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.

5vhg

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of pentad mutant GAPR-1

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 3: / Line 3: @@
 <StructureSection load='5vhg' size='340' side='right'caption='[[5vhg]], [[Resolution|resolution]] 1.27&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5vhg]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VHG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5VHG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5vhg]] 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=5VHG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VHG FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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]] 1.27&#8491;</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=5vhg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vhg OCA], [http://pdbe.org/5vhg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vhg RCSB], [http://www.ebi.ac.uk/pdbsum/5vhg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vhg ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5vhg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vhg OCA], [https://pdbe.org/5vhg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vhg RCSB], [https://www.ebi.ac.uk/pdbsum/5vhg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vhg ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/GAPR1_HUMAN GAPR1_HUMAN]
-Mammalian Golgi-associated plant pathogenesis-related protein 1 (GAPR-1) is a negative autophagy regulator that binds Beclin 1, a key component of the autophagosome nucleation complex. Beclin 1 residues 267-284 are required for binding GAPR-1. Here, sequence analyses, structural modeling, mutagenesis combined with pull-down assays, X-ray crystal structure determination and small-angle X-ray scattering were used to investigate the Beclin 1-GAPR-1 interaction. Five conserved residues line an equatorial GAPR-1 surface groove that is large enough to bind a peptide. A model of a peptide comprising Beclin 1 residues 267-284 docked onto GAPR-1, built using the CABS-dock server, indicates that this peptide binds to this GAPR-1 groove. Mutation of the five conserved residues lining this groove, H54A/E86A/G102K/H103A/N138G, abrogates Beclin 1 binding. The 1.27 A resolution X-ray crystal structure of this pentad mutant GAPR-1 was determined. Comparison with the wild-type (WT) GAPR-1 structure shows that the equatorial groove of the pentad mutant is shallower and more positively charged, and therefore may not efficiently bind Beclin 1 residues 267-284, which include many hydrophobic residues. Both WT and pentad mutant GAPR-1 crystallize as dimers, and in each case the equatorial groove of one subunit is partially occluded by the other subunit, indicating that dimeric GAPR-1 is unlikely to bind Beclin 1. SAXS analysis of WT and pentad mutant GAPR-1 indicates that in solution the WT forms monomers, while the pentad mutant is primarily dimeric. Thus, changes in the structure of the equatorial groove combined with the improved dimerization of pentad mutant GAPR-1 are likely to abrogate binding to Beclin 1.
-Structural insights into the interaction of the conserved mammalian proteins GAPR-1 and Beclin 1, a key autophagy protein.,Li Y, Zhao Y, Su M, Glover K, Chakravarthy S, Colbert CL, Levine B, Sinha SC Acta Crystallogr D Struct Biol. 2017 Sep 1;73(Pt 9):775-792. doi:, 10.1107/S2059798317011822. Epub 2017 Aug 29. PMID:28876241<ref>PMID:28876241</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 5vhg" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Chakravarthy, S]]
+[[Category: Chakravarthy S]]
-[[Category: Colbert, C L]]
+[[Category: Colbert CL]]
-[[Category: Levine, B]]
+[[Category: Levine B]]
-[[Category: Li, Y]]
+[[Category: Li Y]]
-[[Category: Sinha, S C]]
+[[Category: Sinha SC]]
-[[Category: Su, M]]
+[[Category: Su M]]
-[[Category: Zhao, Y]]
+[[Category: Zhao Y]]
-[[Category: Autophagy]]
-[[Category: Beclin 1]]
-[[Category: Gapr-1]]
-[[Category: Plant protein]]

5vhg

From Proteopedia

Current revision

Crystal structure of pentad mutant GAPR-1

Structural highlights

Function

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox