3bdm

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (01:37, 21 November 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3bdm.png|left|200px]]
 
-
<!--
+
==yeast 20S proteasome:glidobactin A-complex==
-
The line below this paragraph, containing "STRUCTURE_3bdm", creates the "Structure Box" on the page.
+
<StructureSection load='3bdm' size='340' side='right'caption='[[3bdm]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[3bdm]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BDM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BDM FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDT:(2E,4E)-N-[(2S,3R)-3-HYDROXY-1-[[(3Z,5S,8S,10S)-10-HYDROXY-5-METHYL-2,7-DIOXO-1,6-DIAZACYCLODODEC-3-EN-8-YL]AMINO]-1-OXOBUTAN-2-YL]DODECA-2,4-DIENAMIDE'>GDT</scene></td></tr>
-
{{STRUCTURE_3bdm| PDB=3bdm | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bdm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bdm OCA], [https://pdbe.org/3bdm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bdm RCSB], [https://www.ebi.ac.uk/pdbsum/3bdm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bdm ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/PSB2_YEAST PSB2_YEAST] The proteasome degrades poly-ubiquitinated proteins in the cytoplasm and in the nucleus. It is essential for the regulated turnover of proteins and for the removal of misfolded proteins. The proteasome is a multicatalytic proteinase complex that is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. It has an ATP-dependent proteolytic activity.
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bd/3bdm_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3bdm ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Pathogenic bacteria often use effector molecules to increase virulence. In most cases, the mode of action of effectors remains unknown. Strains of Pseudomonas syringae pv. syringae (Pss) secrete syringolin A (SylA), a product of a mixed non-ribosomal peptide/polyketide synthetase, in planta. Here we identify SylA as a virulence factor because a SylA-negative mutant in Pss strain B728a obtained by gene disruption was markedly less virulent on its host, Phaseolus vulgaris (bean). We show that SylA irreversibly inhibits all three catalytic activities of eukaryotic proteasomes, thus adding proteasome inhibition to the repertoire of modes of action of virulence factors. The crystal structure of the yeast proteasome in complex with SylA revealed a novel mechanism of covalent binding to the catalytic subunits. Thus, SylA defines a new class of proteasome inhibitors that includes glidobactin A (GlbA), a structurally related compound from an unknown species of the order Burkholderiales, for which we demonstrate a similar proteasome inhibition mechanism. As proteasome inhibitors are a promising class of anti-tumour agents, the discovery of a novel family of inhibitory natural products, which we refer to as syrbactins, may also have implications for the development of anti-cancer drugs. Homologues of SylA and GlbA synthetase genes are found in some other pathogenic bacteria, including the human pathogen Burkholderia pseudomallei, the causative agent of melioidosis. It is thus possible that these bacteria are capable of producing proteasome inhibitors of the syrbactin class.
-
===yeast 20S proteasome:glidobactin A-complex===
+
A plant pathogen virulence factor inhibits the eukaryotic proteasome by a novel mechanism.,Groll M, Schellenberg B, Bachmann AS, Archer CR, Huber R, Powell TK, Lindow S, Kaiser M, Dudler R Nature. 2008 Apr 10;452(7188):755-8. PMID:18401409<ref>PMID:18401409</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 3bdm" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_18401409}}, adds the Publication Abstract to the page
+
*[[Proteasome 3D structures|Proteasome 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 18401409 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_18401409}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
3BDM is a 28 chains structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BDM OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:18401409</ref><references group="xtra"/>
+
-
[[Category: Proteasome endopeptidase complex]]
+
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
-
[[Category: Dudler, R.]]
+
[[Category: Dudler R]]
-
[[Category: Groll, M.]]
+
[[Category: Groll M]]
-
[[Category: Kaiser, M.]]
+
[[Category: Kaiser M]]
-
[[Category: Cytoplasm]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Nucleus]]
+
-
[[Category: Pathogen]]
+
-
[[Category: Phosphoprotein]]
+
-
[[Category: Protease]]
+
-
[[Category: Proteasome]]
+
-
[[Category: Proteolysis]]
+
-
[[Category: Threonine protease]]
+
-
[[Category: Ubiquitin]]
+
-
[[Category: Ubl conjugation]]
+
-
[[Category: Virulence factor]]
+
-
[[Category: Zymogen]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 16:19:09 2009''
+

Current revision

yeast 20S proteasome:glidobactin A-complex

PDB ID 3bdm

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools