6l5g
From Proteopedia
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==Crystal structure of yak lactoperoxidase with disordered heme moiety at 2.50 A resolution== | ==Crystal structure of yak lactoperoxidase with disordered heme moiety at 2.50 A resolution== | ||
| - | <StructureSection load='6l5g' size='340' side='right'caption='[[6l5g]]' scene=''> | + | <StructureSection load='6l5g' size='340' side='right'caption='[[6l5g]], [[Resolution|resolution]] 2.50Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L5G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6L5G FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6l5g]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_mutus Bos mutus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L5G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6L5G FirstGlance]. <br> |
| - | </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=6l5g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l5g OCA], [https://pdbe.org/6l5g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6l5g RCSB], [https://www.ebi.ac.uk/pdbsum/6l5g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6l5g ProSAT]</span></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]] 2.5Å</td></tr> |
| + | <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=GOL:GLYCEROL'>GOL</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> | ||
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6l5g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l5g OCA], [https://pdbe.org/6l5g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6l5g RCSB], [https://www.ebi.ac.uk/pdbsum/6l5g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6l5g ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/PERL_BOVIN PERL_BOVIN] LPO is an antimicrobial agent. It is thought to help protect the udder from infection and promote growth in newborn calves. | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | 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. | ||
| + | |||
| + | 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> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6l5g" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
*[[Lactoperoxidase|Lactoperoxidase]] | *[[Lactoperoxidase|Lactoperoxidase]] | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Bos mutus]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Rani C]] | [[Category: Rani C]] | ||
Revision as of 10:51, 22 November 2023
Crystal structure of yak lactoperoxidase with disordered heme moiety at 2.50 A resolution
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Categories: Bos mutus | Large Structures | Rani C | Sharma P | Sharma S | Singh PK | Singh TP
