3h4m: Difference between revisions

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 <StructureSection load='3h4m' size='340' side='right'caption='[[3h4m]], [[Resolution|resolution]] 3.11&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3h4m]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3H4M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3H4M FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3h4m]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3H4M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3H4M FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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]] 3.106&#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;'>[[3h43|3h43]], [[3h4p|3h4p]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pan, MJ1176 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</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=3h4m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3h4m OCA], [https://pdbe.org/3h4m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3h4m RCSB], [https://www.ebi.ac.uk/pdbsum/3h4m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3h4m ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/PAN_METJA PAN_METJA]] ATPase which is responsible for recognizing, binding, unfolding and translocation of substrate proteins into the archaeal 20S proteasome core particle. Is essential for opening the gate of the 20S proteasome via an interaction with its C-terminus, thereby allowing substrate entry and access to the site of proteolysis. Thus, the C-termini of the proteasomal ATPase function like a 'key in a lock' to induce gate opening and therefore regulate proteolysis. Unfolding activity requires energy from ATP hydrolysis, whereas ATP binding alone promotes ATPase-20S proteasome association which triggers gate opening, and supports translocation of unfolded substrates. In addition to ATP, is able to cleave other nucleotide triphosphates such as CTP, GTP and UTP, but hydrolysis of these other nucleotides is less effective in promoting proteolysis than ATP. Moreover, PAN by itself can function as a chaperone in vitro.[HAMAP-Rule:MF_00553]<ref>PMID:10473546</ref> <ref>PMID:10692374</ref> <ref>PMID:16337593</ref> <ref>PMID:17803938</ref> <ref>PMID:19481528</ref>
+[https://www.uniprot.org/uniprot/PAN_METJA PAN_METJA] ATPase which is responsible for recognizing, binding, unfolding and translocation of substrate proteins into the archaeal 20S proteasome core particle. Is essential for opening the gate of the 20S proteasome via an interaction with its C-terminus, thereby allowing substrate entry and access to the site of proteolysis. Thus, the C-termini of the proteasomal ATPase function like a 'key in a lock' to induce gate opening and therefore regulate proteolysis. Unfolding activity requires energy from ATP hydrolysis, whereas ATP binding alone promotes ATPase-20S proteasome association which triggers gate opening, and supports translocation of unfolded substrates. In addition to ATP, is able to cleave other nucleotide triphosphates such as CTP, GTP and UTP, but hydrolysis of these other nucleotides is less effective in promoting proteolysis than ATP. Moreover, PAN by itself can function as a chaperone in vitro.[HAMAP-Rule:MF_00553]<ref>PMID:10473546</ref> <ref>PMID:10692374</ref> <ref>PMID:16337593</ref> <ref>PMID:17803938</ref> <ref>PMID:19481528</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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 </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=3h4m ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Eukaryotic proteasome consists of a core particle (CP), which degrades unfolded protein, and a regulatory particle (RP), which is responsible for recognition, ATP-dependent unfolding, and translocation of polyubiquitinated substrate protein. In the archaea Methanocaldococcus jannaschii, the RP is a homohexameric complex of proteasome-activating nucleotidase (PAN). Here, we report the crystal structures of essential elements of the archaeal proteasome: the CP, the ATPase domain of PAN, and a distal subcomplex that is likely the first to encounter substrate. The distal subcomplex contains a coiled-coil segment and an OB-fold domain, both of which appear to be conserved in the eukaryotic proteasome. The OB domains of PAN form a hexameric ring with a 13 A pore, which likely constitutes the outermost constriction of the substrate translocation channel. These studies reveal structural codes and architecture of the complete proteasome, identify potential substrate-binding sites, and uncover unexpected asymmetry in the RP of archaea and eukaryotes.
-Structural insights into the regulatory particle of the proteasome from Methanocaldococcus jannaschii.,Zhang F, Hu M, Tian G, Zhang P, Finley D, Jeffrey PD, Shi Y Mol Cell. 2009 May 14;34(4):473-84. PMID:19481527<ref>PMID:19481527</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3h4m" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 43067]]
 [[Category: Large Structures]]
-[[Category: Finley, D]]
+[[Category: Methanocaldococcus jannaschii]]
-[[Category: Hu, M]]
+[[Category: Finley D]]
-[[Category: Jeffrey, P]]
+[[Category: Hu M]]
-[[Category: Shi, Y]]
+[[Category: Jeffrey P]]
-[[Category: Tian, G]]
+[[Category: Shi Y]]
-[[Category: Zhang, F]]
+[[Category: Tian G]]
-[[Category: Zhang, P]]
+[[Category: Zhang F]]
-[[Category: Atp-binding]]
+[[Category: Zhang P]]
-[[Category: Atpase]]
-[[Category: Hydrolase]]
-[[Category: Nucleotide-binding]]
-[[Category: Pan]]
-[[Category: Proteasome]]