3w06

From Proteopedia

(Difference between revisions)

Revision as of 15:55, 5 August 2016

Crystal structure of Arabidopsis thaliana DWARF14 Like (AtD14L)

Structural highlights

3w06 is a 1 chain structure with sequence from Arath. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	3w04, 3w05
Gene:	AT4g37470, F6G17.120 (ARATH)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[KAI2_ARATH] Involved in seed germination and seedling development. Essential for plant responses to karrikins, a class of butenolide compounds, structurally similar to strigolactones, released from burning vegetation that stimulate seed germination and enhance seedling photomorphogenesis. KAI2 is not required for strigolactone-mediated responses, but MAX2 is necessary for responses to karrikins and strigolactones.^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

Strigolactones (SLs) are plant hormones that inhibit shoot branching. DWARF14 (D14) inhibits rice tillering and is an SL receptor candidate in the branching inhibition pathway, whereas the close homologue DWARF14-LIKE (D14L) participates in the signaling pathway of karrikins (KARs), which are derived from burnt vegetation as smoke stimulants of seed germination. We provide the first evidence for direct binding of the bioactive SL analogue GR24 to D14. Isothermal titration calorimetry measurements show a D14-GR24 binding affinity in the sub-micromolar range. Similarly, bioactive KAR1 directly binds D14L in the micromolar range. The crystal structure of rice D14 shows a compact alpha-/beta-fold hydrolase domain forming a deep ligand-binding pocket capable of accommodating GR24. Insertion of four alpha-helices between beta6 strand and alphaD helix forms the helical cap of the pocket, although the pocket is open to the solvent. The pocket contains the conserved catalytic triad Ser-His-Asp aligned with the oxyanion hole, suggesting hydrolase activity. Although these structural characteristics are conserved in D14L, the D14L pocket is smaller than that of D14. The KAR-insensitive mutation kai2-1 is located at the prominent long beta6-alphaD1 loop, which is characteristic in D14 and D14L, but not in related alpha-/beta-fold hydrolases.

Structures of D14 and D14L in the strigolactone and karrikin signaling pathways.,Kagiyama M, Hirano Y, Mori T, Kim SY, Kyozuka J, Seto Y, Yamaguchi S, Hakoshima T Genes Cells. 2013 Jan 10. doi: 10.1111/gtc.12025. PMID:23301669^[5]

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

References

↑ Sun XD, Ni M. HYPOSENSITIVE TO LIGHT, an alpha/beta fold protein, acts downstream of ELONGATED HYPOCOTYL 5 to regulate seedling de-etiolation. Mol Plant. 2011 Jan;4(1):116-26. doi: 10.1093/mp/ssq055. Epub 2010 Sep 23. PMID:20864454 doi:10.1093/mp/ssq055
↑ Waters MT, Nelson DC, Scaffidi A, Flematti GR, Sun YK, Dixon KW, Smith SM. Specialisation within the DWARF14 protein family confers distinct responses to karrikins and strigolactones in Arabidopsis. Development. 2012 Apr;139(7):1285-95. doi: 10.1242/dev.074567. Epub 2012 Feb 22. PMID:22357928 doi:10.1242/dev.074567
↑ Waters MT, Smith SM. KAI2- and MAX2-mediated responses to karrikins and strigolactones are largely independent of HY5 in Arabidopsis seedlings. Mol Plant. 2013 Jan;6(1):63-75. doi: 10.1093/mp/sss127. Epub 2012 Nov 9. PMID:23142794 doi:10.1093/mp/sss127
↑ Kagiyama M, Hirano Y, Mori T, Kim SY, Kyozuka J, Seto Y, Yamaguchi S, Hakoshima T. Structures of D14 and D14L in the strigolactone and karrikin signaling pathways. Genes Cells. 2013 Jan 10. doi: 10.1111/gtc.12025. PMID:23301669 doi:10.1111/gtc.12025
↑ Kagiyama M, Hirano Y, Mori T, Kim SY, Kyozuka J, Seto Y, Yamaguchi S, Hakoshima T. Structures of D14 and D14L in the strigolactone and karrikin signaling pathways. Genes Cells. 2013 Jan 10. doi: 10.1111/gtc.12025. PMID:23301669 doi:10.1111/gtc.12025

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3w06"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Arabidopsis thaliana DWARF14 Like (AtD14L)==
 <StructureSection load='3w06' size='340' side='right' caption='[[3w06]], [[Resolution|resolution]] 1.15&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3w06]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W06 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3W06 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3w06]] is a 1 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=3W06 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3W06 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3w04|3w04]], [[3w05|3w05]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AT4g37470, F6G17.120 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AT4g37470, F6G17.120 ([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=3w06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w06 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3w06 RCSB], [http://www.ebi.ac.uk/pdbsum/3w06 PDBsum]</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=3w06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w06 OCA], [http://pdbe.org/3w06 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3w06 RCSB], [http://www.ebi.ac.uk/pdbsum/3w06 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3w06 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/Q9SZU7_ARATH Q9SZU7_ARATH]] Involved in seed germination and seedling development. Essential for plant responses to karrikins, a class of butenolide compounds, structurally similar to strigolactones, released from burning vegetation that stimulate seed germination and enhance seedling photomorphogenesis. KAI2 is not required for strigolactone-mediated responses, but MAX2 is necessary for responses to karrikins and strigolactones.<ref>PMID:20864454</ref> <ref>PMID:22357928</ref> <ref>PMID:23142794</ref> <ref>PMID:23301669</ref>
+[[http://www.uniprot.org/uniprot/KAI2_ARATH KAI2_ARATH]] Involved in seed germination and seedling development. Essential for plant responses to karrikins, a class of butenolide compounds, structurally similar to strigolactones, released from burning vegetation that stimulate seed germination and enhance seedling photomorphogenesis. KAI2 is not required for strigolactone-mediated responses, but MAX2 is necessary for responses to karrikins and strigolactones.<ref>PMID:20864454</ref> <ref>PMID:22357928</ref> <ref>PMID:23142794</ref> <ref>PMID:23301669</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 19: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3w06" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Arabidopsis thaliana]]
+[[Category: Arath]]
 [[Category: Hakoshima, T]]
 [[Category: Hirano, Y]]

3w06

From Proteopedia

Revision as of 15:55, 5 August 2016

Crystal structure of Arabidopsis thaliana DWARF14 Like (AtD14L)

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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