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| | ==Structure of deoxyadenosine kinase from M.mycoides with products dcmp and a flexible dcdp bound== | | ==Structure of deoxyadenosine kinase from M.mycoides with products dcmp and a flexible dcdp bound== |
| - | <StructureSection load='2jat' size='340' side='right' caption='[[2jat]], [[Resolution|resolution]] 2.60Å' scene=''> | + | <StructureSection load='2jat' size='340' side='right'caption='[[2jat]], [[Resolution|resolution]] 2.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2jat]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycmi Mycmi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JAT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JAT FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2jat]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycoplasma_mycoides_subsp._mycoides_SC Mycoplasma mycoides subsp. mycoides SC]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JAT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JAT FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCM:2-DEOXYCYTIDINE-5-MONOPHOSPHATE'>DCM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</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">[[2jaq|2jaq]], [[2jas|2jas]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCM:2-DEOXYCYTIDINE-5-MONOPHOSPHATE'>DCM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyguanosine_kinase Deoxyguanosine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.113 2.7.1.113] </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=2jat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jat OCA], [https://pdbe.org/2jat PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jat RCSB], [https://www.ebi.ac.uk/pdbsum/2jat PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jat 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=2jat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jat OCA], [http://pdbe.org/2jat PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jat RCSB], [http://www.ebi.ac.uk/pdbsum/2jat PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2jat ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q93IG4_MYCMI Q93IG4_MYCMI] |
| | == 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: Deoxyguanosine kinase]] | + | [[Category: Large Structures]] |
| - | [[Category: Mycmi]] | + | [[Category: Mycoplasma mycoides subsp. mycoides SC]] |
| - | [[Category: Eklund, H]] | + | [[Category: Eklund H]] |
| - | [[Category: Eriksson, S]] | + | [[Category: Eriksson S]] |
| - | [[Category: Wang, L]] | + | [[Category: Wang L]] |
| - | [[Category: Welin, M]] | + | [[Category: Welin M]] |
| - | [[Category: Deoxyribonucleoside kinase]]
| + | |
| - | [[Category: Kinase]]
| + | |
| - | [[Category: Transferase]]
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| Structural highlights
Function
Q93IG4_MYCMI
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
Deoxyribonucleoside kinases (dNKs) catalyze the transfer of a phosphoryl group from ATP to a deoxyribonucleoside (dN), a key step in DNA precursor synthesis. Recently structural information concerning dNKs has been obtained, but no structure of a bacterial dCK/dGK enzyme is known. Here we report the structure of such an enzyme, represented by deoxyadenosine kinase from Mycoplasma mycoides subsp. mycoides small colony type (Mm-dAK). Superposition of Mm-dAK with its human counterpart's deoxyguanosine kinase (dGK) and deoxycytidine kinase (dCK) reveals that the overall structures are very similar with a few amino acid alterations in the proximity of the active site. To investigate the substrate specificity, Mm-dAK has been crystallized in complex with dATP and dCTP, as well as the products dCMP and dCDP. Both dATP and dCTP bind to the enzyme in a feedback-inhibitory manner with the dN part in the deoxyribonucleoside binding site and the triphosphates in the P-loop. Substrate specificity studies with clinically important nucleoside analogs as well as several phosphate donors were performed. Thus, in this study we combine structural and kinetic data to gain a better understanding of the substrate specificity of the dCK/dGK family of enzymes. The structure of Mm-dAK provides a starting point for making new anti bacterial agents against pathogenic bacteria.
Structure-function analysis of a bacterial deoxyadenosine kinase reveals the basis for substrate specificity.,Welin M, Wang L, Eriksson S, Eklund H J Mol Biol. 2007 Mar 9;366(5):1615-23. Epub 2006 Dec 8. PMID:17229440[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Welin M, Wang L, Eriksson S, Eklund H. Structure-function analysis of a bacterial deoxyadenosine kinase reveals the basis for substrate specificity. J Mol Biol. 2007 Mar 9;366(5):1615-23. Epub 2006 Dec 8. PMID:17229440 doi:http://dx.doi.org/10.1016/j.jmb.2006.12.010
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