3bq7: Difference between revisions

Revision as of 19:00, 20 October 2021

SAM domain of Diacylglycerol Kinase delta1 (E35G)

Structural highlights

3bq7 is a 6 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:	DGKD, KIAA0145 (HUMAN)
Activity:	Diacylglycerol kinase, with EC number 2.7.1.107
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DGKD_HUMAN] May function as signaling molecule.^[1] Isoform 2 may be involved in cell growth and tumorigenesis. Involved in clathrin-dependent endocytosis.^[2]

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 diacylglycerol kinase (DGK) enzymes function as regulators of intracellular signaling by altering the levels of the second messengers, diacylglycerol and phosphatidic acid. The DGK delta and eta isozymes possess a common protein-protein interaction module known as a sterile alpha-motif (SAM) domain. In DGK delta, SAM domain self-association inhibits the translocation of DGK delta to the plasma membrane. Here we show that DGK delta SAM forms a polymer and map the polymeric interface by a genetic selection for soluble mutants. A crystal structure reveals that DGKSAM forms helical polymers through a head-to-tail interaction similar to other SAM domain polymers. Disrupting polymerization by polymer interface mutations constitutively localizes DGK delta to the plasma membrane. Thus, polymerization of DGK delta regulates the activity of the enzyme by sequestering DGK delta in an inactive cellular location. Regulation by dynamic polymerization is an emerging theme in signal transduction.

Regulation of enzyme localization by polymerization: polymer formation by the SAM domain of diacylglycerol kinase delta1.,Harada BT, Knight MJ, Imai S, Qiao F, Ramachander R, Sawaya MR, Gingery M, Sakane F, Bowie JU Structure. 2008 Mar;16(3):380-7. PMID:18334213^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Kawasaki T, Kobayashi T, Ueyama T, Shirai Y, Saito N. Regulation of clathrin-dependent endocytosis by diacylglycerol kinase delta: importance of kinase activity and binding to AP2alpha. Biochem J. 2008 Jan 15;409(2):471-9. PMID:17880279 doi:https://dx.doi.org/10.1042/BJ20070755
↑ Kawasaki T, Kobayashi T, Ueyama T, Shirai Y, Saito N. Regulation of clathrin-dependent endocytosis by diacylglycerol kinase delta: importance of kinase activity and binding to AP2alpha. Biochem J. 2008 Jan 15;409(2):471-9. PMID:17880279 doi:https://dx.doi.org/10.1042/BJ20070755
↑ Harada BT, Knight MJ, Imai S, Qiao F, Ramachander R, Sawaya MR, Gingery M, Sakane F, Bowie JU. Regulation of enzyme localization by polymerization: polymer formation by the SAM domain of diacylglycerol kinase delta1. Structure. 2008 Mar;16(3):380-7. PMID:18334213 doi:10.1016/j.str.2007.12.017

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Kawasaki T, Kobayashi T, Ueyama T, Shirai Y, Saito N. Regulation of clathrin-dependent endocytosis by diacylglycerol kinase delta: importance of kinase activity and binding to AP2alpha. Biochem J. 2008 Jan 15;409(2):471-9. PMID:17880279 doi:https://dx.doi.org/10.1042/BJ20070755

[2] Kawasaki T, Kobayashi T, Ueyama T, Shirai Y, Saito N. Regulation of clathrin-dependent endocytosis by diacylglycerol kinase delta: importance of kinase activity and binding to AP2alpha. Biochem J. 2008 Jan 15;409(2):471-9. PMID:17880279 doi:https://dx.doi.org/10.1042/BJ20070755

[3] Harada BT, Knight MJ, Imai S, Qiao F, Ramachander R, Sawaya MR, Gingery M, Sakane F, Bowie JU. Regulation of enzyme localization by polymerization: polymer formation by the SAM domain of diacylglycerol kinase delta1. Structure. 2008 Mar;16(3):380-7. PMID:18334213 doi:10.1016/j.str.2007.12.017

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==SAM domain of Diacylglycerol Kinase delta1 (E35G)==
-<StructureSection load='3bq7' size='340' side='right' caption='[[3bq7]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+<StructureSection load='3bq7' size='340' side='right'caption='[[3bq7]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3bq7]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BQ7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3bq7]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BQ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BQ7 FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DGKD, KIAA0145 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DGKD, KIAA0145 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diacylglycerol_kinase Diacylglycerol kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.107 2.7.1.107] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Diacylglycerol_kinase Diacylglycerol kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.107 2.7.1.107] </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=3bq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bq7 OCA], [http://pdbe.org/3bq7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bq7 RCSB], [http://www.ebi.ac.uk/pdbsum/3bq7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3bq7 ProSAT]</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=3bq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bq7 OCA], [https://pdbe.org/3bq7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bq7 RCSB], [https://www.ebi.ac.uk/pdbsum/3bq7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bq7 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DGKD_HUMAN DGKD_HUMAN]] May function as signaling molecule.<ref>PMID:17880279</ref>   Isoform 2 may be involved in cell growth and tumorigenesis. Involved in clathrin-dependent endocytosis.<ref>PMID:17880279</ref>
+[[https://www.uniprot.org/uniprot/DGKD_HUMAN DGKD_HUMAN]] May function as signaling molecule.<ref>PMID:17880279</ref>   Isoform 2 may be involved in cell growth and tumorigenesis. Involved in clathrin-dependent endocytosis.<ref>PMID:17880279</ref>
 == 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/bq/3bq7_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bq/3bq7_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 29: / Line 29: @@
 </div>
 <div class="pdbe-citations 3bq7" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Diacylglycerol kinase 3D structures|Diacylglycerol kinase 3D structures]]
 == References ==
 <references/>
@@ Line 35: / Line 38: @@
 [[Category: Diacylglycerol kinase]]
 [[Category: Human]]
+[[Category: Large Structures]]
 [[Category: Bowie, J U]]
 [[Category: Knight, M J]]

3bq7: Difference between revisions

Revision as of 19:00, 20 October 2021

SAM domain of Diacylglycerol Kinase delta1 (E35G)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

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