4b0r

From Proteopedia

(Difference between revisions)

Current revision

Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-like Modification Pathway

Structural highlights

4b0r is a 1 chain structure with sequence from Acidothermus cellulolyticus 11B. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.6Å
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/4b0r"

@@ Line 3: / Line 3: @@
 <StructureSection load='4b0r' size='340' side='right'caption='[[4b0r]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4b0r]] 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=4B0R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4B0R FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4b0r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acidothermus_cellulolyticus_11B Acidothermus cellulolyticus 11B]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4B0R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4B0R FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4b0s|4b0s]], [[4b0t|4b0t]]</div></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]] 2.6&#8491;</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=4b0r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4b0r OCA], [https://pdbe.org/4b0r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4b0r RCSB], [https://www.ebi.ac.uk/pdbsum/4b0r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4b0r ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[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>
+[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 ==
@@ Line 22: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Acic1]]
+[[Category: Acidothermus cellulolyticus 11B]]
 [[Category: Large Structures]]
-[[Category: Allain, F H.T]]
+[[Category: Allain FH-T]]
-[[Category: Ban, N]]
+[[Category: Ban N]]
-[[Category: Barandun, J]]
+[[Category: Barandun J]]
-[[Category: Damberger, F F]]
+[[Category: Damberger FF]]
-[[Category: Guth, E]]
+[[Category: Guth E]]
-[[Category: Ozcelik, D]]
+[[Category: Ozcelik D]]
-[[Category: Schmitz, N]]
+[[Category: Schmitz N]]
-[[Category: Sutter, M]]
+[[Category: Sutter M]]
-[[Category: Weber-Ban, E]]
+[[Category: Weber-Ban E]]
-[[Category: Depupylation]]
-[[Category: Hydrolase]]
-[[Category: Proteasome]]
-[[Category: Pupylation]]

4b0r

From Proteopedia

Current revision

Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-like Modification Pathway

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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