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4b0s

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Revision as of 05:53, 25 August 2022

Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-like Modification Pathway in Complex with ATP

Structural highlights

4b0s is a 1 chain structure with sequence from Acic1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	4b0r, 4b0t
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DOP_ACIC1] Displays depupylase (DPUP) activity, removing conjugated Pup from target proteins; is thus involved in the recycling of Pup and may function similarly to deubiquitinases (DUBs) in eukaryotes to prevent or promote proteasomal degradation of certain proteins. Is also able to catalyze the deamidation of the C-terminal glutamine to glutamate in a variant of the prokaryotic ubiquitin-like protein Pup; however, since Pup from A.cellulolyticus possesses a C-terminal glutamate, this deamidase activity may be of no significance in vivo.^[1]

Publication Abstract from PubMed

Pupylation is a posttranslational protein modification occurring in mycobacteria and other actinobacteria that is functionally analogous to ubiquitination. Here we report the crystal structures of the modification enzymes involved in this pathway, the prokaryotic ubiquitin-like protein (Pup) ligase PafA and the depupylase/deamidase Dop. Both feature a larger amino-terminal domain consisting of a central beta-sheet packed against a cluster of helices, a fold characteristic for carboxylate-amine ligases, and a smaller C-terminal domain unique to PafA/Dop members. The active site is located on the concave surface of the beta-sheet with the nucleotide bound in a deep pocket. A conserved groove leading into the active site could have a role in Pup-binding. Nuclear magnetic resonance and biochemical experiments determine the region of Pup that interacts with PafA and Dop. Structural data and mutational studies identify crucial residues for the catalysis of both enzymes.

Structures of Pup ligase PafA and depupylase Dop from the prokaryotic ubiquitin-like modification pathway.,Ozcelik D, Barandun J, Schmitz N, Sutter M, Guth E, Damberger FF, Allain FH, Ban N, Weber-Ban E Nat Commun. 2012 Aug 21;3:1014. doi: 10.1038/ncomms2009. PMID:22910360^[2]

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

References

↑ Ozcelik D, Barandun J, Schmitz N, Sutter M, Guth E, Damberger FF, Allain FH, Ban N, Weber-Ban E. Structures of Pup ligase PafA and depupylase Dop from the prokaryotic ubiquitin-like modification pathway. Nat Commun. 2012 Aug 21;3:1014. doi: 10.1038/ncomms2009. PMID:22910360 doi:http://dx.doi.org/10.1038/ncomms2009
↑ Ozcelik D, Barandun J, Schmitz N, Sutter M, Guth E, Damberger FF, Allain FH, Ban N, Weber-Ban E. Structures of Pup ligase PafA and depupylase Dop from the prokaryotic ubiquitin-like modification pathway. Nat Commun. 2012 Aug 21;3:1014. doi: 10.1038/ncomms2009. PMID:22910360 doi:http://dx.doi.org/10.1038/ncomms2009

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4b0s"

@@ Line 3: / Line 3: @@
 <StructureSection load='4b0s' size='340' side='right'caption='[[4b0s]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4b0s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Acic1 Acic1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4B0S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4B0S FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4b0s]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acic1 Acic1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4B0S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4B0S FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4b0r|4b0r]], [[4b0t|4b0t]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4b0r|4b0r]], [[4b0t|4b0t]]</div></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=4b0s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4b0s OCA], [http://pdbe.org/4b0s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4b0s RCSB], [http://www.ebi.ac.uk/pdbsum/4b0s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4b0s ProSAT]</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=4b0s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4b0s OCA], [https://pdbe.org/4b0s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4b0s RCSB], [https://www.ebi.ac.uk/pdbsum/4b0s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4b0s ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DOP_ACIC1 DOP_ACIC1]] Displays depupylase (DPUP) activity, removing conjugated Pup from target proteins; is thus involved in the recycling of Pup and may function similarly to deubiquitinases (DUBs) in eukaryotes to prevent or promote proteasomal degradation of certain proteins. Is also able to catalyze the deamidation of the C-terminal glutamine to glutamate in a variant of the prokaryotic ubiquitin-like protein Pup; however, since Pup from A.cellulolyticus possesses a C-terminal glutamate, this deamidase activity may be of no significance in vivo.<ref>PMID:22910360</ref>
+[[https://www.uniprot.org/uniprot/DOP_ACIC1 DOP_ACIC1]] Displays depupylase (DPUP) activity, removing conjugated Pup from target proteins; is thus involved in the recycling of Pup and may function similarly to deubiquitinases (DUBs) in eukaryotes to prevent or promote proteasomal degradation of certain proteins. Is also able to catalyze the deamidation of the C-terminal glutamine to glutamate in a variant of the prokaryotic ubiquitin-like protein Pup; however, since Pup from A.cellulolyticus possesses a C-terminal glutamate, this deamidase activity may be of no significance in vivo.<ref>PMID:22910360</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==

4b0s

From Proteopedia

Revision as of 05:53, 25 August 2022

Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-like Modification Pathway in Complex with ATP

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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