2qv7: Difference between revisions

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{{Seed}}
[[Image:2qv7.png|left|200px]]


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==Crystal Structure of Diacylglycerol Kinase DgkB in complex with ADP and Mg==
The line below this paragraph, containing "STRUCTURE_2qv7", creates the "Structure Box" on the page.
<StructureSection load='2qv7' size='340' side='right'caption='[[2qv7]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2qv7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QV7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QV7 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
{{STRUCTURE_2qv7|  PDB=2qv7  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2qv7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qv7 OCA], [https://pdbe.org/2qv7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qv7 RCSB], [https://www.ebi.ac.uk/pdbsum/2qv7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qv7 ProSAT]</span></td></tr>
</table>
== 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/qv/2qv7_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2qv7 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Soluble diacylglycerol (DAG) kinases function as regulators of diacylglycerol metabolism in cell signaling and intermediary metabolism. We report the structure of a DAG kinase, DgkB from Staphylococcus aureus, both as the free enzyme and in complex with ADP. The molecule is a tight homodimer, and each monomer comprises two domains with the catalytic center located within the interdomain cleft. Two distinctive features of DkgB are a structural Mg2+ site and an associated Asp*water*Mg2+ network that extends toward the active site locale. Site-directed mutagenesis revealed that these features play important roles in the catalytic mechanism. The key active site residues and the components of the Asp*water*Mg2+ network are conserved in the catalytic cores of the mammalian signaling DAG kinases, indicating that these enzymes use the same mechanism and have similar structures as DgkB.


===Crystal Structure of Diacylglycerol Kinase DgkB in complex with ADP and Mg===
Analysis of the Staphylococcus aureus DgkB structure reveals a common catalytic mechanism for the soluble diacylglycerol kinases.,Miller DJ, Jerga A, Rock CO, White SW Structure. 2008 Jul;16(7):1036-46. PMID:18611377<ref>PMID:18611377</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2qv7" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_18611377}}, adds the Publication Abstract to the page
*[[Diacylglycerol kinase|Diacylglycerol kinase]]
(as it appears on PubMed at http://www.pubmed.gov), where 18611377 is the PubMed ID number.
*[[Diacylglycerol kinase 3D structures|Diacylglycerol kinase 3D structures]]
-->
== References ==
{{ABSTRACT_PUBMED_18611377}}
<references/>
 
__TOC__
==About this Structure==
</StructureSection>
2QV7 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QV7 OCA].
[[Category: Large Structures]]
 
==Reference==
<ref group="xtra">PMID:18611377</ref><references group="xtra"/>
[[Category: Diacylglycerol kinase]]
[[Category: Staphylococcus aureus]]
[[Category: Staphylococcus aureus]]
[[Category: Jerga, A.]]
[[Category: Jerga A]]
[[Category: Miller, D J.]]
[[Category: Miller DJ]]
[[Category: Rock, C O.]]
[[Category: Rock CO]]
[[Category: White, S W.]]
[[Category: White SW]]
[[Category: Alpha-beta domain 1]]
[[Category: Beta sandwich domain 2]]
[[Category: Protein-adp complex]]
[[Category: Transferase]]
 
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Retrieved from "https://proteopedia.org/2qv7"