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| | <StructureSection load='5ee3' size='340' side='right'caption='[[5ee3]], [[Resolution|resolution]] 2.90Å' scene=''> | | <StructureSection load='5ee3' size='340' side='right'caption='[[5ee3]], [[Resolution|resolution]] 2.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5ee3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Japanese_rice Japanese rice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EE3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5EE3 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5ee3]] 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=5EE3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EE3 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.9Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5ee0|5ee0]], [[5ee1|5ee1]], [[5ee9|5ee9]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">OS08G0199300, OSYCHF1 ([http://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=5ee3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ee3 OCA], [https://pdbe.org/5ee3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ee3 RCSB], [https://www.ebi.ac.uk/pdbsum/5ee3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ee3 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5ee3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ee3 OCA], [http://pdbe.org/5ee3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ee3 RCSB], [http://www.ebi.ac.uk/pdbsum/5ee3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ee3 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/OLA1_ORYSJ OLA1_ORYSJ]] Hydrolyzes ATP, and can also hydrolyze GTP with lower efficiency. Has lower affinity for GTP (Potential). Exhibits GTPase activity (PubMed:19086295). Confers sensitivity to salinity stress by suppressing the anti-oxidation enzymatic activities and increasing lipid peroxidation thus leading to the accumulation of reactive oxygen species (ROS) (PubMed:23550829).[HAMAP-Rule:MF_03167]<ref>PMID:19086295</ref> <ref>PMID:23550829</ref> | + | [https://www.uniprot.org/uniprot/OLA1_ORYSJ OLA1_ORYSJ] Hydrolyzes ATP, and can also hydrolyze GTP with lower efficiency. Has lower affinity for GTP (Potential). Exhibits GTPase activity (PubMed:19086295). Confers sensitivity to salinity stress by suppressing the anti-oxidation enzymatic activities and increasing lipid peroxidation thus leading to the accumulation of reactive oxygen species (ROS) (PubMed:23550829).[HAMAP-Rule:MF_03167]<ref>PMID:19086295</ref> <ref>PMID:23550829</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Japanese rice]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Chen, Z]] | + | [[Category: Oryza sativa Japonica Group]] |
| - | [[Category: Li, X]] | + | [[Category: Chen Z]] |
| - | [[Category: Amp-pnp]] | + | [[Category: Li X]] |
| - | [[Category: Atp]]
| + | |
| - | [[Category: Gtp-binding protein]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Osychf1]]
| + | |
| - | [[Category: P-loop ntpase]]
| + | |
| - | [[Category: Ychf-type]]
| + | |
| Structural highlights
5ee3 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 2.9Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
OLA1_ORYSJ Hydrolyzes ATP, and can also hydrolyze GTP with lower efficiency. Has lower affinity for GTP (Potential). Exhibits GTPase activity (PubMed:19086295). Confers sensitivity to salinity stress by suppressing the anti-oxidation enzymatic activities and increasing lipid peroxidation thus leading to the accumulation of reactive oxygen species (ROS) (PubMed:23550829).[HAMAP-Rule:MF_03167][1] [2]
Publication Abstract from PubMed
G proteins are involved in almost all aspects of the cellular regulatory pathways through their ability to bind and hydrolyze GTP. The YchF subfamily, interestingly, possesses the unique ability to bind both ATP and GTP, and is possibly an ancestral form of G proteins based on phylogenetic studies and is present in all kingdoms of life. However, the biological significance of such a relaxed ligand specificity has long eluded researchers. Here, we have elucidated the different conformational changes caused by the binding of a YchF homolog in rice (OsYchF1) to ATP versus GTP by X-ray crystallography. Furthermore, by comparing the 3D relationships of the ligand position and the various amino acid residues at the binding sites in the crystal structures of the apo-bound and ligand-bound versions, a mechanism for the protein's ability to bind both ligands is revealed. Mutation of the noncanonical G4 motif of the OsYchF1 to the canonical sequence for GTP specificity precludes the binding/hydrolysis of ATP and prevents OsYchF1 from functioning as a negative regulator of plant-defense responses, while retaining its ability to bind/hydrolyze GTP and its function as a negative regulator of abiotic stress responses, demonstrating the specific role of ATP-binding/hydrolysis in disease resistance. This discovery will have a significant impact on our understanding of the structure-function relationships of the YchF subfamily of G proteins in all kingdoms of life.
ATP binding by the P-loop NTPase OsYchF1 (an unconventional G protein) contributes to biotic but not abiotic stress responses.,Cheung MY, Li X, Miao R, Fong YH, Li KP, Yung YL, Yu MH, Wong KB, Chen Z, Lam HM Proc Natl Acad Sci U S A. 2016 Mar 8;113(10):2648-53. doi:, 10.1073/pnas.1522966113. Epub 2016 Feb 24. PMID:26912459[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Cheung MY, Zeng NY, Tong SW, Li WY, Xue Y, Zhao KJ, Wang C, Zhang Q, Fu Y, Sun Z, Sun SS, Lam HM. Constitutive expression of a rice GTPase-activating protein induces defense responses. New Phytol. 2008 Jul;179(2):530-45. PMID:19086295
- ↑ Cheung MY, Li MW, Yung YL, Wen CQ, Lam HM. The unconventional P-loop NTPase OsYchF1 and its regulator OsGAP1 play opposite roles in salinity stress tolerance. Plant Cell Environ. 2013 Nov;36(11):2008-20. doi: 10.1111/pce.12108. Epub 2013, Apr 25. PMID:23550829 doi:http://dx.doi.org/10.1111/pce.12108
- ↑ Cheung MY, Li X, Miao R, Fong YH, Li KP, Yung YL, Yu MH, Wong KB, Chen Z, Lam HM. ATP binding by the P-loop NTPase OsYchF1 (an unconventional G protein) contributes to biotic but not abiotic stress responses. Proc Natl Acad Sci U S A. 2016 Mar 8;113(10):2648-53. doi:, 10.1073/pnas.1522966113. Epub 2016 Feb 24. PMID:26912459 doi:http://dx.doi.org/10.1073/pnas.1522966113
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