5vg1: Difference between revisions
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==Neutron crystallographic structure of a Jonesia denitrificans lytic polysaccharide monooxygenase== | |||
<StructureSection load='5vg1' size='340' side='right'caption='[[5vg1]], [[Resolution|resolution]] 2.10Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5vg1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Jonesia_denitrificans_DSM_20603 Jonesia denitrificans DSM 20603]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VG1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VG1 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Neutron Diffraction, [[Resolution|Resolution]] 2.1Å</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=PER:PEROXIDE+ION'>PER</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=5vg1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vg1 OCA], [https://pdbe.org/5vg1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vg1 RCSB], [https://www.ebi.ac.uk/pdbsum/5vg1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vg1 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/C7R4I0_JONDD C7R4I0_JONDD] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
A 1.1 A resolution, room-temperature X-ray structure and a 2.1 A resolution neutron structure of a chitin-degrading lytic polysaccharide monooxygenase domain from the bacterium Jonesia denitrificans (JdLPMO10A) show a putative dioxygen species equatorially bound to the active site copper. Both structures show an elongated density for the dioxygen, most consistent with a Cu(II)-bound peroxide. The coordination environment is consistent with Cu(II). In the neutron and X-ray structures, difference maps reveal the N-terminal amino group, involved in copper coordination, is present as a mixed ND2 and ND-, suggesting a role for the copper ion in shifting the pKa of the amino terminus. | |||
Neutron and Atomic Resolution X-ray Structures of a Lytic Polysaccharide Monooxygenase Reveal Copper-Mediated Dioxygen Binding and Evidence for N-Terminal Deprotonation.,Bacik JP, Mekasha S, Forsberg Z, Kovalevsky AY, Vaaje-Kolstad G, Eijsink VGH, Nix JC, Coates L, Cuneo MJ, Unkefer CJ, Chen JC Biochemistry. 2017 May 23;56(20):2529-2532. doi: 10.1021/acs.biochem.7b00019., Epub 2017 May 11. PMID:28481095<ref>PMID:28481095</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: Bacik | <div class="pdbe-citations 5vg1" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: | ==See Also== | ||
*[[Chitinase 3D structures|Chitinase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Jonesia denitrificans DSM 20603]] | |||
[[Category: Large Structures]] | |||
[[Category: Bacik J-P]] | |||
[[Category: Chen JCH]] | |||
[[Category: Unkefer CJ]] | |||
Latest revision as of 16:48, 4 October 2023
Neutron crystallographic structure of a Jonesia denitrificans lytic polysaccharide monooxygenaseNeutron crystallographic structure of a Jonesia denitrificans lytic polysaccharide monooxygenase
Structural highlights
FunctionPublication Abstract from PubMedA 1.1 A resolution, room-temperature X-ray structure and a 2.1 A resolution neutron structure of a chitin-degrading lytic polysaccharide monooxygenase domain from the bacterium Jonesia denitrificans (JdLPMO10A) show a putative dioxygen species equatorially bound to the active site copper. Both structures show an elongated density for the dioxygen, most consistent with a Cu(II)-bound peroxide. The coordination environment is consistent with Cu(II). In the neutron and X-ray structures, difference maps reveal the N-terminal amino group, involved in copper coordination, is present as a mixed ND2 and ND-, suggesting a role for the copper ion in shifting the pKa of the amino terminus. Neutron and Atomic Resolution X-ray Structures of a Lytic Polysaccharide Monooxygenase Reveal Copper-Mediated Dioxygen Binding and Evidence for N-Terminal Deprotonation.,Bacik JP, Mekasha S, Forsberg Z, Kovalevsky AY, Vaaje-Kolstad G, Eijsink VGH, Nix JC, Coates L, Cuneo MJ, Unkefer CJ, Chen JC Biochemistry. 2017 May 23;56(20):2529-2532. doi: 10.1021/acs.biochem.7b00019., Epub 2017 May 11. PMID:28481095[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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