7d52

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==Crystal structure of yak lactoperoxidase with a disordered propionic group of heme moiety at 2.20 A resolution==
==Crystal structure of yak lactoperoxidase with a disordered propionic group of heme moiety at 2.20 A resolution==
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<StructureSection load='7d52' size='340' side='right'caption='[[7d52]]' scene=''>
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<StructureSection load='7d52' size='340' side='right'caption='[[7d52]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6l4f 6l4f]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7D52 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7D52 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[7d52]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_mutus Bos mutus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6l4f 6l4f]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7D52 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7D52 FirstGlance]. <br>
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</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=7d52 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d52 OCA], [https://pdbe.org/7d52 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7d52 RCSB], [https://www.ebi.ac.uk/pdbsum/7d52 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7d52 ProSAT]</span></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7d52 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d52 OCA], [https://pdbe.org/7d52 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7d52 RCSB], [https://www.ebi.ac.uk/pdbsum/7d52 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7d52 ProSAT]</span></td></tr>
</table>
</table>
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== Function ==
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[https://www.uniprot.org/uniprot/L8ICE9_9CETA L8ICE9_9CETA]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Lactoperoxidase, a heme-containing glycoprotein, catalyzes the oxidation of thiocyanate by hydrogen peroxide into hypothiocyanite which acts as an antibacterial agent. The prosthetic heme moiety is attached to the protein through two ester linkages via Glu258 and Asp108. In lactoperoxidase, the substrate-binding site is formed on the distal heme side. To study the effect of physiologically important potassium ion on the structure and function of lactoperoxidase, the fresh protein samples were isolated from yak (Bos grunniens) colostrum and purified to homogeneity. The biochemical studies with potassium fluoride showed a significant reduction in the catalytic activity. Lactoperoxidase was crystallized using 200 mM ammonium nitrate and 20% PEG-3350 at pH 6.0. The crystals of LPO were soaked in the solution of potassium fluoride and used for the X-ray intensity data collection. Structure determination at 2.20 A resolution revealed the presence of a potassium ion in the distal heme cavity. Structure determination further revealed that the propionic chain attached to pyrrole ring C of the heme moiety, was disordered into two components each having an occupancy of 0.5. One component occupied a position similar to the normally observed position of propionic chain while the second component was found in the distal heme cavity. The potassium ion in the distal heme cavity formed five coordinate bonds with two oxygen atoms of propionic moiety, N(epsilon2) atom of His109 and two oxygen atoms of water molecules. The presence of potassium ion in the distal heme cavity hampered the catalytic activity of lactoperoxidase.
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Potassium-induced partial inhibition of lactoperoxidase: structure of the complex of lactoperoxidase with potassium ion at 2.20 A resolution.,Singh PK, Pandey S, Rani C, Ahmad N, Viswanathan V, Sharma P, Kaur P, Sharma S, Singh TP J Biol Inorg Chem. 2021 Feb;26(1):149-159. doi: 10.1007/s00775-020-01844-6. Epub , 2021 Jan 11. PMID:33427997<ref>PMID:33427997</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 7d52" style="background-color:#fffaf0;"></div>
==See Also==
==See Also==
*[[Lactoperoxidase|Lactoperoxidase]]
*[[Lactoperoxidase|Lactoperoxidase]]
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== References ==
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<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bos mutus]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Ahmad N]]
[[Category: Ahmad N]]

Current revision

Crystal structure of yak lactoperoxidase with a disordered propionic group of heme moiety at 2.20 A resolution

PDB ID 7d52

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