4frz: Difference between revisions

Revision as of 20:08, 19 October 2022

Arabidopsis KCBP motor domain dimerized via regulatory domain

Structural highlights

4frz is a 2 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	ADP, EDO, IMD, MG
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

KN14E_ARATH Minus-end microtubule-dependent motor protein involved in the regulation of cell division and trichome morphogenesis through microtubules bundling. Possesses basal and microtubule-stimulated ATPase activities. Acts as a hub that brings together microtubules and actin filaments to modulate the cytoskeleton during trichome formation and morphogenesis (PubMed:26287478). Could be involved in the negative regulation of root growth (PubMed:25262228).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11]

Publication Abstract from PubMed

Kinesin-like calmodulin binding protein (KCBP), a Kinesin-14 family motor protein, is involved in the structural organization of microtubules during mitosis and trichome morphogenesis in plants. The molecular mechanism of microtubule bundling by KCBP remains unknown. KCBP binding to microtubules is regulated by Ca2+-binding proteins that recognize its C-terminal regulatory domain. In this work, we have discovered a new function of the regulatory domain. We present a crystal structure of an Arabidopsis KCBP fragment showing that the C-terminal regulatory domain forms a dimerization interface for KCBP. This dimerization site is distinct from the dimerization interface within the N-terminal domain. Side chains of hydrophobic residues of the calmodulin binding helix of the regulatory domain form the C-terminal dimerization interface. Biochemical experiments show that another segment of the regulatory domain located beyond the dimerization interface, its negatively charged coil, is unexpectedly and absolutely required to stabilize the dimers. The strong microtubule bundling properties of KCBP are unaffected by deletion of the C-terminal regulatory domain. The slow minus-end directed motility of KCBP is also unchanged in vitro. Although the C-terminal domain is not essential for microtubule bundling, we suggest that KCBP may use its two independent dimerization interfaces to support different types of bundled microtubule structures in cells. Two distinct dimerization sites may provide a mechanism for microtubule rearrangement in response to Ca2+ signaling since Ca2+- binding proteins can disengage KCBP dimers dependent on its C-terminal dimerization interface.

Plant Kinesin-Like Calmodulin Binding Protein Employs Its Regulatory Domain for Dimerization.,Vinogradova MV, Malanina GG, Waitzman JS, Rice SE, Fletterick RJ PLoS One. 2013 Jun 21;8(6):e66669. Print 2013. PMID:23805258^[12]

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

References

↑ Kao YL, Deavours BE, Phelps KK, Walker RA, Reddy AS. Bundling of microtubules by motor and tail domains of a kinesin-like calmodulin-binding protein from Arabidopsis: regulation by Ca(2+)/Calmodulin. Biochem Biophys Res Commun. 2000 Jan 7;267(1):201-7. doi: 10.1006/bbrc.1999.1896. PMID:10623599 doi:https://dx.doi.org/10.1006/bbrc.1999.1896
↑ Reddy VS, Day IS, Thomas T, Reddy AS. KIC, a novel Ca2+ binding protein with one EF-hand motif, interacts with a microtubule motor protein and regulates trichome morphogenesis. Plant Cell. 2004 Jan;16(1):185-200. Epub 2003 Dec 19. PMID:14688294 doi:10.1105/tpc.016600
↑ Reddy AS. Analysis of calcium/calmodulin regulation of a plant kinesin using co-sedimentation and ATPase assays. Methods Mol Biol. 2007;392:23-36. doi: 10.1007/978-1-59745-490-2_2. PMID:17951708 doi:https://dx.doi.org/10.1007/978-1-59745-490-2_2
↑ Humphrey TV, Haasen KE, Aldea-Brydges MG, Sun H, Zayed Y, Indriolo E, Goring DR. PERK-KIPK-KCBP signalling negatively regulates root growth in Arabidopsis thaliana. J Exp Bot. 2015 Jan;66(1):71-83. doi: 10.1093/jxb/eru390. Epub 2014 Sep 26. PMID:25262228 doi:https://dx.doi.org/10.1093/jxb/eru390
↑ Tian J, Han L, Feng Z, Wang G, Liu W, Ma Y, Yu Y, Kong Z. Orchestration of microtubules and the actin cytoskeleton in trichome cell shape determination by a plant-unique kinesin. Elife. 2015 Aug 19;4. doi: 10.7554/eLife.09351. PMID:26287478 doi:https://dx.doi.org/10.7554/eLife.09351
↑ Reddy AS, Safadi F, Narasimhulu SB, Golovkin M, Hu X. A novel plant calmodulin-binding protein with a kinesin heavy chain motor domain. J Biol Chem. 1996 Mar 22;271(12):7052-60. PMID:8636137
↑ Song H, Golovkin M, Reddy AS, Endow SA. In vitro motility of AtKCBP, a calmodulin-binding kinesin protein of Arabidopsis. Proc Natl Acad Sci U S A. 1997 Jan 7;94(1):322-7. doi: 10.1073/pnas.94.1.322. PMID:8990207 doi:https://dx.doi.org/10.1073/pnas.94.1.322
↑ Oppenheimer DG, Pollock MA, Vacik J, Szymanski DB, Ericson B, Feldmann K, Marks MD. Essential role of a kinesin-like protein in Arabidopsis trichome morphogenesis. Proc Natl Acad Sci U S A. 1997 Jun 10;94(12):6261-6. PMID:9177205
↑ Narasimhulu SB, Kao YL, Reddy AS. Interaction of Arabidopsis kinesin-like calmodulin-binding protein with tubulin subunits: modulation by Ca(2+)-calmodulin. Plant J. 1997 Nov;12(5):1139-49. doi: 10.1046/j.1365-313x.1997.12051139.x. PMID:9418053 doi:https://dx.doi.org/10.1046/j.1365-313x.1997.12051139.x
↑ Narasimhulu SB, Reddy AS. Characterization of microtubule binding domains in the Arabidopsis kinesin-like calmodulin binding protein. Plant Cell. 1998 Jun;10(6):957-65. PMID:9634584
↑ Deavours BE, Reddy AS, Walker RA. Ca2+/calmodulin regulation of the Arabidopsis kinesin-like calmodulin-binding protein. Cell Motil Cytoskeleton. 1998;40(4):408-16. PMID:9712269 doi:<408::AID-CM8>3.0.CO;2-6 10.1002/(SICI)1097-0169(1998)40:4<408::AID-CM8>3.0.CO;2-6
↑ Vinogradova MV, Malanina GG, Waitzman JS, Rice SE, Fletterick RJ. Plant Kinesin-Like Calmodulin Binding Protein Employs Its Regulatory Domain for Dimerization. PLoS One. 2013 Jun 21;8(6):e66669. Print 2013. PMID:23805258 doi:10.1371/journal.pone.0066669

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OCA

[1] Kao YL, Deavours BE, Phelps KK, Walker RA, Reddy AS. Bundling of microtubules by motor and tail domains of a kinesin-like calmodulin-binding protein from Arabidopsis: regulation by Ca(2+)/Calmodulin. Biochem Biophys Res Commun. 2000 Jan 7;267(1):201-7. doi: 10.1006/bbrc.1999.1896. PMID:10623599 doi:https://dx.doi.org/10.1006/bbrc.1999.1896

[2] Reddy VS, Day IS, Thomas T, Reddy AS. KIC, a novel Ca2+ binding protein with one EF-hand motif, interacts with a microtubule motor protein and regulates trichome morphogenesis. Plant Cell. 2004 Jan;16(1):185-200. Epub 2003 Dec 19. PMID:14688294 doi:10.1105/tpc.016600

[3] Reddy AS. Analysis of calcium/calmodulin regulation of a plant kinesin using co-sedimentation and ATPase assays. Methods Mol Biol. 2007;392:23-36. doi: 10.1007/978-1-59745-490-2_2. PMID:17951708 doi:https://dx.doi.org/10.1007/978-1-59745-490-2_2

[4] Humphrey TV, Haasen KE, Aldea-Brydges MG, Sun H, Zayed Y, Indriolo E, Goring DR. PERK-KIPK-KCBP signalling negatively regulates root growth in Arabidopsis thaliana. J Exp Bot. 2015 Jan;66(1):71-83. doi: 10.1093/jxb/eru390. Epub 2014 Sep 26. PMID:25262228 doi:https://dx.doi.org/10.1093/jxb/eru390

[5] Tian J, Han L, Feng Z, Wang G, Liu W, Ma Y, Yu Y, Kong Z. Orchestration of microtubules and the actin cytoskeleton in trichome cell shape determination by a plant-unique kinesin. Elife. 2015 Aug 19;4. doi: 10.7554/eLife.09351. PMID:26287478 doi:https://dx.doi.org/10.7554/eLife.09351

[6] Reddy AS, Safadi F, Narasimhulu SB, Golovkin M, Hu X. A novel plant calmodulin-binding protein with a kinesin heavy chain motor domain. J Biol Chem. 1996 Mar 22;271(12):7052-60. PMID:8636137

[7] Song H, Golovkin M, Reddy AS, Endow SA. In vitro motility of AtKCBP, a calmodulin-binding kinesin protein of Arabidopsis. Proc Natl Acad Sci U S A. 1997 Jan 7;94(1):322-7. doi: 10.1073/pnas.94.1.322. PMID:8990207 doi:https://dx.doi.org/10.1073/pnas.94.1.322

[8] Oppenheimer DG, Pollock MA, Vacik J, Szymanski DB, Ericson B, Feldmann K, Marks MD. Essential role of a kinesin-like protein in Arabidopsis trichome morphogenesis. Proc Natl Acad Sci U S A. 1997 Jun 10;94(12):6261-6. PMID:9177205

[9] Narasimhulu SB, Kao YL, Reddy AS. Interaction of Arabidopsis kinesin-like calmodulin-binding protein with tubulin subunits: modulation by Ca(2+)-calmodulin. Plant J. 1997 Nov;12(5):1139-49. doi: 10.1046/j.1365-313x.1997.12051139.x. PMID:9418053 doi:https://dx.doi.org/10.1046/j.1365-313x.1997.12051139.x

[10] Narasimhulu SB, Reddy AS. Characterization of microtubule binding domains in the Arabidopsis kinesin-like calmodulin binding protein. Plant Cell. 1998 Jun;10(6):957-65. PMID:9634584

[11] Deavours BE, Reddy AS, Walker RA. Ca2+/calmodulin regulation of the Arabidopsis kinesin-like calmodulin-binding protein. Cell Motil Cytoskeleton. 1998;40(4):408-16. PMID:9712269 doi:<408::AID-CM8>3.0.CO;2-6 10.1002/(SICI)1097-0169(1998)40:4<408::AID-CM8>3.0.CO;2-6

[12] Vinogradova MV, Malanina GG, Waitzman JS, Rice SE, Fletterick RJ. Plant Kinesin-Like Calmodulin Binding Protein Employs Its Regulatory Domain for Dimerization. PLoS One. 2013 Jun 21;8(6):e66669. Print 2013. PMID:23805258 doi:10.1371/journal.pone.0066669

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@@ Line 1: / Line 1: @@
 ==Arabidopsis KCBP motor domain dimerized via regulatory domain==
-<StructureSection load='4frz' size='340' side='right' caption='[[4frz]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+<StructureSection load='4frz' size='340' side='right'caption='[[4frz]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4frz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FRZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FRZ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4frz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FRZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FRZ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3h4s|3h4s]]</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=4frz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4frz OCA], [https://pdbe.org/4frz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4frz RCSB], [https://www.ebi.ac.uk/pdbsum/4frz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4frz ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">KCBP, ZWI, At5g65930, K14B20.10 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=4frz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4frz OCA], [http://pdbe.org/4frz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4frz RCSB], [http://www.ebi.ac.uk/pdbsum/4frz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4frz ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/KCBP_ARATH KCBP_ARATH]] Minus-end microtubule-dependent motor protein involved in the regulation of cell division and trichome morphogenesis. Possesses basal and microtubule-stimulated ATPase activities.<ref>PMID:8636137</ref> <ref>PMID:9177205</ref> <ref>PMID:9712269</ref> <ref>PMID:9634584</ref> <ref>PMID:14688294</ref>
+[https://www.uniprot.org/uniprot/KN14E_ARATH KN14E_ARATH] Minus-end microtubule-dependent motor protein involved in the regulation of cell division and trichome morphogenesis through microtubules bundling. Possesses basal and microtubule-stimulated ATPase activities. Acts as a hub that brings together microtubules and actin filaments to modulate the cytoskeleton during trichome formation and morphogenesis (PubMed:26287478). Could be involved in the negative regulation of root growth (PubMed:25262228).<ref>PMID:10623599</ref> <ref>PMID:14688294</ref> <ref>PMID:17951708</ref> <ref>PMID:25262228</ref> <ref>PMID:26287478</ref> <ref>PMID:8636137</ref> <ref>PMID:8990207</ref> <ref>PMID:9177205</ref> <ref>PMID:9418053</ref> <ref>PMID:9634584</ref> <ref>PMID:9712269</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
-[[Category: Vinogradova, M]]
+[[Category: Large Structures]]
-[[Category: Calmodulin binding motif]]
+[[Category: Vinogradova M]]
-[[Category: Kinesin dimer]]
-[[Category: Kinesin motor domain]]
-[[Category: Motor protein]]

4frz: Difference between revisions

Revision as of 20:08, 19 October 2022

Arabidopsis KCBP motor domain dimerized via regulatory domain

Structural highlights

Function

Publication Abstract from PubMed

References

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