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| | ==Crystal structure of a E138A Escherichia coli dCTP deaminase mutant enzyme in complex with dTTP== | | ==Crystal structure of a E138A Escherichia coli dCTP deaminase mutant enzyme in complex with dTTP== |
| - | <StructureSection load='2j4q' size='340' side='right' caption='[[2j4q]], [[Resolution|resolution]] 2.60Å' scene=''> | + | <StructureSection load='2j4q' size='340' side='right'caption='[[2j4q]], [[Resolution|resolution]] 2.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2j4q]] is a 2 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=2J4Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2J4Q FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2j4q]] is a 2 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=2J4Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2J4Q FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</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]] 2.6Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1xs1|1xs1]], [[1xs4|1xs4]], [[1xs6|1xs6]], [[2j4h|2j4h]]</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=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=2j4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j4q OCA], [https://pdbe.org/2j4q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2j4q RCSB], [https://www.ebi.ac.uk/pdbsum/2j4q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2j4q ProSAT]</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=2j4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j4q OCA], [http://pdbe.org/2j4q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2j4q RCSB], [http://www.ebi.ac.uk/pdbsum/2j4q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2j4q 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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| | </div> | | </div> |
| | <div class="pdbe-citations 2j4q" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 2j4q" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Deaminase 3D structures|Deaminase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| - | [[Category: DCTP deaminase]] | + | [[Category: Large Structures]] |
| - | [[Category: Bynck, J H]] | + | [[Category: Bynck JH]] |
| - | [[Category: Fanoe, M]] | + | [[Category: Fanoe M]] |
| - | [[Category: Johansson, E]] | + | [[Category: Johansson E]] |
| - | [[Category: Larsen, S]] | + | [[Category: Larsen S]] |
| - | [[Category: Thymark, M]] | + | [[Category: Thymark M]] |
| - | [[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
The trimeric dCTP deaminase produces dUTP that is hydrolysed to dUMP by the structurally closely related dUTPase. This pathway provides 70-80% of the total dUMP as a precursor for dTTP. Accordingly, dCTP deaminase is regulated by dTTP, which increases the substrate concentration for half-maximal activity and the cooperativity of dCTP saturation. Likewise, increasing concentrations of dCTP increase the cooperativity of dTTP inhibition. Previous structural studies showed that the complexes of inactive mutant protein, E138A, with dUTP or dCTP bound, and wild-type enzyme with dUTP bound were all highly similar and characterized by having an ordered C-terminal. When comparing with a new structure in which dTTP is bound to the active site of E138A, the region between Val120 and His125 was found to be in a new conformation. This and the previous conformation were mutually exclusive within the trimer. Also, the dCTP complex of the inactive H121A was found to have residues 120-125 in this new conformation, indicating that it renders the enzyme inactive. The C-terminal fold was found to be disordered for both new complexes. We suggest that the cooperative kinetics are imposed by a dTTP-dependent lag of product formation observed in presteady-state kinetics. This lag may be derived from a slow equilibration between an inactive and an active conformation of dCTP deaminase represented by the dTTP complex and the dUTP/dCTP complex, respectively. The dCTP deaminase then resembles a simple concerted system subjected to effector binding, but without the use of an allosteric site.
Regulation of dCTP deaminase from Escherichia coli by nonallosteric dTTP binding to an inactive form of the enzyme.,Johansson E, Thymark M, Bynck JH, Fano M, Larsen S, Willemoes M FEBS J. 2007 Aug;274(16):4188-98. Epub 2007 Jul 25. PMID:17651436[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Johansson E, Thymark M, Bynck JH, Fano M, Larsen S, Willemoes M. Regulation of dCTP deaminase from Escherichia coli by nonallosteric dTTP binding to an inactive form of the enzyme. FEBS J. 2007 Aug;274(16):4188-98. Epub 2007 Jul 25. PMID:17651436 doi:10.1111/j.1742-4658.2007.05945.x
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