7lnt

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Current revision (07:18, 3 April 2024) (edit) (undo)
 
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<StructureSection load='7lnt' size='340' side='right'caption='[[7lnt]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
<StructureSection load='7lnt' size='340' side='right'caption='[[7lnt]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[7lnt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LNT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LNT FirstGlance]. <br>
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<table><tr><td colspan='2'>[[7lnt]] 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=7LNT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LNT FirstGlance]. <br>
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</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=WZT:(phenylmethyl)+dihydrogen+phosphate'>WZT</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.35&#8491;</td></tr>
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<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>
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<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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=WZT:(phenylmethyl)+dihydrogen+phosphate'>WZT</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=7lnt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lnt OCA], [https://pdbe.org/7lnt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lnt RCSB], [https://www.ebi.ac.uk/pdbsum/7lnt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lnt 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=7lnt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lnt OCA], [https://pdbe.org/7lnt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lnt RCSB], [https://www.ebi.ac.uk/pdbsum/7lnt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lnt ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/M9SEQ1_METAX M9SEQ1_METAX]
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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.
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 7lnt" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Isopentenyl phosphate kinase]]
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[[Category: Candidatus Methanomethylophilus alvus]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Bourne, C R]]
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[[Category: Bourne CR]]
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[[Category: Scull, E M]]
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[[Category: Scull EM]]
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[[Category: Singh, S]]
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[[Category: Singh S]]
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[[Category: Thomas, L M]]
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[[Category: Thomas LM]]
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[[Category: Phosphotransferase atp biocatalysis isoprenoids enzyme promiscuity]]
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[[Category: Transferase]]
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Current revision

Ternary complex of the Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus bound to benzyl monophosphate and ATP

PDB ID 7lnt

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