This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2z0d

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 07:11, 10 November 2021

The crystal structure of human Atg4B- LC3(1-120) complex

Structural highlights

2z0d is a 2 chain structure with sequence from Buffalo rat and Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	2z0e
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[ATG4B_HUMAN] Cysteine protease required for autophagy, which cleaves the C-terminal part of MAP1LC3, GABARAPL1, GABARAPL2 and GABARAP, allowing the liberation of form I. A subpopulation of form I is subsequently converted to a smaller form (form II). Form II, with a revealed C-terminal glycine, is considered to be the phosphatidylethanolamine (PE)-conjugated form, and has the capacity for the binding to autophagosomes. Also mediates the lipid deconjugation required for target recycling.^[1] ^[2] [MLP3B_RAT] Probably involved in formation of autophagosomal vacuoles (autophagosomes).

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Atg8 is conjugated to phosphatidylethanolamine (PE) by ubiquitin-like conjugation reactions. Atg8 has at least two functions in autophagy: membrane biogenesis and target recognition. Regulation of PE conjugation and deconjugation of Atg8 is crucial for these functions in which Atg4 has a critical function by both processing Atg8 precursors and deconjugating Atg8-PE. Here, we report the crystal structures of catalytically inert human Atg4B (HsAtg4B) in complex with processed and unprocessed forms of LC3, a mammalian orthologue of yeast Atg8. On LC3 binding, the regulatory loop and the N-terminal tail of HsAtg4B undergo large conformational changes. The regulatory loop masking the entrance of the active site of free HsAtg4B is lifted by LC3 Phe119, so that a groove is formed along which the LC3 tail enters the active site. At the same time, the N-terminal tail masking the exit of the active site of HsAtg4B in the free form is detached from the enzyme core and a large flat surface is exposed, which might enable the enzyme to access the membrane-bound LC3-PE.

The structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing and delipidation during autophagy.,Satoo K, Noda NN, Kumeta H, Fujioka Y, Mizushima N, Ohsumi Y, Inagaki F EMBO J. 2009 May 6;28(9):1341-50. Epub 2009 Mar 26. PMID:19322194^[3]

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

References

↑ Kabeya Y, Mizushima N, Yamamoto A, Oshitani-Okamoto S, Ohsumi Y, Yoshimori T. LC3, GABARAP and GATE16 localize to autophagosomal membrane depending on form-II formation. J Cell Sci. 2004 Jun 1;117(Pt 13):2805-12. PMID:15169837 doi:10.1242/jcs.01131
↑ Satoo K, Noda NN, Kumeta H, Fujioka Y, Mizushima N, Ohsumi Y, Inagaki F. The structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing and delipidation during autophagy. EMBO J. 2009 May 6;28(9):1341-50. Epub 2009 Mar 26. PMID:19322194 doi:10.1038/emboj.2009.80
↑ Satoo K, Noda NN, Kumeta H, Fujioka Y, Mizushima N, Ohsumi Y, Inagaki F. The structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing and delipidation during autophagy. EMBO J. 2009 May 6;28(9):1341-50. Epub 2009 Mar 26. PMID:19322194 doi:10.1038/emboj.2009.80

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2z0d"

@@ Line 3: / Line 3: @@
 <StructureSection load='2z0d' size='340' side='right'caption='[[2z0d]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2z0d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z0D OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2Z0D FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2z0d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat] and [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z0D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z0D FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2z0e|2z0e]]</td></tr>
+</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2z0e|2z0e]]</div></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=2z0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z0d OCA], [http://pdbe.org/2z0d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z0d RCSB], [http://www.ebi.ac.uk/pdbsum/2z0d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z0d 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=2z0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z0d OCA], [https://pdbe.org/2z0d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z0d RCSB], [https://www.ebi.ac.uk/pdbsum/2z0d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z0d ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ATG4B_HUMAN ATG4B_HUMAN]] Cysteine protease required for autophagy, which cleaves the C-terminal part of MAP1LC3, GABARAPL1, GABARAPL2 and GABARAP, allowing the liberation of form I. A subpopulation of form I is subsequently converted to a smaller form (form II). Form II, with a revealed C-terminal glycine, is considered to be the phosphatidylethanolamine (PE)-conjugated form, and has the capacity for the binding to autophagosomes. Also mediates the lipid deconjugation required for target recycling.<ref>PMID:15169837</ref> <ref>PMID:19322194</ref>  [[http://www.uniprot.org/uniprot/MLP3B_RAT MLP3B_RAT]] Probably involved in formation of autophagosomal vacuoles (autophagosomes).
+[[https://www.uniprot.org/uniprot/ATG4B_HUMAN ATG4B_HUMAN]] Cysteine protease required for autophagy, which cleaves the C-terminal part of MAP1LC3, GABARAPL1, GABARAPL2 and GABARAP, allowing the liberation of form I. A subpopulation of form I is subsequently converted to a smaller form (form II). Form II, with a revealed C-terminal glycine, is considered to be the phosphatidylethanolamine (PE)-conjugated form, and has the capacity for the binding to autophagosomes. Also mediates the lipid deconjugation required for target recycling.<ref>PMID:15169837</ref> <ref>PMID:19322194</ref>  [[https://www.uniprot.org/uniprot/MLP3B_RAT MLP3B_RAT]] Probably involved in formation of autophagosomal vacuoles (autophagosomes).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]

2z0d

From Proteopedia

Revision as of 07:11, 10 November 2021

The crystal structure of human Atg4B- LC3(1-120) complex

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox