAQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[6daq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Dsm_7251 Dsm 7251]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DAQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DAQ FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=9KP:'>9KP</scene>, <scene name='pdbligand=KPI:(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC+ACID'>KPI</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=9KP:'>9KP</scene>, <scene name='pdbligand=KPI:(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC+ACID'>KPI</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phdJ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=110539 DSM 7251])</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=6daq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6daq OCA], [http://pdbe.org/6daq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6daq RCSB], [http://www.ebi.ac.uk/pdbsum/6daq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6daq 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=6daq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6daq OCA], [http://pdbe.org/6daq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6daq RCSB], [http://www.ebi.ac.uk/pdbsum/6daq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6daq ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Dsm 7251]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: LeVieux, J A]]		[[Category: LeVieux, J A]]

OCA at 07:10, 10 April 2019

2019-04-10T07:10:37Z

← Older revision		Revision as of 07:10, 10 April 2019
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 6daq is ~~ON HOLD until Paper~~ Publication		==PhdJ bound to substrate intermediate==
			<StructureSection load='6daq' size='340' side='right'caption='[[6daq]], [[Resolution\|resolution]] 2.00Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[6daq]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DAQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DAQ FirstGlance]. <br>
			</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=9KP:'>9KP</scene>, <scene name='pdbligand=KPI:(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC+ACID'>KPI</scene></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=6daq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6daq OCA], [http://pdbe.org/6daq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6daq RCSB], [http://www.ebi.ac.uk/pdbsum/6daq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6daq ProSAT]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			NahE and PhdJ are bifunctional hydratase-aldolases in bacterial catabolic pathways for naphthalene and phenanthrene, respectively. Bacterial species with these pathways can use polycyclic aromatic hydrocarbons (PAHs) as sole sources of carbon and energy. Because of the harmful properties of PAHs and their widespread distribution and persistence in the environment, there is great interest in understanding these degradative pathways, including the mechanisms and specificities of the enzymes found in the pathways. This knowledge can be used to develop and optimize bioremediation techniques. Although hydratase-aldolases catalyze a major step in the PAH degradative pathways, their mechanisms are poorly understood. Sequence analysis identified NahE and PhdJ as members of the N-acetylneuraminate lyase (NAL) subgroup in the aldolase superfamily. Both have a conserved lysine and tyrosine (for Schiff base formation) as well as a GXXGE motif (to bind the pyruvoyl carboxylate group). Herein, we report the structures of NahE, PhdJ, and PhdJ covalently bound to substrate via a Schiff base. Structural analysis and dynamic light scattering experiments show that both enzymes are tetramers. A hydrophobic helix insert, present in the active sites of NahE and PhdJ, might differentiate them from other NAL subgroup members. The individual specificities of NahE and PhdJ are governed by Asn-281/Glu-285 and Ser-278/Asp-282, respectively. Finally, the PhdJ complex structure suggests a potential mechanism for hydration of substrate and subsequent retro-aldol fission. The combined findings fill a gap in our mechanistic understanding of these enzymes and their place in the NAL subgroup.

	~~Authors~~: ~~Medellin~~, ~~B.P~~., LeVieux, ~~J.A.~~, Zhang, Y.J., ~~Whitman, C.P~~.		Structural Characterization of the Hydratase-Aldolases, NahE and PhdJ: Implications for the Specificity, Catalysis, and N-Acetylneuraminate Lyase Subgroup of the Aldolase Superfamily.,LeVieux JA, Medellin B, Johnson WH Jr, Erwin K, Li W, Johnson IA, Zhang YJ, Whitman CP Biochemistry. 2018 Jun 26;57(25):3524-3536. doi: 10.1021/acs.biochem.8b00532., Epub 2018 Jun 11. PMID:29856600<ref>PMID:29856600</ref>

	~~Description~~: ~~PhdJ bound to substrate intermediate~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	[[Category: ~~Unreleased~~ Structures]]		</div>
	[[Category: Whitman, C.P]]		<div class="pdbe-citations 6daq" style="background-color:#fffaf0;"></div>
	[[Category: Zhang, Y.J]]		== References ==
	[[Category: ~~Levieux, J.A~~]]		<references/>
	[[Category: ~~Medellin, B.P~~]]		__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: LeVieux, J A]]
			[[Category: Medellin, B P]]
			[[Category: Whitman, C P]]
			[[Category: Zhang, Y J]]
			[[Category: Aldolase]]
			[[Category: Lyase]]

OCA at 04:02, 30 May 2018

2018-05-30T04:02:49Z

← Older revision		Revision as of 04:02, 30 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6daq is ON HOLD		The entry 6daq is ON HOLD until Paper Publication

	Authors: Medellin, B.P., LeVieux, J.A., Zhang, Y.J., Whitman, C.P.		Authors: Medellin, B.P., LeVieux, J.A., Zhang, Y.J., Whitman, C.P.

OCA: Protected "6daq" [edit=sysop:move=sysop]

2018-05-09T04:56:05Z

Protected "6daq" [edit=sysop:move=sysop]

← Older revision	Revision as of 04:56, 9 May 2018
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6daq is ON HOLD Authors: Medellin, B.P., LeVieux, J.A., Zhang, Y.J., Whitman, C.P. Description: PhdJ bound to substrate intermediate [[Category: Un...

2018-05-09T04:56:03Z

New page: '''Unreleased structure''' The entry 6daq is ON HOLD Authors: Medellin, B.P., LeVieux, J.A., Zhang, Y.J., Whitman, C.P. Description: PhdJ bound to substrate intermediate [[Category: Un...

New page

'''Unreleased structure'''

The entry 6daq is ON HOLD

Authors: Medellin, B.P., LeVieux, J.A., Zhang, Y.J., Whitman, C.P.

Description: PhdJ bound to substrate intermediate
[[Category: Unreleased Structures]]
[[Category: Whitman, C.P]]
[[Category: Zhang, Y.J]]
[[Category: Levieux, J.A]]
[[Category: Medellin, B.P]]