1kre: Difference between revisions

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-[[Image:1kre.gif|left|200px]]<br /><applet load="1kre" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1kre, resolution 2.20&Aring;" />
-'''STRUCTURE OF P. CITRINUM ALPHA 1,2-MANNOSIDASE REVEALS THE BASIS FOR DIFFERENCES IN SPECIFICITY OF THE ER AND GOLGI CLASS I ENZYMES'''<br />
-==Overview==
+==STRUCTURE OF P. CITRINUM ALPHA 1,2-MANNOSIDASE REVEALS THE BASIS FOR DIFFERENCES IN SPECIFICITY OF THE ER AND GOLGI CLASS I ENZYMES==
-Class I alpha1,2-mannosidases (glycosylhydrolase family 47) are key, enzymes in the maturation of N-glycans. This protein family includes two, distinct enzymatically active subgroups. Subgroup 1 includes the yeast and, human endoplasmic reticulum (ER) alpha1,2-mannosidases that primarily trim, Man(9)GlcNAc(2) to Man(8)GlcNAc(2) isomer B whereas subgroup 2 includes, mammalian Golgi alpha1,2-mannosidases IA, IB, and IC that trim, Man(9)GlcNAc(2) to Man(5)GlcNAc(2) via Man(8)GlcNAc(2) isomers A and C., The structure of the catalytic domain of the subgroup 2, alpha1,2-mannosidase from Penicillium citrinum has been determined by, molecular replacement at 2.2-A resolution. The fungal alpha1,2-mannosidase, is an (alphaalpha)(7)-helix barrel, very similar to the subgroup 1 yeast, (Vallee, F., Lipari, F., Yip, P., Sleno, B., Herscovics, A., and Howell, P. L. (2000) EMBO J. 19, 581-588) and human (Vallee, F., Karaveg, K., Herscovics, A., Moremen, K. W., and Howell, P. L. (2000) J. Biol. Chem., 275, 41287-41298) ER enzymes. The location of the conserved acidic, residues of the catalytic site and the binding of the inhibitors, kifunensine and 1-deoxymannojirimycin, to the essential calcium ion are, conserved in the fungal enzyme. However, there are major structural, differences in the oligosaccharide binding site between the two, alpha1,2-mannosidase subgroups. In the subgroup 1 enzymes, an arginine, residue plays a critical role in stabilizing the oligosaccharide, substrate. In the fungal alpha1,2-mannosidase this arginine is replaced by, glycine. This replacement and other sequence variations result in a more, spacious carbohydrate binding site. Modeling studies of interactions, between the yeast, human and fungal enzymes with different Man(8)GlcNAc(2), isomers indicate that there is a greater degree of freedom to bind the, oligosaccharide in the active site of the fungal enzyme than in the yeast, and human ER alpha1,2-mannosidases.
+<StructureSection load='1kre' size='340' side='right'caption='[[1kre]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1kre]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Penicillium_citrinum Penicillium citrinum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KRE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KRE FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</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=DMJ:1-DEOXYMANNOJIRIMYCIN'>DMJ</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=1kre FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kre OCA], [https://pdbe.org/1kre PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kre RCSB], [https://www.ebi.ac.uk/pdbsum/1kre PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kre 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/kr/1kre_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=1kre ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Class I alpha1,2-mannosidases (glycosylhydrolase family 47) are key enzymes in the maturation of N-glycans. This protein family includes two distinct enzymatically active subgroups. Subgroup 1 includes the yeast and human endoplasmic reticulum (ER) alpha1,2-mannosidases that primarily trim Man(9)GlcNAc(2) to Man(8)GlcNAc(2) isomer B whereas subgroup 2 includes mammalian Golgi alpha1,2-mannosidases IA, IB, and IC that trim Man(9)GlcNAc(2) to Man(5)GlcNAc(2) via Man(8)GlcNAc(2) isomers A and C. The structure of the catalytic domain of the subgroup 2 alpha1,2-mannosidase from Penicillium citrinum has been determined by molecular replacement at 2.2-A resolution. The fungal alpha1,2-mannosidase is an (alphaalpha)(7)-helix barrel, very similar to the subgroup 1 yeast (Vallee, F., Lipari, F., Yip, P., Sleno, B., Herscovics, A., and Howell, P. L. (2000) EMBO J. 19, 581-588) and human (Vallee, F., Karaveg, K., Herscovics, A., Moremen, K. W., and Howell, P. L. (2000) J. Biol. Chem. 275, 41287-41298) ER enzymes. The location of the conserved acidic residues of the catalytic site and the binding of the inhibitors, kifunensine and 1-deoxymannojirimycin, to the essential calcium ion are conserved in the fungal enzyme. However, there are major structural differences in the oligosaccharide binding site between the two alpha1,2-mannosidase subgroups. In the subgroup 1 enzymes, an arginine residue plays a critical role in stabilizing the oligosaccharide substrate. In the fungal alpha1,2-mannosidase this arginine is replaced by glycine. This replacement and other sequence variations result in a more spacious carbohydrate binding site. Modeling studies of interactions between the yeast, human and fungal enzymes with different Man(8)GlcNAc(2) isomers indicate that there is a greater degree of freedom to bind the oligosaccharide in the active site of the fungal enzyme than in the yeast and human ER alpha1,2-mannosidases.
-==About this Structure==
+Structure of Penicillium citrinum alpha 1,2-mannosidase reveals the basis for differences in specificity of the endoplasmic reticulum and Golgi class I enzymes.,Lobsanov YD, Vallee F, Imberty A, Yoshida T, Yip P, Herscovics A, Howell PL J Biol Chem. 2002 Feb 15;277(7):5620-30. Epub 2001 Nov 19. PMID:11714724<ref>PMID:11714724</ref>
-KRE is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Penicillium_citrinum Penicillium citrinum] with CA and DMJ as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KRE OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structure of Penicillium citrinum alpha 1,2-mannosidase reveals the basis for differences in specificity of the endoplasmic reticulum and Golgi class I enzymes., Lobsanov YD, Vallee F, Imberty A, Yoshida T, Yip P, Herscovics A, Howell PL, J Biol Chem. 2002 Feb 15;277(7):5620-30. Epub 2001 Nov 19. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11714724 11714724]
+</div>
-[[Category: Mannosyl-oligosaccharide 1,2-alpha-mannosidase]]
+<div class="pdbe-citations 1kre" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Mannosidase 3D structures|Mannosidase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Penicillium citrinum]]
-[[Category: Single protein]]
+[[Category: Herscovics A]]
-[[Category: Herscovics, A.]]
+[[Category: Howell PL]]
-[[Category: Howell, P.L.]]
+[[Category: Imberty A]]
-[[Category: Imberty, A.]]
+[[Category: Lobsanov YD]]
-[[Category: Lobsanov, Y.D.]]
+[[Category: Vallee F]]
-[[Category: Vallee, F.]]
+[[Category: Yip P]]
-[[Category: Yip, P.]]
+[[Category: Yoshida T]]
-[[Category: Yoshida, T.]]
-[[Category: CA]]
-[[Category: DMJ]]
-[[Category: (alpha/alpha)7-barrel]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:44:30 2007''