View source for 2ri9


==Penicillium citrinum alpha-1,2-mannosidase in complex with a substrate analog==
<StructureSection load='2ri9' size='340' side='right'caption='[[2ri9]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2ri9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_1109 Atcc 1109]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RI9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RI9 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LDY:ALPHA-D-LYXOPYRANOSE'>LDY</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MMA:O1-METHYL-MANNOSE'>MMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1kkt|1kkt]], [[1kre|1kre]], [[1krf|1krf]], [[2ri8|2ri8]]</div></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MSDC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5077 ATCC 1109])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Mannosyl-oligosaccharide_1,2-alpha-mannosidase Mannosyl-oligosaccharide 1,2-alpha-mannosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.113 3.2.1.113] </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=2ri9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ri9 OCA], [https://pdbe.org/2ri9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ri9 RCSB], [https://www.ebi.ac.uk/pdbsum/2ri9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ri9 ProSAT]</span></td></tr>
</table>
== Function ==
[[https://www.uniprot.org/uniprot/MAN12_PENCI MAN12_PENCI]] Involved in the maturation of Asn-linked oligosaccharides. Progressively trim alpha-1,2-linked mannose residues from Man(9)GlcNAc(2) to produce Man(5)GlcNAc(2). 
== 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/ri/2ri9_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=2ri9 ConSurf].
<div style="clear:both"></div>
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== Publication Abstract from PubMed ==
Class I alpha-mannosidases (glycoside hydrolase family GH47) play key roles in the maturation of N-glycans and the ER-associated degradation of unfolded glycoproteins. The 1.95 A resolution structure of a fungal alpha-1,2-mannosidase in complex with the substrate analogue methyl-alpha-D-lyxopyranosyl-(1',2)-alpha-D-mannopyranoside (LM) shows the intact disaccharide spanning the -1/+1 subsites, with the D-lyxoside ring in the -1 subsite in the 1C4 chair conformation, and provides insight into the mechanism of catalysis. The absence of the C5' hydroxymethyl group on the D-lyxoside moiety results in the side chain of Arg407 adopting two alternative conformations: the minor one interacting with Asp375 and the major one interacting with both the D-lyxoside and the catalytic base Glu409, thus disrupting its function. Chemical modification of Asp375 has previously been shown to inactivate the enzyme. Taken together, the data suggest that Arg407, which belongs to the conserved sequence motif RPExxE, may act to modulate the activity of the enzyme. The proposed mechanism for modulating the activity is potentially a general mechanism for this superfamily.

Modulation of activity by Arg407: structure of a fungal alpha-1,2-mannosidase in complex with a substrate analogue.,Lobsanov YD, Yoshida T, Desmet T, Nerinckx W, Yip P, Claeyssens M, Herscovics A, Howell PL Acta Crystallogr D Biol Crystallogr. 2008 Mar;64(Pt 3):227-36. Epub 2008, Feb 20. PMID:18323617<ref>PMID:18323617</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 2ri9" style="background-color:#fffaf0;"></div>

==See Also==
*[[Mannosidase 3D structures|Mannosidase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Atcc 1109]]
[[Category: Large Structures]]
[[Category: Mannosyl-oligosaccharide 1,2-alpha-mannosidase]]
[[Category: Claeyssens, M]]
[[Category: Desmet, T]]
[[Category: Herscovics, A]]
[[Category: Howell, P L]]
[[Category: Lobsanov, Y D]]
[[Category: Nerinckx, W]]
[[Category: Yip, P]]
[[Category: Yoshida, T]]
[[Category: Alternative conformation]]
[[Category: Glycoprotein]]
[[Category: Glycosidase]]
[[Category: Hydrolase]]
[[Category: Modulation of activity]]
[[Category: Secreted]]