|
|
| Line 3: |
Line 3: |
| <StructureSection load='3v1p' size='340' side='right'caption='[[3v1p]], [[Resolution|resolution]] 1.37Å' scene=''> | | <StructureSection load='3v1p' size='340' side='right'caption='[[3v1p]], [[Resolution|resolution]] 1.37Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[3v1p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Metth Metth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V1P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V1P FirstGlance]. <br> | | <table><tr><td colspan='2'>[[3v1p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus_str._Delta_H Methanothermobacter thermautotrophicus str. Delta H]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V1P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V1P FirstGlance]. <br> |
| </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMP:6-HYDROXYURIDINE-5-PHOSPHATE'>BMP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.37Å</td></tr> |
| <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ltp|3ltp]]</div></td></tr>
| | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMP:6-HYDROXYURIDINE-5-PHOSPHATE'>BMP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pyrF, MTH_129 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=187420 METTH])</td></tr> | |
| <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23] </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=3v1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v1p OCA], [https://pdbe.org/3v1p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v1p RCSB], [https://www.ebi.ac.uk/pdbsum/3v1p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v1p 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=3v1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v1p OCA], [https://pdbe.org/3v1p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v1p RCSB], [https://www.ebi.ac.uk/pdbsum/3v1p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v1p ProSAT]</span></td></tr> |
| </table> | | </table> |
| == Function == | | == 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]
| | [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 ==
| |
| The binding of a ligand to orotidine 5'-monophosphate decarboxylase (OMPDC) is accompanied by a conformational change from an open, inactive conformation (E(o)) to a closed, active conformation (E(c)). As the substrate traverses the reaction coordinate to form the stabilized vinyl carbanion/carbene intermediate, interactions that destabilize the carboxylate group of the substrate and stabilize the intermediate (in the E(c).S() complex) are enforced. Focusing on the OMPDC from Methanothermobacter thermautotrophicus, we find the "remote" 5'-phosphate group of the substrate activates the enzyme 2.4 x 10(8)-fold; the activation is equivalently described by an intrinsic binding energy (IBE) of 11.4 kcal/mol. We studied residues in the activation that (1) directly contact the 5'-phosphate group, (2) participate in a hydrophobic cluster near the base of the active site loop that sequesters the bound substrate from the solvent, and (3) form hydrogen bonding interactions across the interface between the "mobile" and "fixed" half-barrel domains of the (beta/alpha)(8)-barrel structure. Our data support a model in which the IBE provided by the 5'-phosphate group is used to allow interactions both near the N-terminus of the active site loop and across the domain interface that stabilize both the E(c).S and E(c).S() complexes relative to the E(o).S complex. The conclusion that the IBE of the 5'-phosphate group provides stabilization to both the E(c).S and E(c).S() complexes, not just the E(c).S() complex, is central to understanding the structural origins of enzymatic catalysis as well as the requirements for the de novo design of enzymes that catalyze novel reactions.
| |
| | |
| Conformational Changes in Orotidine 5'-Monophosphate Decarboxylase: A Structure-Based Explanation for How the 5'-Phosphate Group Activates the Enzyme.,Desai BJ, Wood BM, Fedorov AA, Fedorov EV, Goryanova B, Amyes TL, Richard JP, Almo SC, Gerlt JA Biochemistry. 2012 Oct 17. PMID:23030629<ref>PMID:23030629</ref>
| |
| | |
| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| |
| </div>
| |
| <div class="pdbe-citations 3v1p" style="background-color:#fffaf0;"></div>
| |
|
| |
|
| ==See Also== | | ==See Also== |
| *[[Uridine 5'-monophosphate synthase 3D structures|Uridine 5'-monophosphate synthase 3D structures]] | | *[[Uridine 5'-monophosphate synthase 3D structures|Uridine 5'-monophosphate synthase 3D structures]] |
| == References ==
| |
| <references/>
| |
| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| [[Category: Large Structures]] | | [[Category: Large Structures]] |
| [[Category: Metth]] | | [[Category: Methanothermobacter thermautotrophicus str. Delta H]] |
| [[Category: Orotidine-5'-phosphate decarboxylase]]
| | [[Category: Almo SC]] |
| [[Category: Almo, S C]] | | [[Category: Desai B]] |
| [[Category: Desai, B]] | | [[Category: Fedorov AA]] |
| [[Category: Fedorov, A A]] | | [[Category: Fedorov EV]] |
| [[Category: Fedorov, E V]] | | [[Category: Gerlt JA]] |
| [[Category: Gerlt, J A]] | |
| [[Category: Inhibitor bmp]]
| |
| [[Category: Lyase]]
| |
| [[Category: Lyase-lyase inhibitor complex]]
| |
| [[Category: Orotidine 5'-monophosphate decarboxylase]]
| |
| [[Category: Tim barrel]]
| |