7bzm: Difference between revisions
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==Crystal structure of rice Os3BGlu7 with glucoimidazole== | ==Crystal structure of rice Os3BGlu7 with glucoimidazole== | ||
<StructureSection load='7bzm' size='340' side='right'caption='[[7bzm]]' scene=''> | <StructureSection load='7bzm' size='340' side='right'caption='[[7bzm]], [[Resolution|resolution]] 2.30Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BZM OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[7bzm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa_Japonica_Group Oryza sativa Japonica Group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BZM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BZM FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GIM:GLUCOIMIDAZOLE'>GIM</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=7bzm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bzm OCA], [https://pdbe.org/7bzm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bzm RCSB], [https://www.ebi.ac.uk/pdbsum/7bzm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bzm ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/BGL07_ORYSJ BGL07_ORYSJ] Hydrolyzes p-nitrophenyl beta-D-glucoside, p-nitrophenyl beta-D-mannoside, p-nitrophenyl beta-D-galactoside, p-nitrophenyl beta-D-xyloside, p-nitrophenyl beta-D-fucoside, p-nitrophenyl beta-L-arabinoside, oligosaccharides, pyridoxine beta-D-glucoside and the cyanogenic glucosides amygdalin, prunasin and dhurrin. Possesses pyridoxine transglucosylation activity.<ref>PMID:14692878</ref> <ref>PMID:19766588</ref> <ref>PMID:18308333</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
beta-Glucosidases and beta-mannosidases hydrolyze substrates that differ only in the epimer of the nonreducing terminal sugar moiety, but most such enzymes show a strong preference for one activity or the other. Rice Os3BGlu7 and Os7BGlu26 beta-glycosidases show a less strong preference, but Os3BGlu7 and Os7BGlu26 prefer glucosides and mannosides, respectively. Previous studies of crystal structures with glucoimidazole (GIm) and mannoimidazole (MIm) complexes and metadynamic simulations suggested that Os7BGlu26 hydrolyzes mannosides via the B2,5 transition state (TS) conformation preferred for mannosides and glucosides via their preferred (4)H3/(4)E TS conformation. However, MIm is weakly bound by both enzymes. In the present study, we found that MIm was not bound in the active site of crystallized Os3BGlu7, but GIm was tightly bound in the -1 subsite in a (4)H3/(4)E conformation via hydrogen bonds with the surrounding residues. One-microsecond molecular dynamics simulations showed that GIm was stably bound in the Os3BGlu7 active site and the glycone-binding site with little distortion. In contrast, MIm initialized in the B2,5 conformation rapidly relaxed to a E3/(4)H3 conformation and moved out into a position in the entrance of the active site, where it bound more stably despite making fewer interactions. The lack of MIm binding in the glycone site in protein crystals and simulations implies that the energy required to distort MIm to the B2,5 conformation for optimal active site residue interactions is sufficient to offset the energy of those interactions in Os3BGlu7. This balance between distortion and binding energy may also provide a rationale for glucosidase versus mannosidase specificity in plant beta-glycosidases. | |||
Structural Basis of Specific Glucoimidazole and Mannoimidazole Binding by Os3BGlu7.,Nutho B, Pengthaisong S, Tankrathok A, Lee VS, Ketudat Cairns JR, Rungrotmongkol T, Hannongbua S Biomolecules. 2020 Jun 15;10(6). pii: biom10060907. doi: 10.3390/biom10060907. PMID:32549280<ref>PMID:32549280</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7bzm" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Beta-glucosidase 3D structures|Beta-glucosidase 3D structures]] | |||
*[[Galactosidase 3D structures|Galactosidase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Oryza sativa Japonica Group]] | |||
[[Category: Ketudat Cairns JR]] | [[Category: Ketudat Cairns JR]] | ||
[[Category: Pengthaisong S]] | [[Category: Pengthaisong S]] | ||
[[Category: Tankrathok A]] | [[Category: Tankrathok A]] | ||
Revision as of 18:44, 29 November 2023
Crystal structure of rice Os3BGlu7 with glucoimidazoleCrystal structure of rice Os3BGlu7 with glucoimidazole
Structural highlights
FunctionBGL07_ORYSJ Hydrolyzes p-nitrophenyl beta-D-glucoside, p-nitrophenyl beta-D-mannoside, p-nitrophenyl beta-D-galactoside, p-nitrophenyl beta-D-xyloside, p-nitrophenyl beta-D-fucoside, p-nitrophenyl beta-L-arabinoside, oligosaccharides, pyridoxine beta-D-glucoside and the cyanogenic glucosides amygdalin, prunasin and dhurrin. Possesses pyridoxine transglucosylation activity.[1] [2] [3] Publication Abstract from PubMedbeta-Glucosidases and beta-mannosidases hydrolyze substrates that differ only in the epimer of the nonreducing terminal sugar moiety, but most such enzymes show a strong preference for one activity or the other. Rice Os3BGlu7 and Os7BGlu26 beta-glycosidases show a less strong preference, but Os3BGlu7 and Os7BGlu26 prefer glucosides and mannosides, respectively. Previous studies of crystal structures with glucoimidazole (GIm) and mannoimidazole (MIm) complexes and metadynamic simulations suggested that Os7BGlu26 hydrolyzes mannosides via the B2,5 transition state (TS) conformation preferred for mannosides and glucosides via their preferred (4)H3/(4)E TS conformation. However, MIm is weakly bound by both enzymes. In the present study, we found that MIm was not bound in the active site of crystallized Os3BGlu7, but GIm was tightly bound in the -1 subsite in a (4)H3/(4)E conformation via hydrogen bonds with the surrounding residues. One-microsecond molecular dynamics simulations showed that GIm was stably bound in the Os3BGlu7 active site and the glycone-binding site with little distortion. In contrast, MIm initialized in the B2,5 conformation rapidly relaxed to a E3/(4)H3 conformation and moved out into a position in the entrance of the active site, where it bound more stably despite making fewer interactions. The lack of MIm binding in the glycone site in protein crystals and simulations implies that the energy required to distort MIm to the B2,5 conformation for optimal active site residue interactions is sufficient to offset the energy of those interactions in Os3BGlu7. This balance between distortion and binding energy may also provide a rationale for glucosidase versus mannosidase specificity in plant beta-glycosidases. Structural Basis of Specific Glucoimidazole and Mannoimidazole Binding by Os3BGlu7.,Nutho B, Pengthaisong S, Tankrathok A, Lee VS, Ketudat Cairns JR, Rungrotmongkol T, Hannongbua S Biomolecules. 2020 Jun 15;10(6). pii: biom10060907. doi: 10.3390/biom10060907. PMID:32549280[4] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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