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| | <StructureSection load='3lhz' size='340' side='right'caption='[[3lhz]], [[Resolution|resolution]] 1.40Å' scene=''> | | <StructureSection load='3lhz' size='340' side='right'caption='[[3lhz]], [[Resolution|resolution]] 1.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3lhz]] 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=3LHZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LHZ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3lhz]] 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=3LHZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LHZ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMQ:1-(5-PHOSPHO-BETA-D-RIBOFURANOSYL)BARBITURIC+ACID'>BMQ</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]] 1.4Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3lht|3lht]], [[3lhu|3lhu]], [[3lhv|3lhv]], [[3lhw|3lhw]], [[3lhy|3lhy]], [[3li0|3li0]], [[3li1|3li1]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMQ:1-(5-PHOSPHO-BETA-D-RIBOFURANOSYL)BARBITURIC+ACID'>BMQ</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=3lhz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lhz OCA], [https://pdbe.org/3lhz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lhz RCSB], [https://www.ebi.ac.uk/pdbsum/3lhz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lhz 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=3lhz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lhz OCA], [https://pdbe.org/3lhz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lhz RCSB], [https://www.ebi.ac.uk/pdbsum/3lhz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lhz 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] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | </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: Fedorov AA]] |
| - | [[Category: Fedorov, A A]] | + | [[Category: Fedorov EV]] |
| - | [[Category: Fedorov, E V]] | + | [[Category: Gerlt JA]] |
| - | [[Category: Gerlt, J A]] | + | [[Category: Wood BM]] |
| - | [[Category: Wood, B M]] | + | |
| - | [[Category: 6-hydroxyuridine-5'-phosphate]]
| + | |
| - | [[Category: Decarboxylase]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Pyrimidine biosynthesis]]
| + | |
| Structural highlights
Function
PYRF_METTH Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_A]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The structural factors responsible for the extraordinary rate enhancement ( approximately 10(17)) of the reaction catalyzed by orotidine 5'-monophosphate decarboxylase (OMPDC) have not been defined. Catalysis requires a conformational change that closes an active site loop and "clamps" the orotate base proximal to hydrogen-bonded networks that destabilize the substrate and stabilize the intermediate. In the OMPDC from Methanobacter thermoautotrophicus, a "remote" structurally conserved cluster of hydrophobic residues that includes Val 182 in the active site loop is assembled in the closed, catalytically active conformation. Substitution of these residues with Ala decreases k(cat)/K(m) with a minimal effect on k(cat), providing evidence that the cluster stabilizes the closed conformation. The intrinsic binding energies of the 5'-phosphate group of orotidine 5'-monophosphate for the mutant enzymes are similar to that for the wild type, supporting this conclusion.
Conformational changes in orotidine 5'-monophosphate decarboxylase: "remote" residues that stabilize the active conformation.,Wood BM, Amyes TL, Fedorov AA, Fedorov EV, Shabila A, Almo SC, Richard JP, Gerlt JA Biochemistry. 2010 May 4;49(17):3514-6. PMID:20369850[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Wood BM, Amyes TL, Fedorov AA, Fedorov EV, Shabila A, Almo SC, Richard JP, Gerlt JA. Conformational changes in orotidine 5'-monophosphate decarboxylase: "remote" residues that stabilize the active conformation. Biochemistry. 2010 May 4;49(17):3514-6. PMID:20369850 doi:10.1021/bi100443a
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