2d1i: Difference between revisions

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New page: left|200px<br /> <applet load="2d1i" size="450" color="white" frame="true" align="right" spinBox="true" caption="2d1i, resolution 2.00Å" /> '''Structure of human ...
 
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[[Image:2d1i.gif|left|200px]]<br />
<applet load="2d1i" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2d1i, resolution 2.00&Aring;" />
'''Structure of human Atg4b'''<br />


==Overview==
==Structure of human Atg4b==
Autophagy is an evolutionarily conserved pathway in which the cytoplasm, and organelles are engulfed within double-membrane vesicles, termed, autophagosomes, for the turnover and recycling of these cellular, constituents. The yeast Atg8 and its human orthologs, such as LC3 and, GABARAP, have a unique feature as they conjugate covalently to, phospholipids, differing from ubiquitin and other ubiquitin-like modifiers, that attach only to protein substrates. The lipidated Atg8 and LC3, localize to autophagosomal membranes and play indispensable roles for, maturation of autophagosomes. Upon completion of autophagosome formation, some populations of lipidated Atg8 and LC3 are delipidated for recycling., Atg4b, a specific protease for LC3 and GABARAP, catalyzes the processing, reaction of LC3 and GABARAP precursors to mature forms and de-conjugating, reaction of the modifiers from phospholipids. Atg4b is a unique enzyme, whose primary structure differs from that of any other proteases that, function as processing and/or de-conjugating enzymes of ubiquitin and, ubiquitin-like modifiers. However, the tertiary structures of the, substrates considerably resemble that of ubiquitin except for the, N-terminal additional domain. Here we determined the crystal structure of, human Atg4b by X-ray crystallography at 2.0 A resolution, and show that, Atg4b is a cysteine protease whose active catalytic triad site consists of, Cys74, His280 and Asp278. The structure is comprised of a left lobe and a, small right lobe, designated the "protease domain" and the "auxiliary, domain", respectively. Whereas the protease domain structure of Atg4b, matches that of papain superfamily cysteine proteinases, the auxiliary, domain contains a unique structure with yet-unknown function. We propose, that the R229 and W142 residues in Atg4b are specifically essential for, recognition of substrates and catalysis of both precursor processing and, de-conjugation of phospholipids.
<StructureSection load='2d1i' size='340' side='right'caption='[[2d1i]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[2d1i]] 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=2D1I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D1I FirstGlance]. <br>
2D1I is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2D1I OCA].  
</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=2d1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1i OCA], [https://pdbe.org/2d1i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d1i RCSB], [https://www.ebi.ac.uk/pdbsum/2d1i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d1i ProSAT]</span></td></tr>
==Reference==
</table>
The crystal structure of human Atg4b, a processing and de-conjugating enzyme for autophagosome-forming modifiers., Kumanomidou T, Mizushima T, Komatsu M, Suzuki A, Tanida I, Sou YS, Ueno T, Kominami E, Tanaka K, Yamane T, J Mol Biol. 2006 Jan 27;355(4):612-8. Epub 2005 Nov 28. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16325851 16325851]
== Function ==
[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>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d1/2d1i_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2d1i ConSurf].
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Komatsu, M.]]
[[Category: Komatsu M]]
[[Category: Kominami, E.]]
[[Category: Kominami E]]
[[Category: Kumanomidou, T.]]
[[Category: Kumanomidou T]]
[[Category: Mizushima, T.]]
[[Category: Mizushima T]]
[[Category: Sou, Y.S.]]
[[Category: Sou YS]]
[[Category: Suzuki, A.]]
[[Category: Suzuki A]]
[[Category: Tanaka, K.]]
[[Category: Tanaka K]]
[[Category: Tanida, I.]]
[[Category: Tanida I]]
[[Category: Ueno, T.]]
[[Category: Ueno T]]
[[Category: Yamane, T.]]
[[Category: Yamane T]]
[[Category: apg]]
[[Category: atg]]
[[Category: autophagy]]
[[Category: cysteine protease]]
 
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Latest revision as of 13:45, 13 March 2024

Structure of human Atg4b

2d1i, resolution 2.00Å

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