This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

6lhn

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

RLGSGG-AtPRT6 UBR box

Structural highlights

6lhn 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.
Method:	X-ray diffraction, Resolution 2.5Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PRT6_ARATH Ubiquitin protein ligase which is a component of the N-end rule pathway with arginine specificity, and functions with the arginyltransferases ATE1 and ATE2. Recognizes and binds to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation (PubMed:17572409, PubMed:19255443, PubMed:19620738, PubMed:22020282). Does not participate in degradation of proteins with N-terminal Phe or Leu (PubMed:17572409). The N-end rule pathway regulates seed after-ripening, seedling sugar sensitivity, seedling lipid breakdown, and abscisic acid (ABA) sensitivity of germination (PubMed:19255443). The N-end rule pathway regulates various aspects of leaf and shoot development (PubMed:19620738). Involved in the ubiquitination and subsequent degradation of RAP2-12, an activator of hypoxic gene expression. The ubiquitination occurs after the N-arginylation of RAP2-12 by ATE1 or ATE2 under aerobic conditions (PubMed:22020282). The end-rule pathway plays a role in regulating the timing and amplitude of the immune response following infection with the bacterial pathogen Pseudomonas syringae pv tomato (PubMed:27173012, PubMed:30117535). Regulates the biosynthesis of plant-defense metabolites such as glucosinolates, and the biosynthesis and response to the phytohormone jasmonate (JA), which plays a key role in plant immunity (PubMed:27173012). Controls the expression of specific defense-response genes, activates the synthesis pathway for the phytoalexin camalexin, and influences basal resistance to the hemibiotroph pathogen Pseudomonas syringae pv tomato (PubMed:30117535). Coordinates the mobilization of seed storage reserves and regulates the abundance and activities of several proteases following seed germination (PubMed:29168982).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7]

Publication Abstract from PubMed

The N-degron pathway, formerly the N-end rule pathway, is a protein degradation process that determines the half-life of proteins based on their N-terminal residues. In contrast to the well-established in vivo studies over decades, in vitro studies of this pathway, including biochemical characterization and high-resolution structures, are relatively limited. In this study, we have developed a unique fusion technique using microtubule-associated protein 1A/1B light chain 3B, a key marker protein of autophagy, to tag the N-terminus of the proteins involved in the N-degron pathway, which enables high yield of homogeneous target proteins with variable N-terminal residues for diverse biochemical studies including enzymatic and binding assays and substrate identification. Intriguingly, crystallization showed a markedly enhanced probability, even for the N-degron complexes. To validate our results, we determined the structures of select proteins in the N-degron pathway and compared them to the PDB-deposited proteins. Furthermore, several biochemical applications of this technique were introduced. Therefore, this technique can be used as a general tool for the in vitro study of the N-degron pathway.

Use of the LC3B-fusion technique for biochemical and structural studies of proteins involved in the N-degron pathway.,Kim L, Kwon DH, Heo J, Park MR, Song HK J Biol Chem. 2020 Jan 9. pii: RA119.010912. doi: 10.1074/jbc.RA119.010912. PMID:31919097^[8]

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

References

↑ Garzon M, Eifler K, Faust A, Scheel H, Hofmann K, Koncz C, Yephremov A, Bachmair A. PRT6/At5g02310 encodes an Arabidopsis ubiquitin ligase of the N-end rule pathway with arginine specificity and is not the CER3 locus. FEBS Lett. 2007 Jul 10;581(17):3189-96. doi: 10.1016/j.febslet.2007.06.005. Epub , 2007 Jun 12. PMID:17572409 doi:http://dx.doi.org/10.1016/j.febslet.2007.06.005
↑ Holman TJ, Jones PD, Russell L, Medhurst A, Ubeda Tomas S, Talloji P, Marquez J, Schmuths H, Tung SA, Taylor I, Footitt S, Bachmair A, Theodoulou FL, Holdsworth MJ. The N-end rule pathway promotes seed germination and establishment through removal of ABA sensitivity in Arabidopsis. Proc Natl Acad Sci U S A. 2009 Mar 17;106(11):4549-54. doi:, 10.1073/pnas.0810280106. Epub 2009 Mar 2. PMID:19255443 doi:http://dx.doi.org/10.1073/pnas.0810280106
↑ Graciet E, Walter F, O'Maoileidigh DS, Pollmann S, Meyerowitz EM, Varshavsky A, Wellmer F. The N-end rule pathway controls multiple functions during Arabidopsis shoot and leaf development. Proc Natl Acad Sci U S A. 2009 Aug 11;106(32):13618-23. doi:, 10.1073/pnas.0906404106. Epub 2009 Jul 20. PMID:19620738 doi:http://dx.doi.org/10.1073/pnas.0906404106
↑ Licausi F, Kosmacz M, Weits DA, Giuntoli B, Giorgi FM, Voesenek LA, Perata P, van Dongen JT. Oxygen sensing in plants is mediated by an N-end rule pathway for protein destabilization. Nature. 2011 Oct 23;479(7373):419-22. doi: 10.1038/nature10536. PMID:22020282 doi:http://dx.doi.org/10.1038/nature10536
↑ de Marchi R, Sorel M, Mooney B, Fudal I, Goslin K, Kwasniewska K, Ryan PT, Pfalz M, Kroymann J, Pollmann S, Feechan A, Wellmer F, Rivas S, Graciet E. The N-end rule pathway regulates pathogen responses in plants. Sci Rep. 2016 May 13;6:26020. doi: 10.1038/srep26020. PMID:27173012 doi:http://dx.doi.org/10.1038/srep26020
↑ Zhang H, Gannon L, Hassall KL, Deery MJ, Gibbs DJ, Holdsworth MJ, van der Hoorn RAL, Lilley KS, Theodoulou FL. N-terminomics reveals control of Arabidopsis seed storage proteins and proteases by the Arg/N-end rule pathway. New Phytol. 2018 May;218(3):1106-1126. doi: 10.1111/nph.14909. Epub 2017 Nov 23. PMID:29168982 doi:http://dx.doi.org/10.1111/nph.14909
↑ Vicente J, Mendiondo GM, Pauwels J, Pastor V, Izquierdo Y, Naumann C, Movahedi M, Rooney D, Gibbs DJ, Smart K, Bachmair A, Gray JE, Dissmeyer N, Castresana C, Ray RV, Gevaert K, Holdsworth MJ. Distinct branches of the N-end rule pathway modulate the plant immune response. New Phytol. 2019 Jan;221(2):988-1000. doi: 10.1111/nph.15387. Epub 2018 Aug 17. PMID:30117535 doi:http://dx.doi.org/10.1111/nph.15387
↑ Kim L, Kwon DH, Heo J, Park MR, Song HK. Use of the LC3B-fusion technique for biochemical and structural studies of proteins involved in the N-degron pathway. J Biol Chem. 2020 Jan 9. pii: RA119.010912. doi: 10.1074/jbc.RA119.010912. PMID:31919097 doi:http://dx.doi.org/10.1074/jbc.RA119.010912

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6lhn"

Categories: Arabidopsis thaliana | Large Structures | Kim L | Kwon DH | Song HK

@@ Line 3: / Line 3: @@
 <StructureSection load='6lhn' size='340' side='right'caption='[[6lhn]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6lhn]] 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=6LHN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6LHN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6lhn]] 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=6LHN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LHN FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.5&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PRT6, CER3, GED1, At5g02310/At5g02300, T1E22.70/T1E22.60 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RING-type_E3_ubiquitin_transferase RING-type E3 ubiquitin transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.27 2.3.2.27] </span></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=6lhn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lhn OCA], [https://pdbe.org/6lhn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lhn RCSB], [https://www.ebi.ac.uk/pdbsum/6lhn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lhn ProSAT]</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=6lhn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lhn OCA], [http://pdbe.org/6lhn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lhn RCSB], [http://www.ebi.ac.uk/pdbsum/6lhn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lhn ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PRT6_ARATH PRT6_ARATH]] Ubiquitin protein ligase which is a component of the N-end rule pathway with arginine specificity, and functions with the arginyltransferases ATE1 and ATE2. Recognizes and binds to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation (PubMed:17572409, PubMed:19255443, PubMed:19620738, PubMed:22020282). Does not participate in degradation of proteins with N-terminal Phe or Leu (PubMed:17572409). The N-end rule pathway regulates seed after-ripening, seedling sugar sensitivity, seedling lipid breakdown, and abscisic acid (ABA) sensitivity of germination (PubMed:19255443). The N-end rule pathway regulates various aspects of leaf and shoot development (PubMed:19620738). Involved in the ubiquitination and subsequent degradation of RAP2-12, an activator of hypoxic gene expression. The ubiquitination occurs after the N-arginylation of RAP2-12 by ATE1 or ATE2 under aerobic conditions (PubMed:22020282). The end-rule pathway plays a role in regulating the timing and amplitude of the immune response following infection with the bacterial pathogen Pseudomonas syringae pv tomato (PubMed:27173012, PubMed:30117535). Regulates the biosynthesis of plant-defense metabolites such as glucosinolates, and the biosynthesis and response to the phytohormone jasmonate (JA), which plays a key role in plant immunity (PubMed:27173012). Controls the expression of specific defense-response genes, activates the synthesis pathway for the phytoalexin camalexin, and influences basal resistance to the hemibiotroph pathogen Pseudomonas syringae pv tomato (PubMed:30117535). Coordinates the mobilization of seed storage reserves and regulates the abundance and activities of several proteases following seed germination (PubMed:29168982).<ref>PMID:17572409</ref> <ref>PMID:19255443</ref> <ref>PMID:19620738</ref> <ref>PMID:22020282</ref> <ref>PMID:27173012</ref> <ref>PMID:29168982</ref> <ref>PMID:30117535</ref>
+[https://www.uniprot.org/uniprot/PRT6_ARATH PRT6_ARATH] Ubiquitin protein ligase which is a component of the N-end rule pathway with arginine specificity, and functions with the arginyltransferases ATE1 and ATE2. Recognizes and binds to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation (PubMed:17572409, PubMed:19255443, PubMed:19620738, PubMed:22020282). Does not participate in degradation of proteins with N-terminal Phe or Leu (PubMed:17572409). The N-end rule pathway regulates seed after-ripening, seedling sugar sensitivity, seedling lipid breakdown, and abscisic acid (ABA) sensitivity of germination (PubMed:19255443). The N-end rule pathway regulates various aspects of leaf and shoot development (PubMed:19620738). Involved in the ubiquitination and subsequent degradation of RAP2-12, an activator of hypoxic gene expression. The ubiquitination occurs after the N-arginylation of RAP2-12 by ATE1 or ATE2 under aerobic conditions (PubMed:22020282). The end-rule pathway plays a role in regulating the timing and amplitude of the immune response following infection with the bacterial pathogen Pseudomonas syringae pv tomato (PubMed:27173012, PubMed:30117535). Regulates the biosynthesis of plant-defense metabolites such as glucosinolates, and the biosynthesis and response to the phytohormone jasmonate (JA), which plays a key role in plant immunity (PubMed:27173012). Controls the expression of specific defense-response genes, activates the synthesis pathway for the phytoalexin camalexin, and influences basal resistance to the hemibiotroph pathogen Pseudomonas syringae pv tomato (PubMed:30117535). Coordinates the mobilization of seed storage reserves and regulates the abundance and activities of several proteases following seed germination (PubMed:29168982).<ref>PMID:17572409</ref> <ref>PMID:19255443</ref> <ref>PMID:19620738</ref> <ref>PMID:22020282</ref> <ref>PMID:27173012</ref> <ref>PMID:29168982</ref> <ref>PMID:30117535</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 19: @@
 </div>
 <div class="pdbe-citations 6lhn" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Ubiquitin protein ligase 3D structures|Ubiquitin protein ligase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Arath]]
-[[Category: Large Structures]]
-[[Category: RING-type E3 ubiquitin transferase]]
-[[Category: Kim, L]]
-[[Category: Kwon, D H]]
-[[Category: Song, H K]]
 [[Category: Arabidopsis thaliana]]
-[[Category: Ligase]]
+[[Category: Large Structures]]
-[[Category: Prt6]]
+[[Category: Kim L]]
+[[Category: Kwon DH]]
+[[Category: Song HK]]

6lhn

From Proteopedia

Current revision

RLGSGG-AtPRT6 UBR box

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox