2kap

From Proteopedia

(Difference between revisions)

Current revision

Solution structure of DLC1-SAM

Structural highlights

2kap is a 1 chain structure with sequence from Homo sapiens. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RHG07_HUMAN Functions as a GTPase-activating protein for the small GTPases RHOA, RHOB, RHOC and CDC42, terminating their downstream signaling. This induces morphological changes and detachment through cytoskeletal reorganization, playing a critical role in biological processes such as cell migration and proliferation. Also functions in vivo as an activator of the phospholipase PLCD1. Active DLC1 increases cell migration velocity but reduces directionality.^[1] ^[2] ^[3]

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

Sterile alpha motif (SAM) domains are found in many different proteins and shown to play important roles in various biological processes. The N-terminal domain of deleted in liver cancer 1 (DLC1) protein is a SAM domain which exists in a monomeric form in aqueous solution and facilitates the distribution of EF1A1 to the membrane periphery and ruffles upon growth factor stimulation. Here, we report the structure of an N-terminal truncated DLC1 SAM domain (DLC1-SAM) and its urea-induced equilibrium unfolding investigated with various biophysical methods such as CD, fluorescence emission spectroscopy, and NMR. CD and tryptophan intrinsic fluorescence emission data imply that the unfolding of DLC1-SAM follows a simple two-state mechanism, yet the NMR data suggest the presence of at least one intermediate state. The intermediate cannot be detected by NMR, but it does not exist in large aggregates as shown by analytical ultracentrifugation experiments. Analysis of the free energy values for different residues shows that in the transition from the native state to non-native states the C-terminal helix is somewhat more stable than the other parts of the protein, whereas in the transition from the native and intermediate states to the denatured state, the stabilities of different residues are similar except for that of the region surrounding residues D37-F40 which has lower stability and is more readily denatured at high urea concentrations. Analysis of the midpoints of the transitions shows that the unfolding of the native state and formation of the denatured state are not cooperative and the unfolding of only a few residues seems to follow a two-state mechanism.

Characterization of DLC1-SAM equilibrium unfolding at the amino acid residue level.,Yang S, Noble CG, Yang D Biochemistry. 2009 May 19;48(19):4040-9. PMID:19317456^[4]

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

References

↑ Kim TY, Healy KD, Der CJ, Sciaky N, Bang YJ, Juliano RL. Effects of structure of Rho GTPase-activating protein DLC-1 on cell morphology and migration. J Biol Chem. 2008 Nov 21;283(47):32762-70. doi: 10.1074/jbc.M800617200. Epub 2008, Sep 11. PMID:18786931 doi:10.1074/jbc.M800617200
↑ Kawai K, Iwamae Y, Yamaga M, Kiyota M, Ishii H, Hirata H, Homma Y, Yagisawa H. Focal adhesion-localization of START-GAP1/DLC1 is essential for cell motility and morphology. Genes Cells. 2009 Feb;14(2):227-41. doi: 10.1111/j.1365-2443.2008.01265.x. Epub, 2008 Jan 15. PMID:19170769 doi:10.1111/j.1365-2443.2008.01265.x
↑ Erlmann P, Schmid S, Horenkamp FA, Geyer M, Pomorski TG, Olayioye MA. DLC1 activation requires lipid interaction through a polybasic region preceding the RhoGAP domain. Mol Biol Cell. 2009 Oct;20(20):4400-11. doi: 10.1091/mbc.E09-03-0247. Epub 2009, Aug 26. PMID:19710422 doi:10.1091/mbc.E09-03-0247
↑ Yang S, Noble CG, Yang D. Characterization of DLC1-SAM equilibrium unfolding at the amino acid residue level. Biochemistry. 2009 May 19;48(19):4040-9. PMID:19317456 doi:10.1021/bi9000936

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2kap"

Categories: Homo sapiens | Large Structures | Yang D | Yang S

@@ Line 1: / Line 1: @@
 ==Solution structure of DLC1-SAM==
-<StructureSection load='2kap' size='340' side='right' caption='[[2kap]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''>
+<StructureSection load='2kap' size='340' side='right'caption='[[2kap]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2kap]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KAP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KAP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2kap]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KAP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KAP FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DLC1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2kap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kap OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2kap RCSB], [http://www.ebi.ac.uk/pdbsum/2kap PDBsum]</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=2kap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kap OCA], [https://pdbe.org/2kap PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kap RCSB], [https://www.ebi.ac.uk/pdbsum/2kap PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kap ProSAT]</span></td></tr>
-<table>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RHG07_HUMAN RHG07_HUMAN] Functions as a GTPase-activating protein for the small GTPases RHOA, RHOB, RHOC and CDC42, terminating their downstream signaling. This induces morphological changes and detachment through cytoskeletal reorganization, playing a critical role in biological processes such as cell migration and proliferation. Also functions in vivo as an activator of the phospholipase PLCD1. Active DLC1 increases cell migration velocity but reduces directionality.<ref>PMID:18786931</ref> <ref>PMID:19170769</ref> <ref>PMID:19710422</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/ka/2kap_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ka/2kap_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2kap ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 24: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2kap" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Rho GTPase activating protein 3D structures|Rho GTPase activating protein 3D structures]]
 == References ==
 <references/>
@@ Line 29: / Line 36: @@
 </StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Yang, D.]]
+[[Category: Large Structures]]
-[[Category: Yang, S.]]
+[[Category: Yang D]]
-[[Category: Dlc-1]]
+[[Category: Yang S]]
-[[Category: Gtpase activation]]
-[[Category: Phosphoprotein]]
-[[Category: Sam domain]]
-[[Category: Signaling protein]]
-[[Category: Solution structure]]

2kap

From Proteopedia

Current revision

Solution structure of DLC1-SAM

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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