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2dur

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Revision as of 06:34, 6 June 2018

Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+/Man2-bound form

Structural highlights

2dur is a 2 chain structure with sequence from Canlf. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
Related:	1gv9, 1r1z, 2duo, 2dup, 2duq, 2dus
Gene:	LMAN2 (CANLF)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[LMAN2_CANFA] Plays a role as an intracellular lectin in the early secretory pathway. Interacts with N-acetyl-D-galactosamine and high-mannose type glycans and may also bind to O-linked glycans. Involved in the transport and sorting of glycoproteins carrying high mannose-type glycans.^[1] ^[2]

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

VIP36 functions as a transport lectin for trafficking certain high mannose type glycoproteins in the secretory pathway. Here we report the crystal structure of VIP36 exoplasmic/luminal domain comprising a carbohydrate recognition domain and a stalk domain. The structures of VIP36 in complex with Ca(2+) and mannosyl ligands are also described. The carbohydrate recognition domain is composed of a 17-stranded antiparallel beta-sandwich and binds one Ca(2+) adjoining the carbohydrate-binding site. The structure reveals that a coordinated Ca(2+) ion orients the side chains of Asp(131), Asn(166), and His(190) for carbohydrate binding. This result explains the Ca(2+)-dependent carbohydrate binding of this protein. The Man-alpha-1,2-Man-alpha-1,2-Man, which corresponds to the D1 arm of high mannose type glycan, is recognized by eight residues through extensive hydrogen bonds. The complex structures reveal the structural basis for high mannose type glycoprotein recognition by VIP36 in a Ca(2+)-dependent and D1 arm-specific manner.

Structural basis for recognition of high mannose type glycoproteins by mammalian transport lectin VIP36.,Satoh T, Cowieson NP, Hakamata W, Ideo H, Fukushima K, Kurihara M, Kato R, Yamashita K, Wakatsuki S J Biol Chem. 2007 Sep 21;282(38):28246-55. Epub 2007 Jul 25. PMID:17652092^[3]

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

References

↑ Hara-Kuge S, Ohkura T, Ideo H, Shimada O, Atsumi S, Yamashita K. Involvement of VIP36 in intracellular transport and secretion of glycoproteins in polarized Madin-Darby canine kidney (MDCK) cells. J Biol Chem. 2002 May 3;277(18):16332-9. Epub 2002 Feb 28. PMID:11872745 doi:http://dx.doi.org/10.1074/jbc.M112188200
↑ Satoh T, Cowieson NP, Hakamata W, Ideo H, Fukushima K, Kurihara M, Kato R, Yamashita K, Wakatsuki S. Structural basis for recognition of high mannose type glycoproteins by mammalian transport lectin VIP36. J Biol Chem. 2007 Sep 21;282(38):28246-55. Epub 2007 Jul 25. PMID:17652092 doi:10.1074/jbc.M703064200
↑ Satoh T, Cowieson NP, Hakamata W, Ideo H, Fukushima K, Kurihara M, Kato R, Yamashita K, Wakatsuki S. Structural basis for recognition of high mannose type glycoproteins by mammalian transport lectin VIP36. J Biol Chem. 2007 Sep 21;282(38):28246-55. Epub 2007 Jul 25. PMID:17652092 doi:10.1074/jbc.M703064200

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 1: / Line 1: @@
 ==Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+/Man2-bound form==
 <StructureSection load='2dur' size='340' side='right' caption='[[2dur]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2dur]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Canfa Canfa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DUR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2dur]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Canlf Canlf]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DUR FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1gv9|1gv9]], [[1r1z|1r1z]], [[2duo|2duo]], [[2dup|2dup]], [[2duq|2duq]], [[2dus|2dus]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">LMAN2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9615 CANFA])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">LMAN2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9615 CANLF])</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=2dur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dur OCA], [http://pdbe.org/2dur PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dur RCSB], [http://www.ebi.ac.uk/pdbsum/2dur PDBsum]</span></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=2dur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dur OCA], [http://pdbe.org/2dur PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dur RCSB], [http://www.ebi.ac.uk/pdbsum/2dur PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dur ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 14: / Line 15: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/du/2dur_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/du/2dur_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 33: / Line 34: @@
 __TOC__
 </StructureSection>
-[[Category: Canfa]]
+[[Category: Canlf]]
 [[Category: Cowieson, N P]]
 [[Category: Kato, R]]

2dur

From Proteopedia

Revision as of 06:34, 6 June 2018

Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+/Man2-bound form

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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