7de5: Difference between revisions
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==Crystal structure of yak lactoperoxidase at 1.55 A resolution.== | ==Crystal structure of yak lactoperoxidase at 1.55 A resolution.== | ||
<StructureSection load='7de5' size='340' side='right'caption='[[7de5]]' scene=''> | <StructureSection load='7de5' size='340' side='right'caption='[[7de5]], [[Resolution|resolution]] 1.55Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=7ch2 7ch2], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=7byz 7byz] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6l2v 6l2v]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DE5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DE5 FirstGlance]. <br> | <table><tr><td colspan='2'>[[7de5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_grunniens Bos grunniens]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=7ch2 7ch2], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=7byz 7byz] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6l2v 6l2v]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DE5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DE5 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=7de5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7de5 OCA], [https://pdbe.org/7de5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7de5 RCSB], [https://www.ebi.ac.uk/pdbsum/7de5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7de5 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]] 1.55Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</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=7de5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7de5 OCA], [https://pdbe.org/7de5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7de5 RCSB], [https://www.ebi.ac.uk/pdbsum/7de5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7de5 ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/L8ICE9_9CETA L8ICE9_9CETA] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Lactoperoxidase (LPO) is a heme containing oxido-reductase enzyme. It is secreted from mammary, salivary, lachrymal and mucosal glands. It catalyses the conversion of thiocyanate into hypothiocyanate and halides into hypohalides. LPO belongs to the superfamily of mammalian heme peroxidases which also includes myeloperoxidase (MPO), eosinophil peroxidase (EPO) and thyroid peroxidase (TPO). The heme prosthetic group is covalently linked in LPO through two ester bonds involving conserved residues Glu258 and Asp108. It was isolated from colostrum of yak (Bos grunniens), purified to homogeneity and crystallized using ammonium iodide as a precipitating agent. The crystals belonged to monoclinic space group P2(1) with cell dimensions of a = 53.91 A, b = 78.98 A, c = 67.82 A and beta = 92.96 degrees . The structure was determined at 1.55 A resolution. This is the first structure of LPO from yak. Also, this is the highest resolution structure of LPO determined so far from any source. The structure determination revealed that three segments (Ser1-Cys15), (Thr117-Asn138) and (Cys167-Leu175) were disordered and formed one surface of LPO structure. In the substrate binding site, the iodide ions were observed in three subsites which are formed by (1) heme moiety and residues, Gln105, Asp108, His109, Phe113, Arg255, Glu258, Phe380 and Phe381, (2) residues, Asn230, Lys232, Pro236, Cys248, Phe254, Phe381 and Pro424 and (3) residues, Ser198, Leu199 and Arg202. The structure determination also revealed that the side chain of Phe254 was disordered. It was observed to adopt two conformations in the structures of LPO. | |||
Structure of Yak Lactoperoxidase at 1.55 A Resolution.,Viswanathan V, Rani C, Ahmad N, Singh PK, Sharma P, Kaur P, Sharma S, Singh TP Protein J. 2021 Feb;40(1):8-18. doi: 10.1007/s10930-020-09957-2. Epub 2021 Jan 3. PMID:33389415<ref>PMID:33389415</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7de5" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Lactoperoxidase|Lactoperoxidase]] | *[[Lactoperoxidase|Lactoperoxidase]] | ||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Bos grunniens]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Ahmad N]] | [[Category: Ahmad N]] | ||
Latest revision as of 19:31, 29 November 2023
Crystal structure of yak lactoperoxidase at 1.55 A resolution.Crystal structure of yak lactoperoxidase at 1.55 A resolution.
Structural highlights
FunctionPublication Abstract from PubMedLactoperoxidase (LPO) is a heme containing oxido-reductase enzyme. It is secreted from mammary, salivary, lachrymal and mucosal glands. It catalyses the conversion of thiocyanate into hypothiocyanate and halides into hypohalides. LPO belongs to the superfamily of mammalian heme peroxidases which also includes myeloperoxidase (MPO), eosinophil peroxidase (EPO) and thyroid peroxidase (TPO). The heme prosthetic group is covalently linked in LPO through two ester bonds involving conserved residues Glu258 and Asp108. It was isolated from colostrum of yak (Bos grunniens), purified to homogeneity and crystallized using ammonium iodide as a precipitating agent. The crystals belonged to monoclinic space group P2(1) with cell dimensions of a = 53.91 A, b = 78.98 A, c = 67.82 A and beta = 92.96 degrees . The structure was determined at 1.55 A resolution. This is the first structure of LPO from yak. Also, this is the highest resolution structure of LPO determined so far from any source. The structure determination revealed that three segments (Ser1-Cys15), (Thr117-Asn138) and (Cys167-Leu175) were disordered and formed one surface of LPO structure. In the substrate binding site, the iodide ions were observed in three subsites which are formed by (1) heme moiety and residues, Gln105, Asp108, His109, Phe113, Arg255, Glu258, Phe380 and Phe381, (2) residues, Asn230, Lys232, Pro236, Cys248, Phe254, Phe381 and Pro424 and (3) residues, Ser198, Leu199 and Arg202. The structure determination also revealed that the side chain of Phe254 was disordered. It was observed to adopt two conformations in the structures of LPO. Structure of Yak Lactoperoxidase at 1.55 A Resolution.,Viswanathan V, Rani C, Ahmad N, Singh PK, Sharma P, Kaur P, Sharma S, Singh TP Protein J. 2021 Feb;40(1):8-18. doi: 10.1007/s10930-020-09957-2. Epub 2021 Jan 3. PMID:33389415[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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