5hkh: Difference between revisions

Latest revision as of 10:44, 16 August 2023

Crystal structure of Ufm1 in complex with UBA5

Structural highlights

5hkh is a 3 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 2.55Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

UFM1_HUMAN Ubiquitin-like modifier protein which binds to a number of target proteins, such as DDRGK1.^[1] ^[2]

Publication Abstract from PubMed

The covalent conjugation of ubiquitin-fold modifier 1 (UFM1) to proteins generates a signal that regulates transcription, response to cell stress, and differentiation. Ufmylation is initiated by ubiquitin-like modifier activating enzyme 5 (UBA5), which activates and transfers UFM1 to ubiquitin-fold modifier-conjugating enzyme 1 (UFC1). The details of the interaction between UFM1 and UBA5 required for UFM1 activation and its downstream transfer are however unclear. In this study, we described and characterized a combined linear LC3-interacting region/UFM1-interacting motif (LIR/UFIM) within the C terminus of UBA5. This single motif ensures that UBA5 binds both UFM1 and light chain 3/gamma-aminobutyric acid receptor-associated proteins (LC3/GABARAP), two ubiquitin (Ub)-like proteins. We demonstrated that LIR/UFIM is required for the full biological activity of UBA5 and for the effective transfer of UFM1 onto UFC1 and a downstream protein substrate both in vitro and in cells. Taken together, our study provides important structural and functional insights into the interaction between UBA5 and Ub-like modifiers, improving the understanding of the biology of the ufmylation pathway.

Structural and Functional Analysis of a Novel Interaction Motif within UFM1-activating Enzyme 5 (UBA5) Required for Binding to Ubiquitin-like Proteins and Ufmylation.,Habisov S, Huber J, Ichimura Y, Akutsu M, Rogova N, Loehr F, McEwan DG, Johansen T, Dikic I, Doetsch V, Komatsu M, Rogov VV, Kirkin V J Biol Chem. 2016 Apr 22;291(17):9025-41. doi: 10.1074/jbc.M116.715474. Epub 2016, Feb 29. PMID:26929408^[3]

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

References

↑ Komatsu M, Chiba T, Tatsumi K, Iemura S, Tanida I, Okazaki N, Ueno T, Kominami E, Natsume T, Tanaka K. A novel protein-conjugating system for Ufm1, a ubiquitin-fold modifier. EMBO J. 2004 May 5;23(9):1977-86. Epub 2004 Apr 8. PMID:15071506 doi:https://dx.doi.org/10.1038/sj.emboj.7600205
↑ Tatsumi K, Sou YS, Tada N, Nakamura E, Iemura S, Natsume T, Kang SH, Chung CH, Kasahara M, Kominami E, Yamamoto M, Tanaka K, Komatsu M. A novel type of E3 ligase for the Ufm1 conjugation system. J Biol Chem. 2010 Feb 19;285(8):5417-27. doi: 10.1074/jbc.M109.036814. Epub 2009 , Dec 14. PMID:20018847 doi:https://dx.doi.org/10.1074/jbc.M109.036814
↑ Habisov S, Huber J, Ichimura Y, Akutsu M, Rogova N, Loehr F, McEwan DG, Johansen T, Dikic I, Doetsch V, Komatsu M, Rogov VV, Kirkin V. Structural and Functional Analysis of a Novel Interaction Motif within UFM1-activating Enzyme 5 (UBA5) Required for Binding to Ubiquitin-like Proteins and Ufmylation. J Biol Chem. 2016 Apr 22;291(17):9025-41. doi: 10.1074/jbc.M116.715474. Epub 2016, Feb 29. PMID:26929408 doi:https://dx.doi.org/10.1074/jbc.M116.715474

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Komatsu M, Chiba T, Tatsumi K, Iemura S, Tanida I, Okazaki N, Ueno T, Kominami E, Natsume T, Tanaka K. A novel protein-conjugating system for Ufm1, a ubiquitin-fold modifier. EMBO J. 2004 May 5;23(9):1977-86. Epub 2004 Apr 8. PMID:15071506 doi:https://dx.doi.org/10.1038/sj.emboj.7600205

[2] Tatsumi K, Sou YS, Tada N, Nakamura E, Iemura S, Natsume T, Kang SH, Chung CH, Kasahara M, Kominami E, Yamamoto M, Tanaka K, Komatsu M. A novel type of E3 ligase for the Ufm1 conjugation system. J Biol Chem. 2010 Feb 19;285(8):5417-27. doi: 10.1074/jbc.M109.036814. Epub 2009 , Dec 14. PMID:20018847 doi:https://dx.doi.org/10.1074/jbc.M109.036814

[3] Habisov S, Huber J, Ichimura Y, Akutsu M, Rogova N, Loehr F, McEwan DG, Johansen T, Dikic I, Doetsch V, Komatsu M, Rogov VV, Kirkin V. Structural and Functional Analysis of a Novel Interaction Motif within UFM1-activating Enzyme 5 (UBA5) Required for Binding to Ubiquitin-like Proteins and Ufmylation. J Biol Chem. 2016 Apr 22;291(17):9025-41. doi: 10.1074/jbc.M116.715474. Epub 2016, Feb 29. PMID:26929408 doi:https://dx.doi.org/10.1074/jbc.M116.715474

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==Crystal structure of Ufm1 in complex with UBA5==
-<StructureSection load='5hkh' size='340' side='right' caption='[[5hkh]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
+<StructureSection load='5hkh' size='340' side='right'caption='[[5hkh]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5hkh]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HKH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HKH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5hkh]] is a 3 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=5HKH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HKH FirstGlance]. <br>
-</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=5hkh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hkh OCA], [http://pdbe.org/5hkh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hkh RCSB], [http://www.ebi.ac.uk/pdbsum/5hkh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hkh ProSAT]</span></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]] 2.55&#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=5hkh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hkh OCA], [https://pdbe.org/5hkh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hkh RCSB], [https://www.ebi.ac.uk/pdbsum/5hkh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hkh ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/UFM1_HUMAN UFM1_HUMAN]] Ubiquitin-like modifier protein which binds to a number of target proteins, such as DDRGK1.<ref>PMID:15071506</ref> <ref>PMID:20018847</ref>
+[https://www.uniprot.org/uniprot/UFM1_HUMAN UFM1_HUMAN] Ubiquitin-like modifier protein which binds to a number of target proteins, such as DDRGK1.<ref>PMID:15071506</ref> <ref>PMID:20018847</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 17: / Line 18: @@
 </div>
 <div class="pdbe-citations 5hkh" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Ubiquitin-fold modifier|Ubiquitin-fold modifier]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Akutsu, M]]
+[[Category: Homo sapiens]]
-[[Category: Doetsch, V]]
+[[Category: Large Structures]]
-[[Category: Huber, J]]
+[[Category: Akutsu M]]
-[[Category: Rogov, V V]]
+[[Category: Doetsch V]]
-[[Category: Signaling protein]]
+[[Category: Huber J]]
+[[Category: Rogov VV]]

5hkh: Difference between revisions

Latest revision as of 10:44, 16 August 2023

Crystal structure of Ufm1 in complex with UBA5

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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