7lnu - Revision history

OCA at 07:18, 3 April 2024

OCA — Wed, 03 Apr 2024 07:18:28 GMT

←Older revision		Revision as of 07:18, 3 April 2024
Line 3:		Line 3:
	<StructureSection load='7lnu' size='340' side='right'caption='[[7lnu]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='7lnu' size='340' side='right'caption='[[7lnu]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7lnu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LNU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LNU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7lnu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Candidatus_Methanomethylophilus_alvus Candidatus Methanomethylophilus alvus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LNU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LNU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=IP8:ISOPENTENYL+PHOSPHATE'>IP8</scene>, <scene name='pdbligand=IPE:3-METHYLBUT-3-ENYL+TRIHYDROGEN+DIPHOSPHATE'>IPE</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]] 2.5Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Isopentenyl_phosphate_kinase Isopentenyl phosphate kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.26 2.7.4.26] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=IP8:ISOPENTENYL+PHOSPHATE'>IP8</scene>, <scene name='pdbligand=IPE:3-METHYLBUT-3-ENYL+TRIHYDROGEN+DIPHOSPHATE'>IPE</scene></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=7lnu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lnu OCA], [https://pdbe.org/7lnu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lnu RCSB], [https://www.ebi.ac.uk/pdbsum/7lnu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lnu 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=7lnu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lnu OCA], [https://pdbe.org/7lnu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lnu RCSB], [https://www.ebi.ac.uk/pdbsum/7lnu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lnu ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/M9SEQ1_METAX M9SEQ1_METAX]
-	Isopentenyl phosphate kinases (IPKs) catalyze the ATP-dependent phosphorylation of isopentenyl monophosphate (IP) to isopentenyl diphosphate (IPP) in the alternate mevalonate pathways of the archaea and plant cytoplasm. In recent years, IPKs have also been employed in artificial biosynthetic pathways called "(iso) prenol pathways" that utilize promiscuous kinases to sequentially phosphorylate (iso) prenol and generate the isoprenoid precursors IPP and dimethylallyl diphosphate (DMAPP). Furthermore, IPKs have garnered attention for their impressive substrate promiscuity toward non-natural alkyl-monophosphates (alkyl-Ps), which has prompted their utilization as biocatalysts for the generation of novel isoprenoids. However, none of the IPK crystal structures currently available contain non-natural substrates, leaving the roles of active-site residues in substrate promiscuity ambiguous. To address this, we present herein the high-resolution crystal structures of an IPK from Candidatus methanomethylophilus alvus (CMA) in the apo form and bound to natural and non-natural substrates. Additionally, we describe active-site engineering studies leading to enzyme variants with broadened substrate scope, as well as structure determination of two such variants (Ile74Ala and Ile146Ala) bound to non-natural alkyl-Ps. Collectively, our crystallographic studies compare six structures of CMA variants in different ligand-bound forms and highlight contrasting structural dynamics of the two substrate-binding sites. Furthermore, the structural and mutational studies confirm a novel role of the highly conserved DVTGG motif in catalysis, both in CMA and in IPKs at large. As such, the current study provides a molecular basis for the substrate-binding modes and catalytic performance of CMA toward the goal of developing IPKs into useful biocatalysts.	+
-		+
-	Molecular Basis for the Substrate Promiscuity of Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus.,Johnson BP, Kumar V, Scull EM, Thomas LM, Bourne CR, Singh S ACS Chem Biol. 2021 Dec 14. doi: ~~10.1021~~/~~acschembio.1c00655. PMID:34905349<ref>PMID:34905349<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 7lnu" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Isopentenyl phosphate kinase~~]]	+	[[Category: Candidatus Methanomethylophilus alvus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bourne~~, C R~~]]	+	[[Category: Bourne CR]]
-	[[Category: Scull~~, E M~~]]	+	[[Category: Scull EM]]
-	[[Category: Singh, S]]	+	[[Category: Singh S]]
-	[[Category: Thomas~~, L M]]~~	+	[[Category: Thomas LM]]
-	~~[[Category: Phosphotransferase atp biocatalysis isoprenoids enzyme promiscuity]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 14:16, 29 December 2021

OCA — Wed, 29 Dec 2021 14:16:19 GMT

←Older revision		Revision as of 14:16, 29 December 2021
Line 1:		Line 1:

	==Ternary complex of the Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus bound to isopentenyl monophosphate and ATP==		==Ternary complex of the Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus bound to isopentenyl monophosphate and ATP==
-	<StructureSection load='7lnu' size='340' side='right'caption='[[7lnu]]' scene=''>	+	<StructureSection load='7lnu' size='340' side='right'caption='[[7lnu]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LNU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LNU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7lnu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LNU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LNU FirstGlance]. <br>
-	</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=7lnu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lnu OCA], [https://pdbe.org/7lnu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lnu RCSB], [https://www.ebi.ac.uk/pdbsum/7lnu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lnu ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=IP8:ISOPENTENYL+PHOSPHATE'>IP8</scene>, <scene name='pdbligand=IPE:3-METHYLBUT-3-ENYL+TRIHYDROGEN+DIPHOSPHATE'>IPE</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Isopentenyl_phosphate_kinase Isopentenyl phosphate kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.26 2.7.4.26] </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=7lnu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lnu OCA], [https://pdbe.org/7lnu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lnu RCSB], [https://www.ebi.ac.uk/pdbsum/7lnu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lnu ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Isopentenyl phosphate kinases (IPKs) catalyze the ATP-dependent phosphorylation of isopentenyl monophosphate (IP) to isopentenyl diphosphate (IPP) in the alternate mevalonate pathways of the archaea and plant cytoplasm. In recent years, IPKs have also been employed in artificial biosynthetic pathways called "(iso) prenol pathways" that utilize promiscuous kinases to sequentially phosphorylate (iso) prenol and generate the isoprenoid precursors IPP and dimethylallyl diphosphate (DMAPP). Furthermore, IPKs have garnered attention for their impressive substrate promiscuity toward non-natural alkyl-monophosphates (alkyl-Ps), which has prompted their utilization as biocatalysts for the generation of novel isoprenoids. However, none of the IPK crystal structures currently available contain non-natural substrates, leaving the roles of active-site residues in substrate promiscuity ambiguous. To address this, we present herein the high-resolution crystal structures of an IPK from Candidatus methanomethylophilus alvus (CMA) in the apo form and bound to natural and non-natural substrates. Additionally, we describe active-site engineering studies leading to enzyme variants with broadened substrate scope, as well as structure determination of two such variants (Ile74Ala and Ile146Ala) bound to non-natural alkyl-Ps. Collectively, our crystallographic studies compare six structures of CMA variants in different ligand-bound forms and highlight contrasting structural dynamics of the two substrate-binding sites. Furthermore, the structural and mutational studies confirm a novel role of the highly conserved DVTGG motif in catalysis, both in CMA and in IPKs at large. As such, the current study provides a molecular basis for the substrate-binding modes and catalytic performance of CMA toward the goal of developing IPKs into useful biocatalysts.
		+
		+	Molecular Basis for the Substrate Promiscuity of Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus.,Johnson BP, Kumar V, Scull EM, Thomas LM, Bourne CR, Singh S ACS Chem Biol. 2021 Dec 14. doi: 10.1021/acschembio.1c00655. PMID:34905349<ref>PMID:34905349</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7lnu" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Isopentenyl phosphate kinase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bourne CR]]	+	[[Category: Bourne, C R]]
-	[[Category: Scull EM]]	+	[[Category: Scull, E M]]
-	[[Category: Singh S]]	+	[[Category: Singh, S]]
-	[[Category: Thomas LM]]	+	[[Category: Thomas, L M]]
		+	[[Category: Phosphotransferase atp biocatalysis isoprenoids enzyme promiscuity]]
		+	[[Category: Transferase]]

OCA at 15:25, 22 December 2021

OCA — Wed, 22 Dec 2021 15:25:54 GMT

←Older revision		Revision as of 15:25, 22 December 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 7lnu is ON HOLD until Paper Publication~~	+	==Ternary complex of the Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus bound to isopentenyl monophosphate and ATP==
-		+	<StructureSection load='7lnu' size='340' side='right'caption='[[7lnu]]' scene=''>
-	~~Authors: Thomas, L.M., Singh, S., Scull, E.M., Bourne, C.R.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LNU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LNU FirstGlance]. <br>
-	~~Description:~~ Ternary complex of the Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus bound to isopentenyl monophosphate and ATP	+	</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=7lnu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lnu OCA], [https://pdbe.org/7lnu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lnu RCSB], [https://www.ebi.ac.uk/pdbsum/7lnu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lnu ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Scull~~, E.M]]	+	__TOC__
-	[[Category: ~~Thomas, L.M~~]]	+	</StructureSection>
-	[[Category: Bourne~~, C.R~~]]	+	[[Category: Large Structures]]
-	[[Category: Singh, S]]	+	[[Category: Bourne CR]]
		+	[[Category: Scull EM]]
		+	[[Category: Singh S]]
		+	[[Category: Thomas LM]]

OCA at 13:23, 3 March 2021

OCA — Wed, 03 Mar 2021 13:23:19 GMT

←Older revision		Revision as of 13:23, 3 March 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7lnu is ON HOLD	+	The entry 7lnu is ON HOLD until Paper Publication

	Authors: Thomas, L.M., Singh, S., Scull, E.M., Bourne, C.R.		Authors: Thomas, L.M., Singh, S., Scull, E.M., Bourne, C.R.

OCA: Protected "7lnu" [edit=sysop:move=sysop]

OCA — Wed, 17 Feb 2021 08:48:01 GMT

Protected "7lnu" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:48, 17 February 2021

OCA: New page: '''Unreleased structure''' The entry 7lnu is ON HOLD Authors: Thomas, L.M., Singh, S., Scull, E.M., Bourne, C.R. Description: Ternary complex of the Isopentenyl Phosphate Kinase from C...

OCA — Wed, 17 Feb 2021 08:47:59 GMT

New page: '''Unreleased structure''' The entry 7lnu is ON HOLD Authors: Thomas, L.M., Singh, S., Scull, E.M., Bourne, C.R. Description: Ternary complex of the Isopentenyl Phosphate Kinase from C...

New page

'''Unreleased structure'''

The entry 7lnu is ON HOLD

Authors: Thomas, L.M., Singh, S., Scull, E.M., Bourne, C.R.

Description: Ternary complex of the Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus bound to isopentenyl monophosphate and ATP
[[Category: Unreleased Structures]]
[[Category: Scull, E.M]]
[[Category: Thomas, L.M]]
[[Category: Bourne, C.R]]
[[Category: Singh, S]]