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| - | ==Crystal struture of lactoperoxidase complex with cyanide== | + | ==Crystal structure of lactoperoxidase complex with cyanide== |
| - | <StructureSection load='3faq' size='340' side='right' caption='[[3faq]], [[Resolution|resolution]] 2.70Å' scene=''> | + | <StructureSection load='3faq' size='340' side='right'caption='[[3faq]], [[Resolution|resolution]] 2.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3faq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bubalus_bubalis Bubalus bubalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FAQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FAQ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3faq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bubalus_bubalis Bubalus bubalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FAQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FAQ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></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]] 2.7Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></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=CYN:CYANIDE+ION'>CYN</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>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3erh|3erh]]</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=3faq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3faq OCA], [https://pdbe.org/3faq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3faq RCSB], [https://www.ebi.ac.uk/pdbsum/3faq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3faq ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3faq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3faq OCA], [http://pdbe.org/3faq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3faq RCSB], [http://www.ebi.ac.uk/pdbsum/3faq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3faq ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PERL_BUBBU PERL_BUBBU]] Antimicrobial agent which utilizes hydrogen peroxide and thiocyanate (SCN) to generate the antimicrobial substance hypothiocyanous acid (HOSCN). May protect the udder from infection and promote growth in newborn calves. Inhibits growth of the following bacterial species: E.coli, K.pneumoniae, P.aeruginosa, S.sonnei, S.saphrophyticus, S.epidermidis, and S.dysenteriae.<ref>PMID:12071645</ref> | + | [https://www.uniprot.org/uniprot/PERL_BUBBU PERL_BUBBU] Antimicrobial agent which utilizes hydrogen peroxide and thiocyanate (SCN) to generate the antimicrobial substance hypothiocyanous acid (HOSCN). May protect the udder from infection and promote growth in newborn calves. Inhibits growth of the following bacterial species: E.coli, K.pneumoniae, P.aeruginosa, S.sonnei, S.saphrophyticus, S.epidermidis, and S.dysenteriae.<ref>PMID:12071645</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fa/3faq_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fa/3faq_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Bubalus bubalis]] | | [[Category: Bubalus bubalis]] |
| - | [[Category: Kaur, P]] | + | [[Category: Large Structures]] |
| - | [[Category: Sharma, S]] | + | [[Category: Kaur P]] |
| - | [[Category: Sheikh, I A]] | + | [[Category: Sharma S]] |
| - | [[Category: Singh, N]] | + | [[Category: Sheikh IA]] |
| - | [[Category: Singh, T P]] | + | [[Category: Singh N]] |
| - | [[Category: Srinivasan, A]] | + | [[Category: Singh TP]] |
| - | [[Category: Complex]]
| + | [[Category: Srinivasan A]] |
| - | [[Category: Heme]]
| + | |
| - | [[Category: Inhibitor]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Peroxidase]]
| + | |
| Structural highlights
3faq is a 1 chain structure with sequence from Bubalus bubalis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.7Å |
| Ligands: | , , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
PERL_BUBBU Antimicrobial agent which utilizes hydrogen peroxide and thiocyanate (SCN) to generate the antimicrobial substance hypothiocyanous acid (HOSCN). May protect the udder from infection and promote growth in newborn calves. Inhibits growth of the following bacterial species: E.coli, K.pneumoniae, P.aeruginosa, S.sonnei, S.saphrophyticus, S.epidermidis, and S.dysenteriae.[1]
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 PubMed
The crystal structure of the complex of lactoperoxidase (LPO) with its physiological substrate thiocyanate (SCN(-)) has been determined at 2.4A resolution. It revealed that the SCN(-) ion is bound to LPO in the distal heme cavity. The observed orientation of the SCN(-) ion shows that the sulfur atom is closer to the heme iron than the nitrogen atom. The nitrogen atom of SCN(-) forms a hydrogen bond with a water (Wat) molecule at position 6'. This water molecule is stabilized by two hydrogen bonds with Gln(423) N(epsilon2) and Phe(422) oxygen. In contrast, the placement of the SCN(-) ion in the structure of myeloperoxidase (MPO) occurs with an opposite orientation, in which the nitrogen atom is closer to the heme iron than the sulfur atom. The site corresponding to the positions of Gln(423), Phe(422) oxygen, and Wat(6)' in LPO is occupied primarily by the side chain of Phe(407) in MPO due to an entirely different conformation of the loop corresponding to the segment Arg(418)-Phe(431) of LPO. This arrangement in MPO does not favor a similar orientation of the SCN(-) ion. The orientation of the catalytic product OSCN(-) as reported in the structure of LPO.OSCN(-) is similar to the orientation of SCN(-) in the structure of LPO.SCN(-). Similarly, in the structure of LPO.SCN(-).CN(-), in which CN(-) binds at Wat(1), the position and orientation of the SCN(-) ion are also identical to that observed in the structure of LPO.SCN.
Structural evidence of substrate specificity in mammalian peroxidases: structure of the thiocyanate complex with lactoperoxidase and its interactions at 2.4 A resolution.,Sheikh IA, Singh AK, Singh N, Sinha M, Singh SB, Bhushan A, Kaur P, Srinivasan A, Sharma S, Singh TP J Biol Chem. 2009 May 29;284(22):14849-56. Epub 2009 Apr 1. PMID:19339248[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Ozdemir H, Hacibeyoglu HI, Uslu H. Purification of lactoperoxidase from creek-water buffalo milk and investigation of kinetic and antibacterial properties. Prep Biochem Biotechnol. 2002 May;32(2):143-55. PMID:12071645 doi:http://dx.doi.org/10.1081/PB-120004127
- ↑ Sheikh IA, Singh AK, Singh N, Sinha M, Singh SB, Bhushan A, Kaur P, Srinivasan A, Sharma S, Singh TP. Structural evidence of substrate specificity in mammalian peroxidases: structure of the thiocyanate complex with lactoperoxidase and its interactions at 2.4 A resolution. J Biol Chem. 2009 May 29;284(22):14849-56. Epub 2009 Apr 1. PMID:19339248 doi:10.1074/jbc.M807644200
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