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| | ==The structure of E. coli UMP kinase in complex with UTP== | | ==The structure of E. coli UMP kinase in complex with UTP== |
| - | <StructureSection load='2bnf' size='340' side='right' caption='[[2bnf]], [[Resolution|resolution]] 2.45Å' scene=''> | + | <StructureSection load='2bnf' size='340' side='right'caption='[[2bnf]], [[Resolution|resolution]] 2.45Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2bnf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BNF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BNF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2bnf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BNF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BNF FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=UTP:URIDINE+5-TRIPHOSPHATE'>UTP</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]] 2.45Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=UTP:URIDINE+5-TRIPHOSPHATE'>UTP</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2bnd|2bnd]], [[2bne|2bne]]</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=2bnf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bnf OCA], [https://pdbe.org/2bnf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bnf RCSB], [https://www.ebi.ac.uk/pdbsum/2bnf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bnf ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-phosphate_kinase Nucleoside-phosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.4 2.7.4.4] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2bnf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bnf OCA], [http://pdbe.org/2bnf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2bnf RCSB], [http://www.ebi.ac.uk/pdbsum/2bnf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2bnf ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/PYRH_ECOLI PYRH_ECOLI] Catalyzes the reversible phosphorylation of UMP to UDP, with ATP as the most efficient phosphate donor.<ref>PMID:7711027</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ecoli]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Nucleoside-phosphate kinase]] | + | [[Category: Large Structures]] |
| - | [[Category: Assairi, L]] | + | [[Category: Assairi L]] |
| - | [[Category: Barzu, O]] | + | [[Category: Barzu O]] |
| - | [[Category: Briozzo, P]] | + | [[Category: Briozzo P]] |
| - | [[Category: Evrin, C]] | + | [[Category: Evrin C]] |
| - | [[Category: Gilles, A M]] | + | [[Category: Gilles AM]] |
| - | [[Category: Joly, N]] | + | [[Category: Joly N]] |
| - | [[Category: Meyer, P]] | + | [[Category: Meyer P]] |
| - | [[Category: Nucleoside monophosphate kinase]]
| + | |
| - | [[Category: Pyrimidine biosynthesis]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
PYRH_ECOLI Catalyzes the reversible phosphorylation of UMP to UDP, with ATP as the most efficient phosphate donor.[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
Bacterial UMP kinases are essential enzymes involved in the multistep synthesis of nucleoside triphosphates. They are hexamers regulated by the allosteric activator GTP and inhibited by UTP. We solved the crystal structure of Escherichia coli UMP kinase bound to the UMP substrate (2.3 A resolution), the UDP product (2.6 A), or UTP (2.45 A). The monomer fold, unrelated to that of other nucleoside monophosphate kinases, belongs to the carbamate kinase-like superfamily. However, the phosphate acceptor binding cleft and subunit assembly are characteristic of UMP kinase. Interactions with UMP explain the high specificity for this natural substrate. UTP, previously described as an allosteric inhibitor, was unexpectedly found in the phosphate acceptor site, suggesting that it acts as a competitive inhibitor. Site-directed mutagenesis of residues Thr-138 and Asn-140, involved in both uracil recognition and active site interaction within the hexamer, decreased the activation by GTP and inhibition by UTP. These experiments suggest a cross-talk mechanism between enzyme subunits involved in cooperative binding at the phosphate acceptor site and in allosteric regulation by GTP. As bacterial UMP kinases have no counterpart in eukaryotes, the information provided here could help the design of new antibiotics.
Structure of Escherichia coli UMP kinase differs from that of other nucleoside monophosphate kinases and sheds new light on enzyme regulation.,Briozzo P, Evrin C, Meyer P, Assairi L, Joly N, Barzu O, Gilles AM J Biol Chem. 2005 Jul 8;280(27):25533-40. Epub 2005 Apr 27. PMID:15857829[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Serina L, Blondin C, Krin E, Sismeiro O, Danchin A, Sakamoto H, Gilles AM, Barzu O. Escherichia coli UMP-kinase, a member of the aspartokinase family, is a hexamer regulated by guanine nucleotides and UTP. Biochemistry. 1995 Apr 18;34(15):5066-74. PMID:7711027
- ↑ Briozzo P, Evrin C, Meyer P, Assairi L, Joly N, Barzu O, Gilles AM. Structure of Escherichia coli UMP kinase differs from that of other nucleoside monophosphate kinases and sheds new light on enzyme regulation. J Biol Chem. 2005 Jul 8;280(27):25533-40. Epub 2005 Apr 27. PMID:15857829 doi:http://dx.doi.org/10.1074/jbc.M501849200
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