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| | <StructureSection load='2zz6' size='340' side='right'caption='[[2zz6]], [[Resolution|resolution]] 1.66Å' scene=''> | | <StructureSection load='2zz6' size='340' side='right'caption='[[2zz6]], [[Resolution|resolution]] 1.66Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2zz6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"methanobacterium_thermoautotrophicus"_(sic)_zeikus_and_wolfe_1972 "methanobacterium thermoautotrophicus" (sic) zeikus and wolfe 1972]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZZ6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZZ6 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2zz6]] is a 2 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=2ZZ6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZZ6 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6AZ:6-AZIDOURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>6AZ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.66Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2e6y|2e6y]], [[1x1z|1x1z]], [[1lp6|1lp6]], [[1los|1los]], [[1lor|1lor]], [[1dv7|1dv7]], [[2zz1|2zz1]], [[2zz2|2zz2]], [[2zz3|2zz3]], [[2zz4|2zz4]], [[2zz5|2zz5]], [[2zz7|2zz7]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6AZ:6-AZIDOURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>6AZ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=2zz6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zz6 OCA], [https://pdbe.org/2zz6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zz6 RCSB], [https://www.ebi.ac.uk/pdbsum/2zz6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zz6 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=2zz6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zz6 OCA], [https://pdbe.org/2zz6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zz6 RCSB], [https://www.ebi.ac.uk/pdbsum/2zz6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zz6 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: Orotidine-5'-phosphate decarboxylase]] | + | [[Category: Methanothermobacter thermautotrophicus]] |
| - | [[Category: Fujihashi, M]] | + | [[Category: Fujihashi M]] |
| - | [[Category: Pai, E F]] | + | [[Category: Pai EF]] |
| - | [[Category: Decarboxylase]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Odcase]]
| + | |
| - | [[Category: Ompdc]]
| + | |
| - | [[Category: Ompdcase]]
| + | |
| - | [[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
Crystal structures of substrate-product complexes of Methanobacterium thermoautotrophicum orotidine 5'-monophosphate decarboxylase, obtained at various steps in its catalysis of the unusual transformation of 6-cyano-uridine 5'-monophosphate (UMP) into barbituric acid ribosyl monophosphate, show that the cyano substituent of the substrate, when bound to the active site, is first bent significantly from the plane of the pyrimidine ring and then replaced by an oxygen atom. Although the K72A and D70A/K72A mutants are either catalytically impaired or even completely inactive, they still display bending of the C6 substituent. Interestingly, high-resolution structures of the D70A and D75N mutants revealed a covalent bond between C6 of UMP and the Lys72 side chain after the -CN moiety's release. The same covalent bond was observed when the native enzyme was incubated with 6-azido-UMP and 6-iodo-UMP; in contrast, the K72A mutant transformed 6-iodo-UMP to barbituric acid ribosyl 5'-monophosphate. These results demonstrate that, given a suitable environment, native orotidine 5'-monophosphate decarboxylase and several of its mutants are not restricted to the physiologically relevant decarboxylation; they are able to catalyze even nucleophilic substitution reactions but consistently maintain distortion on the C6 substituent as an important feature of catalysis.
Structural characterization of the molecular events during a slow substrate-product transition in orotidine 5'-monophosphate decarboxylase.,Fujihashi M, Wei L, Kotra LP, Pai EF J Mol Biol. 2009 Apr 17;387(5):1199-210. Epub 2009 Feb 21. PMID:19236876[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Fujihashi M, Wei L, Kotra LP, Pai EF. Structural characterization of the molecular events during a slow substrate-product transition in orotidine 5'-monophosphate decarboxylase. J Mol Biol. 2009 Apr 17;387(5):1199-210. Epub 2009 Feb 21. PMID:19236876 doi:10.1016/j.jmb.2009.02.037
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