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| | <StructureSection load='1lh0' size='340' side='right'caption='[[1lh0]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='1lh0' size='340' side='right'caption='[[1lh0]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1lh0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LH0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LH0 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1lh0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LH0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LH0 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ORO:OROTIC+ACID'>ORO</scene>, <scene name='pdbligand=PRP:ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC+ACID'>PRP</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]] 2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1i2i|1i2i]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ORO:OROTIC+ACID'>ORO</scene>, <scene name='pdbligand=PRP:ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC+ACID'>PRP</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Orotate_phosphoribosyltransferase Orotate phosphoribosyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.10 2.4.2.10] </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=1lh0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lh0 OCA], [https://pdbe.org/1lh0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lh0 RCSB], [https://www.ebi.ac.uk/pdbsum/1lh0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lh0 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=1lh0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lh0 OCA], [https://pdbe.org/1lh0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lh0 RCSB], [https://www.ebi.ac.uk/pdbsum/1lh0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lh0 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/PYRE_SALTY PYRE_SALTY]] Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP) (By similarity).<ref>PMID:2271660</ref>
| + | [https://www.uniprot.org/uniprot/PYRE_SALTY PYRE_SALTY] Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP) (By similarity).<ref>PMID:2271660</ref> |
| | == 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: Orotate phosphoribosyltransferase]] | + | [[Category: Salmonella enterica subsp. enterica serovar Typhimurium]] |
| - | [[Category: Almo, S C]] | + | [[Category: Almo SC]] |
| - | [[Category: Fedorov, A A]] | + | [[Category: Fedorov AA]] |
| - | [[Category: Grubmeyer, C]] | + | [[Category: Grubmeyer C]] |
| - | [[Category: Panneerselvam, K]] | + | [[Category: Panneerselvam K]] |
| - | [[Category: Shi, W]] | + | [[Category: Shi W]] |
| - | [[Category: Loop closure]]
| + | |
| - | [[Category: Monomer closure]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
PYRE_SALTY Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP) (By similarity).[1]
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
Dimeric Salmonella typhimurium orotate phosphoribosyltransferase (OMP synthase, EC 2.4.2.10), a key enzyme in de novo pyrimidine nucleotide synthesis, has been cocrystallized in a complete substrate E.MgPRPP.orotate complex and the structure determined to 2.2 A resolution. This structure resembles that of Saccharomyces cerevisiae OMP synthase in showing a dramatic and asymmetric reorganization around the active site-bound ligands but shares the same basic topology previously observed in complexes of OMP synthase from S. typhimurium and Escherichia coli. The catalytic loop (residues 99-109) contributed by subunit A is reorganized to close the active site situated in subunit B and to sequester it from solvent. Furthermore, the overall structure of subunit B is more compact, because of movements of the amino-terminal hood and elements of the core domain. The catalytic loop of subunit B remains open and disordered, and subunit A retains the more relaxed conformation observed in loop-open S. typhimurium OMP synthase structures. A non-proline cis-peptide formed between Ala71 and Tyr72 is seen in both subunits. The loop-closed catalytic site of subunit B reveals that both the loop and the hood interact directly with the bound pyrophosphate group of PRPP. In contrast to dimagnesium hypoxanthine-guanine phosphoribosyltransferases, OMP synthase contains a single catalytic Mg(2+) in the closed active site. The remaining pyrophosphate charges of PRPP are neutralized by interactions with Arg99A, Lys100B, Lys103A, and His105A. The new structure confirms the importance of loop movement in catalysis by OMP synthase and identifies several additional movements that must be accomplished in each catalytic cycle. A catalytic mechanism based on enzymic and substrate-assisted stabilization of the previously documented oxocarbenium transition state structure is proposed.
Structure of Salmonella typhimurium OMP Synthase in a Complete Substrate Complex.,Grubmeyer C, Hansen MR, Fedorov AA, Almo SC Biochemistry. 2012 Jun 5;51(22):4397-405. Epub 2012 May 23. PMID:22531064[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Bhatia MB, Vinitsky A, Grubmeyer C. Kinetic mechanism of orotate phosphoribosyltransferase from Salmonella typhimurium. Biochemistry. 1990 Nov 20;29(46):10480-7. PMID:2271660
- ↑ Grubmeyer C, Hansen MR, Fedorov AA, Almo SC. Structure of Salmonella typhimurium OMP Synthase in a Complete Substrate Complex. Biochemistry. 2012 Jun 5;51(22):4397-405. Epub 2012 May 23. PMID:22531064 doi:http://dx.doi.org/10.1021/bi300083p
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