5nyj: Difference between revisions

Latest revision as of 12:16, 22 November 2023

Anbu from Hyphomicrobium sp. strain MC1 - SG: C2

Structural highlights

5nyj is a 16 chain structure with sequence from Hyphomicrobium sp. MC1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.2Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

F8JB59_HYPSM

Publication Abstract from PubMed

The 20S proteasome is a key player in eukaryotic and archaeal protein degradation, but its progenitor in eubacteria is unknown. Recently, the ancestral beta-subunit protein (Anbu) was predicted to be the evolutionary precursor of the proteasome. We crystallized Anbu from Hyphomicrobium sp. strain MC1 in four different space groups and solved the structures by SAD-phasing and Patterson search calculation techniques. Our data reveal that Anbu adopts the classical fold of Ntn-hydrolases, but its oligomeric state differs from that of barrel-shaped proteases. In contrast to their typical architecture, the Anbu protomer is a tightly interacting dimer that can assemble into a helical superstructure. Although Anbu features a catalytic triad of Thr1O(gamma), Asp17O(delta1) and Lys32N(epsilon), it is unable to hydrolyze standard protease substrates. The lack of activity might be caused by the incapacity of Thr1NH2 to function as a Bronsted acid during substrate cleavage due to its missing activation via hydrogen bonding. Altogether, we demonstrate that the topology of the proteasomal fold is conserved in Anbu, but whether it acts as a protease still needs to be clarified.

On the Trails of the Proteasome Fold: Structural and Functional Analysis of the Ancestral beta-Subunit Protein Anbu.,Vielberg MT, Bauer VC, Groll M J Mol Biol. 2018 Feb 2. pii: S0022-2836(18)30007-X. doi:, 10.1016/j.jmb.2018.01.004. PMID:29355501^[1]

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

References

↑ Vielberg MT, Bauer VC, Groll M. On the Trails of the Proteasome Fold: Structural and Functional Analysis of the Ancestral beta-Subunit Protein Anbu. J Mol Biol. 2018 Feb 2. pii: S0022-2836(18)30007-X. doi:, 10.1016/j.jmb.2018.01.004. PMID:29355501 doi:https://dx.doi.org/10.1016/j.jmb.2018.01.004

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OCA

[1] Vielberg MT, Bauer VC, Groll M. On the Trails of the Proteasome Fold: Structural and Functional Analysis of the Ancestral beta-Subunit Protein Anbu. J Mol Biol. 2018 Feb 2. pii: S0022-2836(18)30007-X. doi:, 10.1016/j.jmb.2018.01.004. PMID:29355501 doi:https://dx.doi.org/10.1016/j.jmb.2018.01.004

[1]

@@ Line 1: / Line 1: @@
 ==Anbu from Hyphomicrobium sp. strain MC1 - SG: C2==
-<StructureSection load='5nyj' size='340' side='right' caption='[[5nyj]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
+<StructureSection load='5nyj' size='340' side='right'caption='[[5nyj]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5nyj]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Hypsm Hypsm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NYJ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5nyj]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Hyphomicrobium_sp._MC1 Hyphomicrobium sp. MC1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NYJ FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5nyf|5nyf]]</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]] 3.2&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HYPMC_4374 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=717785 HYPSM])</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=5nyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nyj OCA], [https://pdbe.org/5nyj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nyj RCSB], [https://www.ebi.ac.uk/pdbsum/5nyj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nyj 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=5nyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nyj OCA], [http://pdbe.org/5nyj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nyj RCSB], [http://www.ebi.ac.uk/pdbsum/5nyj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nyj ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/F8JB59_HYPSM F8JB59_HYPSM]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Hypsm]]
+[[Category: Hyphomicrobium sp. MC1]]
-[[Category: Groll, M]]
+[[Category: Large Structures]]
-[[Category: Vielberg, M T]]
+[[Category: Groll M]]
-[[Category: Evolution]]
+[[Category: Vielberg M-T]]
-[[Category: Hydrolase]]
-[[Category: Ntn-hydrolase-fold]]
-[[Category: Proteasome]]

5nyj: Difference between revisions

Latest revision as of 12:16, 22 November 2023

Anbu from Hyphomicrobium sp. strain MC1 - SG: C2

Structural highlights

Function

Publication Abstract from PubMed

References

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