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5ovt

From Proteopedia

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<StructureSection load='5ovt' size='340' side='right'caption='[[5ovt]], [[Resolution|resolution]] 2.95&Aring;' scene=''>
<StructureSection load='5ovt' size='340' side='right'caption='[[5ovt]], [[Resolution|resolution]] 2.95&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5ovt]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/"thiobacillus_denitrificans"_beijerinck_1904 "thiobacillus denitrificans" beijerinck 1904]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OVT OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5OVT FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5ovt]] is a 14 chain structure with sequence from [https://en.wikipedia.org/wiki/Thiobacillus_denitrificans Thiobacillus denitrificans] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OVT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OVT FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.95&#8491;</td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6VO:(3~{R},4~{S})-4-AZANYL-2,6-DIMETHYL-HEPTANE-2,3-DIOL'>6VO</scene>, <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=IML:N-METHYL-ISOLEUCINE'>IML</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6VO:(3~{R},4~{S})-4-AZANYL-2,6-DIMETHYL-HEPTANE-2,3-DIOL'>6VO</scene>, <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=IML:N-METHYL-ISOLEUCINE'>IML</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5ovt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ovt OCA], [http://pdbe.org/5ovt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ovt RCSB], [http://www.ebi.ac.uk/pdbsum/5ovt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ovt ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5ovt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ovt OCA], [https://pdbe.org/5ovt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ovt RCSB], [https://www.ebi.ac.uk/pdbsum/5ovt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ovt ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/A0A2R2JFN0_THIDE A0A2R2JFN0_THIDE]
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Eukaryotic and archaeal proteasomes are paradigms for self-compartmentalizing proteases. To a large extent, their function requires the interplay with hexameric ATPases associated with diverse cellular activities (AAA+) that act as substrate unfoldases. Bacteria have various types of self-compartmentalizing proteases; in addition to the proteasome itself, these include the proteasome homolog HslV, which functions together with the AAA+ ATPase HslU; the ClpP protease with its partner AAA+ ATPase ClpX; and Anbu, a recently characterized ancestral proteasome variant. Previous bioinformatic analysis has revealed a novel bacterial member of the proteasome family, BPH (Beta-proteobacteria proteasome homolog). Using cluster analysis, we here affirmed that BPH evolutionarily descends from HslV. Crystal structures of the Thiobacillus denitrificans and Cupriavidus metallidurans BPHs disclosed a homo-oligomeric double-ring architecture, in which the active sites face the interior of the cylinder. Using small-angle X-ray scattering (SAXS) and electron microscopy averaging, we found that BPH forms tetradecamers in solution, unlike the dodecamers seen in HslV. While the highly acidic inner surface of BPH was in striking contrast to the cavity characteristics of the proteasome and HslV, a classical proteasomal reaction mechanism could be inferred from the covalent binding of the proteasome-specific inhibitor epoxomicin to BPH. A ligand-bound structure implied that the elongated BPH inner pore loop may be involved in substrate recognition. The apparent lack of a partner unfoldase and other unique features, such as Ser replacing Thr as catalytic residue in certain BPH subfamilies, suggest a proteolytic function for BPH distinct from those of known bacterial self-compartmentalizing proteases. .
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Structural characterization of the bacterial proteasome homolog BPH reveals a tetradecameric double-ring complex with unique inner cavity properties.,Fuchs ACD, Maldoner L, Hipp K, Hartmann MD, Martin J J Biol Chem. 2017 Nov 28. pii: M117.815258. doi: 10.1074/jbc.M117.815258. PMID:29183996<ref>PMID:29183996</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5ovt" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Thiobacillus denitrificans beijerinck 1904]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Albrecht, R]]
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[[Category: Synthetic construct]]
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[[Category: Fuchs, A C.D]]
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[[Category: Thiobacillus denitrificans]]
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[[Category: Hartmann, M D]]
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[[Category: Albrecht R]]
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[[Category: Martin, J]]
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[[Category: Fuchs ACD]]
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[[Category: Beta-proteobacteria proteasome homologue]]
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[[Category: Hartmann MD]]
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[[Category: Covalent proteasome inhibitor]]
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[[Category: Martin J]]
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[[Category: Hydrolase]]
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[[Category: Protein degradation]]
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Current revision

Thiobacillus denitrificans BPH in complex with Epoxomicin

PDB ID 5ovt

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