3w04

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of Oryza sativa DWARF14 (D14)

Structural highlights

3w04 is a 2 chain structure with sequence from Oryza sativa Japonica Group. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.45Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

D14_ORYSJ Involved in strigolactone signaling pathway. May function downstream of strigolactone synthesis, as a component of hormone signaling or as an enzyme that participates in the conversion of strigolactones to the bioactive form. Strigolactones are hormones that inhibit tillering and shoot branching through the MAX-dependent pathway, contribute to the regulation of shoot architectural response to phosphate-limiting conditions and function as rhizosphere signal that stimulates hyphal branching of arbuscular mycorrhizal fungi and trigger seed germination of root parasitic weeds.^[1] ^[2]

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^[3]

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

References

↑ Arite T, Umehara M, Ishikawa S, Hanada A, Maekawa M, Yamaguchi S, Kyozuka J. d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers. Plant Cell Physiol. 2009 Aug;50(8):1416-24. doi: 10.1093/pcp/pcp091. Epub 2009, Jun 19. PMID:19542179 doi:http://dx.doi.org/10.1093/pcp/pcp091
↑ 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/3w04"

@@ Line 3: / Line 3: @@
 <StructureSection load='3w04' size='340' side='right'caption='[[3w04]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3w04]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Japanese_rice Japanese rice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W04 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W04 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3w04]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa_Japonica_Group Oryza sativa Japonica Group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W04 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W04 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.45&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3wo6|3wo6]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">D88, LOC_Os03g10620, Os03g0203200 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39947 Japanese rice])</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=3w04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w04 OCA], [https://pdbe.org/3w04 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w04 RCSB], [https://www.ebi.ac.uk/pdbsum/3w04 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w04 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/D14_ORYSJ D14_ORYSJ] Involved in strigolactone signaling pathway. May function downstream of strigolactone synthesis, as a component of hormone signaling or as an enzyme that participates in the conversion of strigolactones to the bioactive form. Strigolactones are hormones that inhibit tillering and shoot branching through the MAX-dependent pathway, contribute to the regulation of shoot architectural response to phosphate-limiting conditions and function as rhizosphere signal that stimulates hyphal branching of arbuscular mycorrhizal fungi and trigger seed germination of root parasitic weeds.<ref>PMID:19542179</ref> <ref>PMID:23301669</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Japanese rice]]
 [[Category: Large Structures]]
-[[Category: Hakoshima, T]]
+[[Category: Oryza sativa Japonica Group]]
-[[Category: Hirano, Y]]
+[[Category: Hakoshima T]]
-[[Category: Kagiyama, M]]
+[[Category: Hirano Y]]
-[[Category: Kim, S Y]]
+[[Category: Kagiyama M]]
-[[Category: Kyozuka, J]]
+[[Category: Kim SY]]
-[[Category: Mori, T]]
+[[Category: Kyozuka J]]
-[[Category: Seto, Y]]
+[[Category: Mori T]]
-[[Category: Yamaguchi, S]]
+[[Category: Seto Y]]
-[[Category: Alpha/beta hydrolase]]
+[[Category: Yamaguchi S]]
-[[Category: Hydrolase]]
-[[Category: Strigolactone hydrolysis]]
-[[Category: Strigolactone signaling]]

3w04

From Proteopedia

Current revision

Crystal structure of Oryza sativa DWARF14 (D14)

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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