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| | <StructureSection load='1xs4' size='340' side='right'caption='[[1xs4]], [[Resolution|resolution]] 2.53Å' scene=''> | | <StructureSection load='1xs4' size='340' side='right'caption='[[1xs4]], [[Resolution|resolution]] 2.53Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1xs4]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XS4 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1XS4 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1xs4]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XS4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XS4 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</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]] 2.53Å</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=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</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;'>[[1xs1|1xs1]], [[1xs6|1xs6]]</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=1xs4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xs4 OCA], [https://pdbe.org/1xs4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xs4 RCSB], [https://www.ebi.ac.uk/pdbsum/1xs4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xs4 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dcd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dCTP_deaminase dCTP deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.13 3.5.4.13] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1xs4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xs4 OCA], [http://pdbe.org/1xs4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xs4 RCSB], [http://www.ebi.ac.uk/pdbsum/1xs4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xs4 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/DCD_ECOLI DCD_ECOLI] |
| | == 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: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: DCTP deaminase]]
| + | [[Category: Bynck JH]] |
| - | [[Category: Bynck, J H]] | + | [[Category: Christensen U]] |
| - | [[Category: Christensen, U]] | + | [[Category: Fano M]] |
| - | [[Category: Fano, M]] | + | [[Category: Johansson E]] |
| - | [[Category: Johansson, E]] | + | [[Category: Larsen S]] |
| - | [[Category: Larsen, S]] | + | [[Category: Neuhard J]] |
| - | [[Category: Neuhard, J]] | + | [[Category: Sigurskjold BW]] |
| - | [[Category: Sigurskjold, B W]] | + | [[Category: Willemoes M]] |
| - | [[Category: Willemoes, M]] | + | |
| - | [[Category: Dctp deaminase]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Nucleotide metabolism]]
| + | |
| - | [[Category: Trimer]]
| + | |
| Structural highlights
Function
DCD_ECOLI
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
dCTP deaminase (EC 3.5.4.13) catalyzes the deamination of dCTP forming dUTP that via dUTPase is the main pathway providing substrate for thymidylate synthase in Escherichia coli and Salmonella typhimurium. dCTP deaminase is unique among nucleoside and nucleotide deaminases as it functions without aid from a catalytic metal ion that facilitates preparation of a water molecule for nucleophilic attack on the substrate. Two active site amino acid residues, Arg(115) and Glu(138), were identified by mutational analysis as important for activity in E. coli dCTP deaminase. None of the mutant enzymes R115A, E138A, or E138Q had any detectable activity but circular dichroism spectra for all mutant enzymes were similar to wild type suggesting that the overall structure was not changed. The crystal structures of wild-type E. coli dCTP deaminase and the E138A mutant enzyme have been determined in complex with dUTP and Mg(2+), and the mutant enzyme also with the substrate dCTP and Mg(2+). The enzyme is a third member of the family of the structurally related trimeric dUTPases and the bifunctional dCTP deaminase-dUTPase from Methanocaldococcus jannaschii. However, the C-terminal fold is completely different from dUTPases resulting in an active site built from residues from two of the trimer subunits, and not from three subunits as in dUTPases. The nucleotides are well defined as well as Mg(2+) that is tridentately coordinated to the nucleotide phosphate chains. We suggest a catalytic mechanism for the dCTP deaminase and identify structural differences to dUTPases that prevent hydrolysis of the dCTP triphosphate.
Structures of dCTP deaminase from Escherichia coli with bound substrate and product: reaction mechanism and determinants of mono- and bifunctionality for a family of enzymes.,Johansson E, Fano M, Bynck JH, Neuhard J, Larsen S, Sigurskjold BW, Christensen U, Willemoes M J Biol Chem. 2005 Jan 28;280(4):3051-9. Epub 2004 Nov 10. PMID:15539408[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Johansson E, Fano M, Bynck JH, Neuhard J, Larsen S, Sigurskjold BW, Christensen U, Willemoes M. Structures of dCTP deaminase from Escherichia coli with bound substrate and product: reaction mechanism and determinants of mono- and bifunctionality for a family of enzymes. J Biol Chem. 2005 Jan 28;280(4):3051-9. Epub 2004 Nov 10. PMID:15539408 doi:10.1074/jbc.M409534200
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