3krq: Difference between revisions
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< | ==Crystal structure of the complex of lactoperoxidase with a potent inhibitor amino-triazole at 2.2a resolution== | ||
<StructureSection load='3krq' size='340' side='right'caption='[[3krq]], [[Resolution|resolution]] 2.25Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3krq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KRQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KRQ FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.25Å</td></tr> | |||
- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3TR:3-AMINO-1,2,4-TRIAZOLE'>3TR</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</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=3krq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3krq OCA], [https://pdbe.org/3krq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3krq RCSB], [https://www.ebi.ac.uk/pdbsum/3krq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3krq ProSAT]</span></td></tr> | |||
</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. | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kr/3krq_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3krq ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The mode of binding of aromatic ligands in the substrate binding site on the distal heme side in heme peroxidases is well understood. However, the mode of diffusion through the extended hydrophobic channel and the regulatory role of the channel are not yet clear. To provide answers to these questions, the crystal structure of the complex of lactoperoxidase and 3-amino-1,2,4-triazole (amitrole) has been determined, which revealed the presence of two ligand molecules, one in the substrate binding site and the second in the hydrophobic channel. The binding of ligand in the channel induced a remarkable conformational change in the side chain of Phe254, which flips from its original distant position to interact with the trapped ligand in the hydrophobic channel. As a result, the channel is completely blocked so that no ligand can diffuse through it to the substrate binding site. Another amitrole molecule is bound to lactoperoxidase in the substrate binding site by replacing three water molecules, including the crucial iron-bound water molecule, W1. In this arrangement, the amino nitrogen atom of amitrole occupies the position of W1 and interacts directly with ferric iron. As a consequence, it prevents the binding of H(2)O(2) to heme iron. Thus, the interactions of amitrole with lactoperoxidase obstruct both the passage of ligands through the hydrophobic channel as well as the binding of H(2)O(2). This explains the amitrole toxicity. From binding studies, the dissociation constant (K (d)) for amitrole with lactoperoxidase was found to be approximately 5.5 x 10(-7) M, indicating high affinity. | |||
First structural evidence for the mode of diffusion of aromatic ligands and ligand-induced closure of the hydrophobic channel in heme peroxidases.,Singh AK, Singh N, Tiwari A, Sinha M, Kushwaha GS, Kaur P, Srinivasan A, Sharma S, Singh TP J Biol Inorg Chem. 2010 May 12. PMID:20461536<ref>PMID:20461536</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3krq" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Lactoperoxidase|Lactoperoxidase]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
== | |||
< | |||
[[Category: Bos taurus]] | [[Category: Bos taurus]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Kaur | [[Category: Kaur P]] | ||
[[Category: Kushwaha | [[Category: Kushwaha GS]] | ||
[[Category: Sharma | [[Category: Sharma S]] | ||
[[Category: Singh | [[Category: Singh AK]] | ||
[[Category: Singh | [[Category: Singh N]] | ||
[[Category: Singh | [[Category: Singh TP]] | ||
[[Category: Sinha | [[Category: Sinha M]] | ||
[[Category: Srinivasan | [[Category: Srinivasan A]] | ||
Latest revision as of 05:02, 21 November 2024
Crystal structure of the complex of lactoperoxidase with a potent inhibitor amino-triazole at 2.2a resolutionCrystal structure of the complex of lactoperoxidase with a potent inhibitor amino-triazole at 2.2a resolution
Structural highlights
FunctionPERL_BOVIN LPO is an antimicrobial agent. It is thought to help protect the udder from infection and promote growth in newborn calves. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe mode of binding of aromatic ligands in the substrate binding site on the distal heme side in heme peroxidases is well understood. However, the mode of diffusion through the extended hydrophobic channel and the regulatory role of the channel are not yet clear. To provide answers to these questions, the crystal structure of the complex of lactoperoxidase and 3-amino-1,2,4-triazole (amitrole) has been determined, which revealed the presence of two ligand molecules, one in the substrate binding site and the second in the hydrophobic channel. The binding of ligand in the channel induced a remarkable conformational change in the side chain of Phe254, which flips from its original distant position to interact with the trapped ligand in the hydrophobic channel. As a result, the channel is completely blocked so that no ligand can diffuse through it to the substrate binding site. Another amitrole molecule is bound to lactoperoxidase in the substrate binding site by replacing three water molecules, including the crucial iron-bound water molecule, W1. In this arrangement, the amino nitrogen atom of amitrole occupies the position of W1 and interacts directly with ferric iron. As a consequence, it prevents the binding of H(2)O(2) to heme iron. Thus, the interactions of amitrole with lactoperoxidase obstruct both the passage of ligands through the hydrophobic channel as well as the binding of H(2)O(2). This explains the amitrole toxicity. From binding studies, the dissociation constant (K (d)) for amitrole with lactoperoxidase was found to be approximately 5.5 x 10(-7) M, indicating high affinity. First structural evidence for the mode of diffusion of aromatic ligands and ligand-induced closure of the hydrophobic channel in heme peroxidases.,Singh AK, Singh N, Tiwari A, Sinha M, Kushwaha GS, Kaur P, Srinivasan A, Sharma S, Singh TP J Biol Inorg Chem. 2010 May 12. PMID:20461536[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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