4put: Difference between revisions

Revision as of 07:32, 8 February 2023

Crystal structure of the Arabidopsis thaliana TOP2 oligopeptidase

Structural highlights

4put is a 1 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:	CL, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

COPDA_ARATH Oligopeptidase that may be involved in the degradation of proteasome-generated peptides (By similarity). Binds salicylic acid.^[1] ^[2]

Publication Abstract from PubMed

Thimet oligopeptidase (TOP) is a zinc-dependent metallopeptidase. Recent studies suggest that Arabidopsis thaliana TOP1 and TOP2 are targets for salicylic acid (SA) binding and participate in SA-mediated plant innate immunity. The crystal structure of A. thaliana TOP2 has been determined at 3.0 A resolution. Comparisons to the structure of human TOP revealed good overall structural conservation, especially in the active-site region, despite their weak sequence conservation. The protein sample was incubated with the photo-activated SA analog 4-azido-SA and exposed to UV irradiation before crystallization. However, there was no conclusive evidence for the binding of SA based on the X-ray diffraction data. Further studies are needed to elucidate the molecular mechanism of how SA regulates the activity of A. thaliana TOP1 and TOP2.

Structure of the Arabidopsis thaliana TOP2 oligopeptidase.,Wang R, Rajagopalan K, Sadre-Bazzaz K, Moreau M, Klessig DF, Tong L Acta Crystallogr F Struct Biol Commun. 2014 May;70(Pt 5):555-9. doi:, 10.1107/S2053230X14006128. Epub 2014 Apr 15. PMID:24817709^[3]

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

References

↑ Moreau M, Westlake T, Zampogna G, Popescu G, Tian M, Noutsos C, Popescu S. The Arabidopsis oligopeptidases TOP1 and TOP2 are salicylic acid targets that modulate SA-mediated signaling and the immune response. Plant J. 2013 Nov;76(4):603-14. doi: 10.1111/tpj.12320. Epub 2013 Oct 18. PMID:24004003 doi:https://dx.doi.org/10.1111/tpj.12320
↑ Kmiec B, Teixeira PF, Berntsson RP, Murcha MW, Branca RM, Radomiljac JD, Regberg J, Svensson LM, Bakali A, Langel U, Lehtio J, Whelan J, Stenmark P, Glaser E. Organellar oligopeptidase (OOP) provides a complementary pathway for targeting peptide degradation in mitochondria and chloroplasts. Proc Natl Acad Sci U S A. 2013 Oct 1;110(40):E3761-9. doi:, 10.1073/pnas.1307637110. Epub 2013 Sep 16. PMID:24043784 doi:https://dx.doi.org/10.1073/pnas.1307637110
↑ Wang R, Rajagopalan K, Sadre-Bazzaz K, Moreau M, Klessig DF, Tong L. Structure of the Arabidopsis thaliana TOP2 oligopeptidase. Acta Crystallogr F Struct Biol Commun. 2014 May;70(Pt 5):555-9. doi:, 10.1107/S2053230X14006128. Epub 2014 Apr 15. PMID:24817709 doi:https://dx.doi.org/10.1107/S2053230X14006128

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Moreau M, Westlake T, Zampogna G, Popescu G, Tian M, Noutsos C, Popescu S. The Arabidopsis oligopeptidases TOP1 and TOP2 are salicylic acid targets that modulate SA-mediated signaling and the immune response. Plant J. 2013 Nov;76(4):603-14. doi: 10.1111/tpj.12320. Epub 2013 Oct 18. PMID:24004003 doi:https://dx.doi.org/10.1111/tpj.12320

[2] Kmiec B, Teixeira PF, Berntsson RP, Murcha MW, Branca RM, Radomiljac JD, Regberg J, Svensson LM, Bakali A, Langel U, Lehtio J, Whelan J, Stenmark P, Glaser E. Organellar oligopeptidase (OOP) provides a complementary pathway for targeting peptide degradation in mitochondria and chloroplasts. Proc Natl Acad Sci U S A. 2013 Oct 1;110(40):E3761-9. doi:, 10.1073/pnas.1307637110. Epub 2013 Sep 16. PMID:24043784 doi:https://dx.doi.org/10.1073/pnas.1307637110

[3] Wang R, Rajagopalan K, Sadre-Bazzaz K, Moreau M, Klessig DF, Tong L. Structure of the Arabidopsis thaliana TOP2 oligopeptidase. Acta Crystallogr F Struct Biol Commun. 2014 May;70(Pt 5):555-9. doi:, 10.1107/S2053230X14006128. Epub 2014 Apr 15. PMID:24817709 doi:https://dx.doi.org/10.1107/S2053230X14006128

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='4put' size='340' side='right'caption='[[4put]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4put]] 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=4PUT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PUT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4put]] is a 1 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=4PUT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PUT FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CYOP, TOP2, At5g10540, F12B17.110 ([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'>[https://proteopedia.org/fgij/fg.htm?mol=4put FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4put OCA], [https://pdbe.org/4put PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4put RCSB], [https://www.ebi.ac.uk/pdbsum/4put PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4put ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oligopeptidase_A Oligopeptidase A], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.70 3.4.24.70] </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=4put FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4put OCA], [http://pdbe.org/4put PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4put RCSB], [http://www.ebi.ac.uk/pdbsum/4put PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4put ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/COPDA_ARATH COPDA_ARATH]] Oligopeptidase that may be involved in the degradation of proteasome-generated peptides (By similarity). Binds salicylic acid.<ref>PMID:24004003</ref> <ref>PMID:24043784</ref>
+[https://www.uniprot.org/uniprot/COPDA_ARATH COPDA_ARATH] Oligopeptidase that may be involved in the degradation of proteasome-generated peptides (By similarity). Binds salicylic acid.<ref>PMID:24004003</ref> <ref>PMID:24043784</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
 [[Category: Large Structures]]
-[[Category: Oligopeptidase A]]
+[[Category: Rajagopalan K]]
-[[Category: Rajagopalan, K]]
+[[Category: Tong L]]
-[[Category: Tong, L]]
+[[Category: Wang R]]
-[[Category: Wang, R]]
-[[Category: Hydrolase]]
-[[Category: Oligopeptidase]]

4put: Difference between revisions

Revision as of 07:32, 8 February 2023

Crystal structure of the Arabidopsis thaliana TOP2 oligopeptidase

Structural highlights

Function

Publication Abstract from PubMed

References

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