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[[Image:2jat.gif|left|200px]]<br />
<applet load="2jat" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2jat, resolution 2.60&Aring;" />
'''STRUCTURE OF DEOXYADENOSINE KINASE FROM M.MYCOIDES WITH PRODUCTS DCMP AND A FLEXIBLE DCDP BOUND'''<br />


==Overview==
==Structure of deoxyadenosine kinase from M.mycoides with products dcmp and a flexible dcdp bound==
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 ... [[http://ispc.weizmann.ac.il/pmbin/getpm?17229440 (full description)]]
<StructureSection load='2jat' size='340' side='right'caption='[[2jat]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
<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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</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='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>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q93IG4_MYCMI Q93IG4_MYCMI]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ja/2jat_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2jat ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== 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.


==About this Structure==
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<ref>PMID:17229440</ref>
2JAT is a [[http://en.wikipedia.org/wiki/Single_protein Single protein]] structure of sequence from [[http://en.wikipedia.org/wiki/Mycoplasma_mycoides_subsp._mycoides_sc Mycoplasma mycoides subsp. mycoides sc]] with MG, POP and DCM as [[http://en.wikipedia.org/wiki/ligands ligands]]. Active as [[http://en.wikipedia.org/wiki/Transferase Transferase]], with EC number [[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.113 2.7.1.113]]. Structure known Active Site: AC1. Full crystallographic information is available from [[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2JAT OCA]].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17229440 17229440]
</div>
[[Category: Mycoplasma mycoides subsp. mycoides sc]]
<div class="pdbe-citations 2jat" style="background-color:#fffaf0;"></div>
[[Category: Single protein]]
== References ==
[[Category: Eklund, H.]]
<references/>
[[Category: Eriksson, S.]]
__TOC__
[[Category: Wang, L.]]
</StructureSection>
[[Category: Welin, M.]]
[[Category: Large Structures]]
[[Category: DCM]]
[[Category: Mycoplasma mycoides subsp. mycoides SC]]
[[Category: MG]]
[[Category: Eklund H]]
[[Category: POP]]
[[Category: Eriksson S]]
[[Category: deoxyribonucleoside kinase]]
[[Category: Wang L]]
[[Category: kinase]]
[[Category: Welin M]]
[[Category: transferase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Oct 30 08:27:33 2007''

Latest revision as of 14:40, 13 December 2023

Structure of deoxyadenosine kinase from M.mycoides with products dcmp and a flexible dcdp bound

2jat, resolution 2.60Å

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