2ri8: Difference between revisions

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New page: left|200px {{Structure |PDB= 2ri8 |SIZE=350|CAPTION= <scene name='initialview01'>2ri8</scene>, resolution 2.16Å |SITE= <scene name='pdbsite=AC1:Nag+Binding+Site+...
 
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[[Image:2ri8.jpg|left|200px]]


{{Structure
==Penicillium citrinum alpha-1,2-mannosidase complex with glycerol==
|PDB= 2ri8 |SIZE=350|CAPTION= <scene name='initialview01'>2ri8</scene>, resolution 2.16&Aring;
<StructureSection load='2ri8' size='340' side='right'caption='[[2ri8]], [[Resolution|resolution]] 2.16&Aring;' scene=''>
|SITE= <scene name='pdbsite=AC1:Nag+Binding+Site+For+Residue+A+1600'>AC1</scene>, <scene name='pdbsite=AC2:Nag+Binding+Site+For+Residue+A+1700'>AC2</scene>, <scene name='pdbsite=AC3:Nag+Binding+Site+For+Residue+A+1701'>AC3</scene>, <scene name='pdbsite=AC4:Man+Binding+Site+For+Residue+A+1702'>AC4</scene>, <scene name='pdbsite=AC5:Man+Binding+Site+For+Residue+A+1703'>AC5</scene>, <scene name='pdbsite=AC6:Man+Binding+Site+For+Residue+A+1704'>AC6</scene>, <scene name='pdbsite=AC7:Nag+Binding+Site+For+Residue+A+1800'>AC7</scene>, <scene name='pdbsite=AC8:Nag+Binding+Site+For+Residue+A+1801'>AC8</scene>, <scene name='pdbsite=AC9:Nag+Binding+Site+For+Residue+B+2600'>AC9</scene>, <scene name='pdbsite=BC1:Nag+Binding+Site+For+Residue+B+2700'>BC1</scene>, <scene name='pdbsite=BC2:Nag+Binding+Site+For+Residue+B+2701'>BC2</scene>, <scene name='pdbsite=BC3:Man+Binding+Site+For+Residue+B+2702'>BC3</scene>, <scene name='pdbsite=BC4:Man+Binding+Site+For+Residue+B+2703'>BC4</scene>, <scene name='pdbsite=BC5:Man+Binding+Site+For+Residue+B+2704'>BC5</scene>, <scene name='pdbsite=BC6:Nag+Binding+Site+For+Residue+B+2800'>BC6</scene>, <scene name='pdbsite=BC7:Ca+Binding+Site+For+Residue+A+1550'>BC7</scene>, <scene name='pdbsite=BC8:Ca+Binding+Site+For+Residue+B+1551'>BC8</scene>, <scene name='pdbsite=BC9:Gol+Binding+Site+For+Residue+A+1900'>BC9</scene>, <scene name='pdbsite=CC1:Gol+Binding+Site+For+Residue+A+1901'>CC1</scene>, <scene name='pdbsite=CC2:Gol+Binding+Site+For+Residue+A+1903'>CC2</scene>, <scene name='pdbsite=CC3:Gol+Binding+Site+For+Residue+A+1904'>CC3</scene>, <scene name='pdbsite=CC4:Gol+Binding+Site+For+Residue+B+2900'>CC4</scene>, <scene name='pdbsite=CC5:Gol+Binding+Site+For+Residue+B+2901'>CC5</scene> and <scene name='pdbsite=CC6:Gol+Binding+Site+For+Residue+B+2903'>CC6</scene>
== Structural highlights ==
|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>
<table><tr><td colspan='2'>[[2ri8]] 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=2RI8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RI8 FirstGlance]. <br>
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannosyl-oligosaccharide_1,2-alpha-mannosidase Mannosyl-oligosaccharide 1,2-alpha-mannosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.113 3.2.1.113] </span>
</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=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
|GENE= MSDC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5077 Penicillium citrinum])
<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]], [[2ri9|2ri9]]</div></td></tr>
|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam01532 Glyco_hydro_47]</span>
<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>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ri8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ri8 OCA], [http://www.ebi.ac.uk/pdbsum/2ri8 PDBsum], [http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1kfv JenaLib], [http://www.rcsb.org/pdb/explore.do?structureId=2ri8 RCSB]</span>
<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=2ri8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ri8 OCA], [https://pdbe.org/2ri8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ri8 RCSB], [https://www.ebi.ac.uk/pdbsum/2ri8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ri8 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/2ri8_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=2ri8 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== 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.


'''Penicillium citrinum alpha-1,2-mannosidase complex with glycerol'''
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>
</div>
<div class="pdbe-citations 2ri8" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
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 (1)C(4) 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.
*[[Mannosidase 3D structures|Mannosidase 3D structures]]
 
== References ==
==About this Structure==
<references/>
2RI8 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Penicillium_citrinum Penicillium citrinum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RI8 OCA].
__TOC__
 
</StructureSection>
==Reference==
[[Category: Atcc 1109]]
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:[http://www.ncbi.nlm.nih.gov/pubmed/18323617 18323617]
[[Category: Large Structures]]
[[Category: Mannosyl-oligosaccharide 1,2-alpha-mannosidase]]
[[Category: Mannosyl-oligosaccharide 1,2-alpha-mannosidase]]
[[Category: Penicillium citrinum]]
[[Category: Claeyssens, M]]
[[Category: Single protein]]
[[Category: Desmet, T]]
[[Category: Claeyssens, M.]]
[[Category: Herscovics, A]]
[[Category: Desmet, T.]]
[[Category: Herscovics, A.]]
[[Category: Howell, P L]]
[[Category: Howell, P L]]
[[Category: Lobsanov, Y D.]]
[[Category: Lobsanov, Y D]]
[[Category: Nerinckx, W.]]
[[Category: Nerinckx, W]]
[[Category: Yip, P.]]
[[Category: Yip, P]]
[[Category: Yoshida, T.]]
[[Category: Yoshida, T]]
[[Category: alternative conformation]]
[[Category: Alternative conformation]]
[[Category: glycoprotein]]
[[Category: Glycoprotein]]
[[Category: glycosidase]]
[[Category: Glycosidase]]
[[Category: hydrolase]]
[[Category: Hydrolase]]
[[Category: modulation of activity]]
[[Category: Modulation of activity]]
[[Category: secreted]]
[[Category: Secreted]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 26 09:53:31 2008''

Latest revision as of 07:26, 2 July 2021

Penicillium citrinum alpha-1,2-mannosidase complex with glycerolPenicillium citrinum alpha-1,2-mannosidase complex with glycerol

Structural highlights

2ri8 is a 2 chain structure with sequence from Atcc 1109. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, , ,
Gene:MSDC (ATCC 1109)
Activity:Mannosyl-oligosaccharide 1,2-alpha-mannosidase, with EC number 3.2.1.113
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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

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

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[1]

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

See Also

References

  1. ↑ Lobsanov YD, Yoshida T, Desmet T, Nerinckx W, Yip P, Claeyssens M, Herscovics A, Howell PL. Modulation of activity by Arg407: structure of a fungal alpha-1,2-mannosidase in complex with a substrate analogue. Acta Crystallogr D Biol Crystallogr. 2008 Mar;64(Pt 3):227-36. Epub 2008, Feb 20. PMID:18323617 doi:http://dx.doi.org/10.1107/S0907444907065572

2ri8, resolution 2.16Å

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