3wk2: Difference between revisions
New page: '''Unreleased structure''' The entry 3wk2 is ON HOLD Authors: Fujihashi, M., Pai, E.F., Miki, K. Description: Orotidine 5'-monophosphate decarboxylase K72A mutant from M. thermoautotro... |
No edit summary |
||
| (7 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
==Orotidine 5'-monophosphate decarboxylase K72A mutant from M. thermoautotrophicus complexed with orotidine 5'-monophosphate methyl ester== | |||
<StructureSection load='3wk2' size='340' side='right'caption='[[3wk2]], [[Resolution|resolution]] 1.69Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3wk2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WK2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WK2 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.69Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=O7M:6-(METHOXYCARBONYL)URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>O7M</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=3wk2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wk2 OCA], [https://pdbe.org/3wk2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wk2 RCSB], [https://www.ebi.ac.uk/pdbsum/3wk2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wk2 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/PYRF_METTH PYRF_METTH] Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_A] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Orotidine 5'-monophosphate decarboxylase (ODCase) accelerates the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP) by 17 orders of magnitude. Eight new crystal structures with ligand analogues combined with computational analyses of the enzyme's short-lived intermediates and the intrinsic electronic energies to distort the substrate and other ligands improve our understanding of the still controversially discussed reaction mechanism. In their respective complexes, 6-methyl-UMP displays significant distortion of its methyl substituent bond, 6-amino-UMP shows the competition between the K72 and C6 substituents for a position close to D70, and the methyl and ethyl esters of OMP both induce rotation of the carboxylate group substituent out of the plane of the pyrimidine ring. Molecular dynamics and quantum mechanics/molecular mechanics computations of the enzyme-substrate complex also show the bond between the carboxylate group and the pyrimidine ring to be distorted, with the distortion contributing a 10-15% decrease of the DeltaDeltaG() value. These results are consistent with ODCase using both substrate distortion and transition-state stabilization, primarily exerted by K72, in its catalysis of the OMP decarboxylation reaction. | |||
Substrate distortion contributes to the catalysis of orotidine 5'-monophosphate decarboxylase.,Fujihashi M, Ishida T, Kuroda S, Kotra LP, Pai EF, Miki K J Am Chem Soc. 2013 Nov 20;135(46):17432-43. doi: 10.1021/ja408197k. Epub 2013, Nov 11. PMID:24151964<ref>PMID:24151964</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3wk2" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Uridine 5'-monophosphate synthase 3D structures|Uridine 5'-monophosphate synthase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Methanothermobacter thermautotrophicus]] | |||
[[Category: Fujihashi M]] | |||
[[Category: Miki K]] | |||
[[Category: Pai EF]] | |||
Latest revision as of 16:13, 8 November 2023
Orotidine 5'-monophosphate decarboxylase K72A mutant from M. thermoautotrophicus complexed with orotidine 5'-monophosphate methyl esterOrotidine 5'-monophosphate decarboxylase K72A mutant from M. thermoautotrophicus complexed with orotidine 5'-monophosphate methyl ester
Structural highlights
FunctionPYRF_METTH Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_A] Publication Abstract from PubMedOrotidine 5'-monophosphate decarboxylase (ODCase) accelerates the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP) by 17 orders of magnitude. Eight new crystal structures with ligand analogues combined with computational analyses of the enzyme's short-lived intermediates and the intrinsic electronic energies to distort the substrate and other ligands improve our understanding of the still controversially discussed reaction mechanism. In their respective complexes, 6-methyl-UMP displays significant distortion of its methyl substituent bond, 6-amino-UMP shows the competition between the K72 and C6 substituents for a position close to D70, and the methyl and ethyl esters of OMP both induce rotation of the carboxylate group substituent out of the plane of the pyrimidine ring. Molecular dynamics and quantum mechanics/molecular mechanics computations of the enzyme-substrate complex also show the bond between the carboxylate group and the pyrimidine ring to be distorted, with the distortion contributing a 10-15% decrease of the DeltaDeltaG() value. These results are consistent with ODCase using both substrate distortion and transition-state stabilization, primarily exerted by K72, in its catalysis of the OMP decarboxylation reaction. Substrate distortion contributes to the catalysis of orotidine 5'-monophosphate decarboxylase.,Fujihashi M, Ishida T, Kuroda S, Kotra LP, Pai EF, Miki K J Am Chem Soc. 2013 Nov 20;135(46):17432-43. doi: 10.1021/ja408197k. Epub 2013, Nov 11. PMID:24151964[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||