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| | <StructureSection load='2bri' size='340' side='right'caption='[[2bri]], [[Resolution|resolution]] 3.00Å' scene=''> | | <StructureSection load='2bri' size='340' side='right'caption='[[2bri]], [[Resolution|resolution]] 3.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2bri]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BRI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BRI FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2bri]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BRI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BRI FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 3Å</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=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2bmu|2bmu]]</div></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=2bri FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bri OCA], [https://pdbe.org/2bri PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bri RCSB], [https://www.ebi.ac.uk/pdbsum/2bri PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bri 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=2bri FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bri OCA], [https://pdbe.org/2bri PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bri RCSB], [https://www.ebi.ac.uk/pdbsum/2bri PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bri ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/PYRH_PYRFU PYRH_PYRFU]] Catalyzes the reversible phosphorylation of UMP to UDP, with ATP as the most efficient phosphate donor.<ref>PMID:15698963</ref>
| + | [https://www.uniprot.org/uniprot/PYRH_PYRFU PYRH_PYRFU] Catalyzes the reversible phosphorylation of UMP to UDP, with ATP as the most efficient phosphate donor.<ref>PMID:15698963</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: Atcc 43587]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Gil-Ortiz, F]] | + | [[Category: Pyrococcus furiosus]] |
| - | [[Category: Marco-Marin, C]] | + | [[Category: Gil-Ortiz F]] |
| - | [[Category: Rubio, V]] | + | [[Category: Marco-Marin C]] |
| - | [[Category: Amino acid kinase]]
| + | [[Category: Rubio V]] |
| - | [[Category: Phosphoryl group transfer]]
| + | |
| - | [[Category: Pyrimidine biosynthesis]]
| + | |
| - | [[Category: Transferase]]
| + | |
| - | [[Category: Ump kinase]]
| + | |
| Structural highlights
Function
PYRH_PYRFU 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
UMP kinase (UMPK), the enzyme responsible for microbial UMP phosphorylation, plays a key role in pyrimidine nucleotide biosynthesis, regulating this process via feed-back control and via gene repression of carbamoyl phosphate synthetase (the first enzyme of the pyrimidine biosynthesis pathway). We present crystal structures of Pyrococcus furiosus UMPK, free or complexed with AMPPNP or AMPPNP and UMP, at 2.4 A, 3 A and 2.55 A resolution, respectively, providing a true snapshot of the catalytically competent bisubstrate complex. The structure proves that UMPK does not resemble other nucleoside monophosphate kinases, including the UMP/CMP kinase found in animals, and thus UMPK may be a potential antimicrobial target. This enzyme has a homohexameric architecture centred around a hollow nucleus, and is organized as a trimer of dimers. The UMPK polypeptide exhibits the amino acid kinase family (AAKF) fold that has been reported in carbamate kinase and acetylglutamate kinase. Comparison with acetylglutamate kinase reveals that the substrates bind within each subunit at equivalent, adequately adapted sites. The UMPK structure contains two bound Mg ions, of which one helps stabilize the transition state, thus having the same catalytic role as one lysine residue found in acetylglutamate kinase, which is missing from P.furiosus UMPK. Relative to carbamate kinase and acetylglutamate kinase, UMPK presents a radically different dimer architecture, lacking the characteristic 16-stranded beta-sheet backbone that was considered a signature of AAKF enzymes. Its hexameric architecture, also a novel trait, results from equatorial contacts between the A and B subunits of adjacent dimers combined with polar contacts between A or B subunits, and may be required for the UMPK regulatory functions, such as gene regulation, proposed here to be mediated by hexamer-hexamer interactions with the DNA-binding protein PepA.
The crystal structure of Pyrococcus furiosus UMP kinase provides insight into catalysis and regulation in microbial pyrimidine nucleotide biosynthesis.,Marco-Marin C, Gil-Ortiz F, Rubio V J Mol Biol. 2005 Sep 16;352(2):438-54. PMID:16095620[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Marco-Marin C, Escamilla-Honrubia JM, Rubio V. First-time crystallization and preliminary X-ray crystallographic analysis of a bacterial-archaeal type UMP kinase, a key enzyme in microbial pyrimidine biosynthesis. Biochim Biophys Acta. 2005 Mar 14;1747(2):271-5. Epub 2004 Dec 9. PMID:15698963 doi:http://dx.doi.org/S1570-9639(04)00322-X
- ↑ Marco-Marin C, Gil-Ortiz F, Rubio V. The crystal structure of Pyrococcus furiosus UMP kinase provides insight into catalysis and regulation in microbial pyrimidine nucleotide biosynthesis. J Mol Biol. 2005 Sep 16;352(2):438-54. PMID:16095620 doi:http://dx.doi.org/10.1016/j.jmb.2005.07.045
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