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5ia8

From Proteopedia

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Structure of a Ubiquitin like protein with an E1 fragment

Structural highlights

5ia8 is a 2 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 2Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

UBA5_HUMAN E1-like enzyme which activates UFM1 and SUMO2.^[1] ^[2] ^[3] UFM1_HUMAN Ubiquitin-like modifier protein which binds to a number of target proteins, such as DDRGK1.^[4] ^[5]

Publication Abstract from PubMed

The modification of proteins by ubiquitin-fold modifier 1 (UFM1) is implicated in many human diseases. Prior to conjugation, UFM1 undergoes activation by its cognate activating enzyme, UBA5. UBA5 is a non-canonical E1 activating enzyme that possesses an adenylation domain but lacks a distinct cysteine domain. Binding of UBA5 to UFM1 is mediated via an amino acid sequence, known as the UFM1-interacting sequence (UIS), located outside the adenylation domain that is required for UFM1 activation. However, the precise boundaries of the UIS are yet not clear and are still under debate. Here we revisit the interaction of UFM1 with UBA5 by determining the crystal structure of UFM1 fused to 13 amino acids of human UBA5. Using binding and activity assays, we found that His 336 of UBA5, previously not reported to be part of the UIS, occupies a negatively charged pocket on UFM1's surface. This His is involved in UFM1 binding and if mutated perturbs activation of UFM1. Surprisingly, we also found that the interaction between two UFM1 molecules mimics how the UIS binds UFM1. Specifically, UFM1 His 70 resembles UBA5 His336 and enters a negatively charged pocked on the other UFM1 molecule. Our results refine our understanding of UFM1-UBA5 binding.

Novel insights into the interaction of UBA5 with UFM1 via a UFM1-interacting sequence.,Padala P, Oweis W, Mashahreh B, Soudah N, Cohen-Kfir E, Todd EA, Berndsen CE, Wiener R Sci Rep. 2017 Mar 30;7(1):508. doi: 10.1038/s41598-017-00610-0. PMID:28360427^[6]

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:http://dx.doi.org/10.1038/sj.emboj.7600205
↑ Zheng M, Gu X, Zheng D, Yang Z, Li F, Zhao J, Xie Y, Ji C, Mao Y. UBE1DC1, an ubiquitin-activating enzyme, activates two different ubiquitin-like proteins. J Cell Biochem. 2008 Aug 15;104(6):2324-34. doi: 10.1002/jcb.21791. PMID:18442052 doi:http://dx.doi.org/10.1002/jcb.21791
↑ Bacik JP, Walker JR, Ali M, Schimmer AD, Dhe-Paganon S. Crystal structure of the human ubiquitin-activating enzyme 5 (UBA5) bound to ATP: mechanistic insights into a minimalistic E1 enzyme. J Biol Chem. 2010 Jun 25;285(26):20273-80. Epub 2010 Apr 5. PMID:20368332 doi:10.1074/jbc.M110.102921
↑ 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:http://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:http://dx.doi.org/10.1074/jbc.M109.036814
↑ Padala P, Oweis W, Mashahreh B, Soudah N, Cohen-Kfir E, Todd EA, Berndsen CE, Wiener R. Novel insights into the interaction of UBA5 with UFM1 via a UFM1-interacting sequence. Sci Rep. 2017 Mar 30;7(1):508. doi: 10.1038/s41598-017-00610-0. PMID:28360427 doi:http://dx.doi.org/10.1038/s41598-017-00610-0

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5ia8"

Categories: Homo sapiens | Large Structures | Oweis W | Padala P | Wiener R

@@ Line 3: / Line 3: @@
 <StructureSection load='5ia8' size='340' side='right'caption='[[5ia8]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ia8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IA8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5IA8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ia8]] is a 2 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=5IA8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IA8 FirstGlance]. <br>
-</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5ia8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ia8 OCA], [http://pdbe.org/5ia8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ia8 RCSB], [http://www.ebi.ac.uk/pdbsum/5ia8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ia8 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&#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=5ia8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ia8 OCA], [https://pdbe.org/5ia8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ia8 RCSB], [https://www.ebi.ac.uk/pdbsum/5ia8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ia8 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/UBA5_HUMAN UBA5_HUMAN] E1-like enzyme which activates UFM1 and SUMO2.<ref>PMID:15071506</ref> <ref>PMID:18442052</ref> <ref>PMID:20368332</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 20: @@
 ==See Also==
-*[[Ubiquitin activating enzyme|Ubiquitin activating enzyme]]
+*[[3D structures of Ubiquitin activating enzyme|3D structures of Ubiquitin activating enzyme]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Oweis, W]]
+[[Category: Oweis W]]
-[[Category: Padala, P]]
+[[Category: Padala P]]
-[[Category: Wiener, R]]
+[[Category: Wiener R]]
-[[Category: Cell cycle]]
-[[Category: Ubiquitin like protein]]

5ia8

From Proteopedia

Current revision

Structure of a Ubiquitin like protein with an E1 fragment

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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