5o2w

From Proteopedia

(Difference between revisions)

Current revision

Extended catalytic domain of Hypocrea jecorina LPMO 9A.

Structural highlights

5o2w is a 1 chain structure with sequence from Trichoderma reesei QM6a. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

LP9A_HYPJQ Lytic polysaccharide monooxygenase (LPMO) that depolymerizes crystalline and amorphous polysaccharides via the oxidation of scissile alpha- or beta-(1-4)-glycosidic bonds, yielding C1 and C4 oxidation products (PubMed:26285758, PubMed:28110665, PubMed:28900033, PubMed:30238672). Catalysis by LPMOs requires the reduction of the active-site copper from Cu(II) to Cu(I) by a reducing agent and H(2)O(2) or O(2) as a cosubstrate (PubMed:28900033, PubMed:32414932, PubMed:34597668). Produces both neutral and oxidized cello-oligosaccharides from cellulose (PubMed:26285758, PubMed:28900033). Acts also on soluble cello-oligosaccharides as short as a tetramer (PubMed:26285758). The oxidative activity displays a synergistic effect capable of boosting endoglucanase activity, and thereby substrate depolymerization of soy cellulose by 27% (PubMed:28110665).^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

Publication Abstract from PubMed

For decades, the enzymes of the fungus Hypocrea jecorina have served as a model system for the breakdown of cellulose. Three-dimensional structures for almost all H. jecorina cellulose-degrading enzymes are available, except for HjLPMO9A, belonging to the AA9 family of lytic polysaccharide monooxygenases (LPMOs). These enzymes enhance the hydrolytic activity of cellulases and are essential for cost-efficient conversion of lignocellulosic biomass. Here, using structural and spectroscopic analyses, we found that native HjLPMO9A contains a catalytic domain and a family-1 carbohydrate-binding module (CBM1) connected via a linker sequence. A C-terminally truncated variant of HjLPMO9A containing 21 residues of the predicted linker expressed at levels sufficient for analysis. Here, using structural, spectroscopic and biochemical analyses, we found that this truncated variant exhibited reduced binding to and activity on cellulose compared with the full-length enzyme. Importantly, a 0.95 A resolution X-ray structure of truncated HjLPMO9A revealed that the linker forms an integral part of the catalytic domain structure, covering a hydrophobic patch on the catalytic AA9 module. We noted that the oxidized catalytic center contains a Cu(II) coordinated by two His ligands, one of which has a Hisbrace in which the His1 terminal amine group also coordinates to a copper. The final equatorial position of the Cu(II) is occupied by a water-derived ligand. The spectroscopic characteristics of the truncated variant were not measurably different from those of full-length HjLPMO9A, indicating that the presence of the CBM1 module increases the affinity of HjLPMO9A for cellulose binding, but does not affect the active site.

High-resolution structure of a lytic polysaccharide monooxygenase from Hypocrea jecorina reveals a predicted linker as an integral part of the catalytic domain.,Hansson H, Karkehabadi S, Mikkelsen N, Douglas NR, Kim S, Lam A, Kaper T, Kelemen B, Meier KK, Jones SM, Solomon EI, Sandgren M J Biol Chem. 2017 Sep 12. pii: jbc.M117.799767. doi: 10.1074/jbc.M117.799767. PMID:28900033^[7]

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

References

↑ Tanghe M, Danneels B, Camattari A, Glieder A, Vandenberghe I, Devreese B, Stals I, Desmet T. Recombinant Expression of Trichoderma reesei Cel61A in Pichia pastoris: Optimizing Yield and N-terminal Processing. Mol Biotechnol. 2015 Dec;57(11-12):1010-7. PMID:26285758 doi:10.1007/s12033-015-9887-9
↑ Pierce BC, Agger JW, Wichmann J, Meyer AS. Oxidative cleavage and hydrolytic boosting of cellulose in soybean spent flakes by Trichoderma reesei Cel61A lytic polysaccharide monooxygenase. Enzyme Microb Technol. 2017 Mar;98:58-66. PMID:28110665 doi:10.1016/j.enzmictec.2016.12.007
↑ Hansson H, Karkehabadi S, Mikkelsen N, Douglas NR, Kim S, Lam A, Kaper T, Kelemen B, Meier KK, Jones SM, Solomon EI, Sandgren M. High-resolution structure of a lytic polysaccharide monooxygenase from Hypocrea jecorina reveals a predicted linker as an integral part of the catalytic domain. J Biol Chem. 2017 Sep 12. pii: jbc.M117.799767. doi: 10.1074/jbc.M117.799767. PMID:28900033 doi:http://dx.doi.org/10.1074/jbc.M117.799767
↑ Danneels B, Tanghe M, Desmet T. Structural Features on the Substrate-Binding Surface of Fungal Lytic Polysaccharide Monooxygenases Determine Their Oxidative Regioselectivity. Biotechnol J. 2019 Mar;14(3):e1800211. PMID:30238672 doi:10.1002/biot.201800211
↑ Jones SM, Transue WJ, Meier KK, Kelemen B, Solomon EI. Kinetic analysis of amino acid radicals formed in H(2)O(2)-driven Cu(I) LPMO reoxidation implicates dominant homolytic reactivity. Proc Natl Acad Sci U S A. 2020 Jun 2;117(22):11916-11922. PMID:32414932 doi:10.1073/pnas.1922499117
↑ Kuusk S, Väljamäe P. Kinetics of H(2)O(2)-driven catalysis by a lytic polysaccharide monooxygenase from the fungus Trichoderma reesei. J Biol Chem. 2021 Nov;297(5):101256. PMID:34597668 doi:10.1016/j.jbc.2021.101256
↑ Hansson H, Karkehabadi S, Mikkelsen N, Douglas NR, Kim S, Lam A, Kaper T, Kelemen B, Meier KK, Jones SM, Solomon EI, Sandgren M. High-resolution structure of a lytic polysaccharide monooxygenase from Hypocrea jecorina reveals a predicted linker as an integral part of the catalytic domain. J Biol Chem. 2017 Sep 12. pii: jbc.M117.799767. doi: 10.1074/jbc.M117.799767. PMID:28900033 doi:http://dx.doi.org/10.1074/jbc.M117.799767

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5o2w"

@@ Line 1: / Line 1: @@
 ==Extended catalytic domain of Hypocrea jecorina LPMO 9A.==
-<StructureSection load='5o2w' size='340' side='right' caption='[[5o2w]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='5o2w' size='340' side='right'caption='[[5o2w]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5o2w]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O2W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O2W FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5o2w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Trichoderma_reesei_QM6a Trichoderma reesei QM6a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O2W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5O2W FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2&#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=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=HIC:4-METHYL-HISTIDINE'>HIC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5o2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o2w OCA], [http://pdbe.org/5o2w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o2w RCSB], [http://www.ebi.ac.uk/pdbsum/5o2w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o2w 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=5o2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o2w OCA], [https://pdbe.org/5o2w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5o2w RCSB], [https://www.ebi.ac.uk/pdbsum/5o2w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5o2w ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/LP9A_HYPJQ LP9A_HYPJQ] Lytic polysaccharide monooxygenase (LPMO) that depolymerizes crystalline and amorphous polysaccharides via the oxidation of scissile alpha- or beta-(1-4)-glycosidic bonds, yielding C1 and C4 oxidation products (PubMed:26285758, PubMed:28110665, PubMed:28900033, PubMed:30238672). Catalysis by LPMOs requires the reduction of the active-site copper from Cu(II) to Cu(I) by a reducing agent and H(2)O(2) or O(2) as a cosubstrate (PubMed:28900033, PubMed:32414932, PubMed:34597668). Produces both neutral and oxidized cello-oligosaccharides from cellulose (PubMed:26285758, PubMed:28900033). Acts also on soluble cello-oligosaccharides as short as a tetramer (PubMed:26285758). The oxidative activity displays a synergistic effect capable of boosting endoglucanase activity, and thereby substrate depolymerization of soy cellulose by 27% (PubMed:28110665).<ref>PMID:26285758</ref> <ref>PMID:28110665</ref> <ref>PMID:28900033</ref> <ref>PMID:30238672</ref> <ref>PMID:32414932</ref> <ref>PMID:34597668</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 17: / Line 19: @@
 </div>
 <div class="pdbe-citations 5o2w" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Monooxygenase 3D structures|Monooxygenase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Hansson, H]]
+[[Category: Large Structures]]
-[[Category: Karkehabadi, S]]
+[[Category: Trichoderma reesei QM6a]]
-[[Category: Mikelssen, N E]]
+[[Category: Hansson H]]
-[[Category: Sandgren, M]]
+[[Category: Karkehabadi S]]
-[[Category: Metalloprotein]]
+[[Category: Mikelssen NE]]
-[[Category: Oxidoreductase]]
+[[Category: Sandgren M]]

5o2w

From Proteopedia

Current revision

Extended catalytic domain of Hypocrea jecorina LPMO 9A.

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox