4d7v

From Proteopedia

(Difference between revisions)

Current revision

The structure of the catalytic domain of NcLPMO9C from the filamentous fungus Neurospora crassa

Structural highlights

4d7v is a 2 chain structure with sequence from Neurospora crassa OR74A. 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

LP9C_NEUCR Lytic polysaccharide monooxygenase (LPMO) that depolymerizes crystalline and amorphous polysaccharides via the oxidation of scissile alpha- or beta-(1-4)-glycosidic bonds, yielding C4 oxidation products (PubMed:23102010, PubMed:24324265, PubMed:24733907, PubMed:26178376, PubMed:30238672, PubMed:31835532, PubMed:35080911, PubMed:36271009). 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:36271009). Degrades various hemicelluloses, in particular xyloglucan (PubMed:24733907, PubMed:31835532). Active on tamarind xyloglucan and konjac glucomannan (PubMed:26178376). Acts on the glucose backbone of xyloglucan, accepting various substitutions (xylose, galactose) in almost allpositions (PubMed:24733907). In contrast to all previously characterized LPMOs, which are active only on polysaccharides, is able to cleave soluble cello-oligosaccharides as short as a tetramer (PubMed:24324265). The cello-oligosaccharide products released by this enzyme contain a C4 gemdiol/keto group at the non-reducing end (PubMed:24324265). Binds to the inner wood cell wall layer and consumes enzymatically generated H(2)O(2) (PubMed:36271009).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8]

Publication Abstract from PubMed

The recently discovered lytic polysaccharide monooxygenases (LPMOs) carry out oxidative cleavage of polysaccharides and are of major im-portance for efficient processing of biomass. NcLP-MO9C from Neurospora crassa acts both on cellu-lose and on non-cellulose beta-glucans, including cello-dextrins and xyloglucan. The crystal structure of the catalytic domain of NcLPMO9C revealed an extend-ed highly polar substrate-binding surface well-suited to interact with a variety of sugar substrates. The ability of NcLPMO9C to act on soluble substrates was exploited to study enzyme-substrate interac-tions. Electron spin resonance (EPR) studies demon-strated that the Cu2+ center environment is altered upon substrate binding, whereas isothermal titration calorimetry (ITC) studies revealed binding affinities in the low micromolar range for polymeric substrates that are in part due to the presence of a carbohydrate-binding module (a CBM1). Importantly, the novel structure of NcLPMO9C enabled a comparative study, revealing that the oxidative regioselectivity of LPMO9s (C1, C4 or both) correlates with distinct structural features of the copper coordination sphere. In strictly C1 oxidizing LPMO9s, access to the sol-vent-facing axial coordination position is restricted by a conserved tyrosine residue, whereas access to this same position seems unrestricted in C4 oxidizing LPMO9s. LPMO9s known to produce a mixture of C-1 and C4-oxidized products show an intermediate situation.

Structural and functional characterization of a lytic polysaccharide monooxygenase with broad substrate specificity.,Borisova AS, Isaksen T, Dimarogona M, Kognole AA, Mathiesen G, Varnai A, Rohr AK, Payne CM, Sorlie M, Sandgren M, Eijsink VG J Biol Chem. 2015 Jul 15. pii: jbc.M115.660183. PMID:26178376^[9]

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

References

↑ Kittl R, Kracher D, Burgstaller D, Haltrich D, Ludwig R. Production of four Neurospora crassa lytic polysaccharide monooxygenases in Pichia pastoris monitored by a fluorimetric assay. Biotechnol Biofuels. 2012 Oct 26;5(1):79. PMID:23102010 doi:10.1186/1754-6834-5-79
↑ Isaksen T, Westereng B, Aachmann FL, Agger JW, Kracher D, Kittl R, Ludwig R, Haltrich D, Eijsink VG, Horn SJ. A C4-oxidizing lytic polysaccharide monooxygenase cleaving both cellulose and cello-oligosaccharides. J Biol Chem. 2014 Jan 31;289(5):2632-42. PMID:24324265 doi:10.1074/jbc.M113.530196
↑ Agger JW, Isaksen T, Várnai A, Vidal-Melgosa S, Willats WG, Ludwig R, Horn SJ, Eijsink VG, Westereng B. Discovery of LPMO activity on hemicelluloses shows the importance of oxidative processes in plant cell wall degradation. Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6287-92. PMID:24733907 doi:10.1073/pnas.1323629111
↑ Borisova AS, Isaksen T, Dimarogona M, Kognole AA, Mathiesen G, Varnai A, Rohr AK, Payne CM, Sorlie M, Sandgren M, Eijsink VG. Structural and functional characterization of a lytic polysaccharide monooxygenase with broad substrate specificity. J Biol Chem. 2015 Jul 15. pii: jbc.M115.660183. PMID:26178376 doi:http://dx.doi.org/10.1074/jbc.M115.660183
↑ 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
↑ Laurent CVFP, Sun P, Scheiblbrandner S, Csarman F, Cannazza P, Frommhagen M, van Berkel WJH, Oostenbrink C, Kabel MA, Ludwig R. Influence of Lytic Polysaccharide Monooxygenase Active Site Segments on Activity and Affinity. Int J Mol Sci. 2019 Dec 10;20(24):6219. PMID:31835532 doi:10.3390/ijms20246219
↑ Tõlgo M, Hegnar OA, Østby H, Várnai A, Vilaplana F, Eijsink VGH, Olsson L. Comparison of Six Lytic Polysaccharide Monooxygenases from Thermothielavioides terrestris Shows That Functional Variation Underlies the Multiplicity of LPMO Genes in Filamentous Fungi. Appl Environ Microbiol. 2022 Mar 22;88(6):e0009622. PMID:35080911 doi:10.1128/aem.00096-22
↑ Chang H, Gacias Amengual N, Botz A, Schwaiger L, Kracher D, Scheiblbrandner S, Csarman F, Ludwig R. Investigating lytic polysaccharide monooxygenase-assisted wood cell wall degradation with microsensors. Nat Commun. 2022 Oct 21;13(1):6258. PMID:36271009 doi:10.1038/s41467-022-33963-w
↑ Borisova AS, Isaksen T, Dimarogona M, Kognole AA, Mathiesen G, Varnai A, Rohr AK, Payne CM, Sorlie M, Sandgren M, Eijsink VG. Structural and functional characterization of a lytic polysaccharide monooxygenase with broad substrate specificity. J Biol Chem. 2015 Jul 15. pii: jbc.M115.660183. PMID:26178376 doi:http://dx.doi.org/10.1074/jbc.M115.660183

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/4d7v"

@@ Line 1: / Line 1: @@
 ==The structure of the catalytic domain of NcLPMO9C from the filamentous fungus Neurospora crassa==
-<StructureSection load='4d7v' size='340' side='right' caption='[[4d7v]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='4d7v' size='340' side='right'caption='[[4d7v]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4d7v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Neucr Neucr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D7V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D7V FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4d7v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Neurospora_crassa_OR74A Neurospora crassa OR74A]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D7V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D7V FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4d7u|4d7u]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GH61-3, NCU02916 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=367110 NEUCR])</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=4d7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d7v OCA], [https://pdbe.org/4d7v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d7v RCSB], [https://www.ebi.ac.uk/pdbsum/4d7v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d7v ProSAT]</span></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=4d7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d7v OCA], [http://pdbe.org/4d7v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4d7v RCSB], [http://www.ebi.ac.uk/pdbsum/4d7v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4d7v ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/LP9C_NEUCR LP9C_NEUCR] Lytic polysaccharide monooxygenase (LPMO) that depolymerizes crystalline and amorphous polysaccharides via the oxidation of scissile alpha- or beta-(1-4)-glycosidic bonds, yielding C4 oxidation products (PubMed:23102010, PubMed:24324265, PubMed:24733907, PubMed:26178376, PubMed:30238672, PubMed:31835532, PubMed:35080911, PubMed:36271009). 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:36271009). Degrades various hemicelluloses, in particular xyloglucan (PubMed:24733907, PubMed:31835532). Active on tamarind xyloglucan and konjac glucomannan (PubMed:26178376). Acts on the glucose backbone of xyloglucan, accepting various substitutions (xylose, galactose) in almost allpositions (PubMed:24733907). In contrast to all previously characterized LPMOs, which are active only on polysaccharides, is able to cleave soluble cello-oligosaccharides as short as a tetramer (PubMed:24324265). The cello-oligosaccharide products released by this enzyme contain a C4 gemdiol/keto group at the non-reducing end (PubMed:24324265). Binds to the inner wood cell wall layer and consumes enzymatically generated H(2)O(2) (PubMed:36271009).<ref>PMID:23102010</ref> <ref>PMID:24324265</ref> <ref>PMID:24733907</ref> <ref>PMID:26178376</ref> <ref>PMID:30238672</ref> <ref>PMID:31835532</ref> <ref>PMID:35080911</ref> <ref>PMID:36271009</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Neucr]]
+[[Category: Large Structures]]
-[[Category: Borisova, A S]]
+[[Category: Neurospora crassa OR74A]]
-[[Category: Dimarogona, M]]
+[[Category: Borisova AS]]
-[[Category: Eijsink, V G.H]]
+[[Category: Dimarogona M]]
-[[Category: Isaksen, T]]
+[[Category: Eijsink VGH]]
-[[Category: Sandgren, M]]
+[[Category: Isaksen T]]
-[[Category: Sorlie, M]]
+[[Category: Sandgren M]]
-[[Category: Aa9]]
+[[Category: Sorlie M]]
-[[Category: Catalytic domain]]
-[[Category: Hemicellulose active]]
-[[Category: Oxidoreductase]]

4d7v

From Proteopedia

Current revision

The structure of the catalytic domain of NcLPMO9C from the filamentous fungus Neurospora crassa

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox