6z90: Difference between revisions

Latest revision as of 13:44, 24 January 2024

Crystal structure of MINDY1 mutant-P138A

Structural highlights

6z90 is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.59Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MINY1_HUMAN Hydrolase that can specifically remove 'Lys-48'-linked conjugated ubiquitin from proteins. Has exodeubiquitinase activity and has a preference for long polyubiquitin chains. May play a regulatory role at the level of protein turnover.^[1] ^[2]

Publication Abstract from PubMed

Of the eight distinct polyubiquitin (polyUb) linkages that can be assembled, the roles of K48-linked polyUb (K48-polyUb) are the most established, with K48-polyUb modified proteins being targeted for degradation. MINDY1 and MINDY2 are members of the MINDY family of deubiquitinases (DUBs) that have exquisite specificity for cleaving K48-polyUb, yet we have a poor understanding of their catalytic mechanism. Here, we analyze the crystal structures of MINDY1 and MINDY2 alone and in complex with monoUb, di-, and penta-K48-polyUb, identifying 5 distinct Ub binding sites in the catalytic domain that explain how these DUBs sense both Ub chain length and linkage type to cleave K48-polyUb chains. The activity of MINDY1/2 is inhibited by the Cys-loop, and we find that substrate interaction relieves autoinhibition to activate these DUBs. We also find that MINDY1/2 use a non-canonical catalytic triad composed of Cys-His-Thr. Our findings highlight multiple layers of regulation modulating DUB activity in MINDY1 and MINDY2.

Mechanism of activation and regulation of deubiquitinase activity in MINDY1 and MINDY2.,Abdul Rehman SA, Armstrong LA, Lange SM, Kristariyanto YA, Grawert TW, Knebel A, Svergun DI, Kulathu Y Mol Cell. 2021 Sep 10. pii: S1097-2765(21)00691-2. doi:, 10.1016/j.molcel.2021.08.024. PMID:34529927^[3]

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

References

↑ Abdul Rehman SA, Kristariyanto YA, Choi SY, Nkosi PJ, Weidlich S, Labib K, Hofmann K, Kulathu Y. MINDY-1 Is a Member of an Evolutionarily Conserved and Structurally Distinct New Family of Deubiquitinating Enzymes. Mol Cell. 2016 Jul 7;63(1):146-55. doi: 10.1016/j.molcel.2016.05.009. Epub 2016, Jun 9. PMID:27292798 doi:https://dx.doi.org/10.1016/j.molcel.2016.05.009
↑ Kristariyanto YA, Abdul Rehman SA, Weidlich S, Knebel A, Kulathu Y. A single MIU motif of MINDY-1 recognizes K48-linked polyubiquitin chains. EMBO Rep. 2017 Jan 12. pii: e201643205. doi: 10.15252/embr.201643205. PMID:28082312 doi:https://dx.doi.org/10.15252/embr.201643205
↑ Abdul Rehman SA, Armstrong LA, Lange SM, Kristariyanto YA, Grawert TW, Knebel A, Svergun DI, Kulathu Y. Mechanism of activation and regulation of deubiquitinase activity in MINDY1 and MINDY2. Mol Cell. 2021 Sep 10. pii: S1097-2765(21)00691-2. doi:, 10.1016/j.molcel.2021.08.024. PMID:34529927 doi:https://dx.doi.org/10.1016/j.molcel.2021.08.024

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OCA

[1] Abdul Rehman SA, Kristariyanto YA, Choi SY, Nkosi PJ, Weidlich S, Labib K, Hofmann K, Kulathu Y. MINDY-1 Is a Member of an Evolutionarily Conserved and Structurally Distinct New Family of Deubiquitinating Enzymes. Mol Cell. 2016 Jul 7;63(1):146-55. doi: 10.1016/j.molcel.2016.05.009. Epub 2016, Jun 9. PMID:27292798 doi:https://dx.doi.org/10.1016/j.molcel.2016.05.009

[2] Kristariyanto YA, Abdul Rehman SA, Weidlich S, Knebel A, Kulathu Y. A single MIU motif of MINDY-1 recognizes K48-linked polyubiquitin chains. EMBO Rep. 2017 Jan 12. pii: e201643205. doi: 10.15252/embr.201643205. PMID:28082312 doi:https://dx.doi.org/10.15252/embr.201643205

[3] Abdul Rehman SA, Armstrong LA, Lange SM, Kristariyanto YA, Grawert TW, Knebel A, Svergun DI, Kulathu Y. Mechanism of activation and regulation of deubiquitinase activity in MINDY1 and MINDY2. Mol Cell. 2021 Sep 10. pii: S1097-2765(21)00691-2. doi:, 10.1016/j.molcel.2021.08.024. PMID:34529927 doi:https://dx.doi.org/10.1016/j.molcel.2021.08.024

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='6z90' size='340' side='right'caption='[[6z90]], [[Resolution|resolution]] 3.59&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6z90]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Z90 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Z90 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6z90]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Z90 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Z90 FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MINDY1, FAM63A, KIAA1390 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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]] 3.59&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ubiquitinyl_hydrolase_1 Ubiquitinyl hydrolase 1], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.19.12 3.4.19.12] </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=6z90 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z90 OCA], [https://pdbe.org/6z90 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6z90 RCSB], [https://www.ebi.ac.uk/pdbsum/6z90 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6z90 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/MINY1_HUMAN MINY1_HUMAN]] Hydrolase that can specifically remove 'Lys-48'-linked conjugated ubiquitin from proteins. Has exodeubiquitinase activity and has a preference for long polyubiquitin chains. May play a regulatory role at the level of protein turnover.<ref>PMID:27292798</ref> <ref>PMID:28082312</ref>
+[https://www.uniprot.org/uniprot/MINY1_HUMAN MINY1_HUMAN] Hydrolase that can specifically remove 'Lys-48'-linked conjugated ubiquitin from proteins. Has exodeubiquitinase activity and has a preference for long polyubiquitin chains. May play a regulatory role at the level of protein turnover.<ref>PMID:27292798</ref> <ref>PMID:28082312</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Ubiquitinyl hydrolase 1]]
+[[Category: Abdul Rehman SA]]
-[[Category: Kulathu, Y]]
+[[Category: Kulathu Y]]
-[[Category: Rehman, S A.Abdul]]
-[[Category: Cysteine protease]]
-[[Category: Hydrolase]]
-[[Category: Isopeptidase and ubiquitin binding]]

6z90: Difference between revisions

Latest revision as of 13:44, 24 January 2024

Crystal structure of MINDY1 mutant-P138A

Structural highlights

Function

Publication Abstract from PubMed

References

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