This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

6ydg

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

X-ray structure of LPMO

Structural highlights

6ydg is a 1 chain structure with sequence from Panus similis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9Å
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A0A0S2GKZ1_9APHY

Publication Abstract from PubMed

Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that cleave polysaccharide substrates oxidatively. First discovered because of their action on recalcitrant crystalline substrates (chitin and cellulose), a number of LPMOs are now reported to act on soluble substrates, including oligosaccharides. However, crystallographic complexes with oligosaccharides have been reported for only a single LPMO so far, an enzyme from the basidiomycete fungus Lentinus similis (LsAA9_A). Here we present a more detailed comparative study of LsAA9_A and an LPMO from the ascomycete fungus Collariella virescens (CvAA9_A) with which it shares 41.5% sequence identity. LsAA9_A is considerably more thermostable than CvAA9_A, and the structural basis for the difference has been investigated. We have compared the patterns of oligosaccharide cleavage and the patterns of binding in several new crystal structures explaining the basis for the product preferences of the two enzymes. Obtaining structural information about complexes of LPMOs with carbohydrates has proven to be very difficult in general judging from the structures reported in the literature thus far, and this can be attributed only partly to the low affinity for small substrates. We have thus evaluated the use of differential scanning fluorimetry as a guide to obtaining complex structures. Furthermore, an analysis of crystal packing of LPMOs and glycoside hydrolases corroborates the hypothesis that active site occlusion is a very significant problem for LPMO-substrate interaction analysis by crystallography, due to their relatively flat and extended substrate binding sites.

Oligosaccharide Binding and Thermostability of Two Related AA9 Lytic Polysaccharide Monooxygenases.,Tandrup T, Tryfona T, Frandsen KEH, Johansen KS, Dupree P, Lo Leggio L Biochemistry. 2020 Sep 15;59(36):3347-3358. doi: 10.1021/acs.biochem.0c00312., Epub 2020 Aug 27. PMID:32818374^[1]

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

References

↑ Tandrup T, Tryfona T, Frandsen KEH, Johansen KS, Dupree P, Lo Leggio L. Oligosaccharide Binding and Thermostability of Two Related AA9 Lytic Polysaccharide Monooxygenases. Biochemistry. 2020 Sep 15;59(36):3347-3358. doi: 10.1021/acs.biochem.0c00312., Epub 2020 Aug 27. PMID:32818374 doi:http://dx.doi.org/10.1021/acs.biochem.0c00312

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6ydg"

@@ Line 3: / Line 3: @@
 <StructureSection load='6ydg' size='340' side='right'caption='[[6ydg]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6ydg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lentinus_similis Lentinus similis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YDG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YDG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6ydg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Panus_similis Panus similis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YDG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YDG FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=HIC:4-METHYL-HISTIDINE'>HIC</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=HIC:4-METHYL-HISTIDINE'>HIC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PRD_900011:beta-cellotetraose'>PRD_900011</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6ydg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ydg OCA], [http://pdbe.org/6ydg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ydg RCSB], [http://www.ebi.ac.uk/pdbsum/6ydg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ydg ProSAT]</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=6ydg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ydg OCA], [https://pdbe.org/6ydg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ydg RCSB], [https://www.ebi.ac.uk/pdbsum/6ydg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ydg ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/A0A0S2GKZ1_9APHY A0A0S2GKZ1_9APHY]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Lentinus similis]]
+[[Category: Panus similis]]
-[[Category: Dupree, P]]
+[[Category: Dupree P]]
-[[Category: Frandsen, K E.H]]
+[[Category: Frandsen KEH]]
-[[Category: Johansen, K S]]
+[[Category: Johansen KS]]
-[[Category: Leggio, L Lo]]
+[[Category: Lo Leggio L]]
-[[Category: Tandrup, T]]
+[[Category: Tandrup T]]
-[[Category: Tryfona, T]]
+[[Category: Tryfona T]]
-[[Category: Cellotetraose]]
-[[Category: Complex]]
-[[Category: Lytic polysaccharide monooxygenase]]
-[[Category: Metal binding protein]]

6ydg

From Proteopedia

Current revision

X-ray structure of LPMO

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox