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| | ==Bacillus subtilis cytidine deaminase with an Arg56 - Ala substitution== | | ==Bacillus subtilis cytidine deaminase with an Arg56 - Ala substitution== |
| - | <StructureSection load='1uwz' size='340' side='right' caption='[[1uwz]], [[Resolution|resolution]] 1.99Å' scene=''> | + | <StructureSection load='1uwz' size='340' side='right'caption='[[1uwz]], [[Resolution|resolution]] 1.99Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1uwz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UWZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UWZ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1uwz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UWZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UWZ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=THU:TETRAHYDRODEOXYURIDINE'>THU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.99Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1jtk|1jtk]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=THU:TETRAHYDRODEOXYURIDINE'>THU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytidine_deaminase Cytidine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.5 3.5.4.5] </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=1uwz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uwz OCA], [https://pdbe.org/1uwz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uwz RCSB], [https://www.ebi.ac.uk/pdbsum/1uwz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uwz 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=1uwz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uwz OCA], [http://pdbe.org/1uwz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1uwz RCSB], [http://www.ebi.ac.uk/pdbsum/1uwz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1uwz ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/CDD_BACSU CDD_BACSU]] This enzyme scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis. | + | [https://www.uniprot.org/uniprot/CDD_BACSU CDD_BACSU] This enzyme scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | ==See Also== | | ==See Also== |
| - | *[[Deaminase|Deaminase]] | + | *[[Deaminase 3D structures|Deaminase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Vibrio subtilis ehrenberg 1835]] | + | [[Category: Bacillus subtilis]] |
| - | [[Category: Cytidine deaminase]] | + | [[Category: Large Structures]] |
| - | [[Category: Johansson, E]] | + | [[Category: Johansson E]] |
| - | [[Category: Larsen, S]] | + | [[Category: Larsen S]] |
| - | [[Category: Neuhard, J]] | + | [[Category: Neuhard J]] |
| - | [[Category: Willemoes, M]] | + | [[Category: Willemoes M]] |
| - | [[Category: Cdd]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Pyrimidine metabolism]]
| + | |
| - | [[Category: Salvage]]
| + | |
| - | [[Category: Tetramer]]
| + | |
| - | [[Category: Zinc binding]]
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| Structural highlights
Function
CDD_BACSU This enzyme scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis.
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 zinc-containing cytidine deaminase (CDA, EC 3.5.4.5) is a pyrimidine salvage enzyme catalyzing the hydrolytic deamination of cytidine and 2'-deoxycytidine forming uridine and 2'-deoxyuridine, respectively. Homodimeric CDA (D-CDA) and homotetrameric CDA (T-CDA) both contain one zinc ion per subunit coordinated to the catalytic water molecule. The zinc ligands in D-CDA are one histidine and two cysteine residues, whereas in T-CDA zinc is coordinated to three cysteines. Two of the zinc coordinating cysteines in T-CDA form hydrogen bonds to the conserved residue Arg56, and this residue together with the dipole moments from two alpha-helices partially neutralizes the additional negative charge in the active site, leading to a catalytic activity similar to D-CDA. Arg56 has been substituted by a glutamine (R56Q), the corresponding residue in D-CDA, an alanine (R56A), and an aspartate (R56D). Moreover, one of the zinc-liganding cysteines has been substituted by histidine to mimic D-CDA, alone (C53H) and in combination with R56Q (C53H/R56Q). R56A, R56Q, and C53H/R56Q contain the same amount of zinc as the wild-type enzyme. The zinc-binding capacity of R56D is reduced. Only R56A, R56Q, and C53H/R56Q yielded measurable CDA activity, R56A and R56Q with similar K(m) but decreased V(max) values compared to wild-type enzyme. Because of dissociation into its inactive subunits, it was impossible to determine the kinetic parameters for C53H/R56Q. R56A and C53H/R56Q display increased apparent pK(a) values compared to the wild-type enzyme and R56Q. On the basis of the structures of R56A, R56Q, and C53H/R56Q an explanation is provided of kinetic results and the apparent instability of C53H/R56Q.
Structural, kinetic, and mutational studies of the zinc ion environment in tetrameric cytidine deaminase.,Johansson E, Neuhard J, Willemoes M, Larsen S Biochemistry. 2004 May 25;43(20):6020-9. PMID:15147186[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Johansson E, Neuhard J, Willemoes M, Larsen S. Structural, kinetic, and mutational studies of the zinc ion environment in tetrameric cytidine deaminase. Biochemistry. 2004 May 25;43(20):6020-9. PMID:15147186 doi:10.1021/bi035893x
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