3bxi: Difference between revisions

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-{{Seed}}
-[[Image:3bxi.png|left|200px]]
-<!--
+==Structure of the complex of bovine lactoperoxidase with its catalyzed product hypothiocyanate ion at 2.3A resolution==
-The line below this paragraph, containing "STRUCTURE_3bxi", creates the "Structure Box" on the page.
+<StructureSection load='3bxi' size='340' side='right'caption='[[3bxi]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3bxi]] 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=3BXI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BXI FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=OSM:1-(OXIDOSULFANYL)METHANAMINE'>OSM</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr>
-{{STRUCTURE_3bxi|  PDB=3bxi  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bxi OCA], [https://pdbe.org/3bxi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bxi RCSB], [https://www.ebi.ac.uk/pdbsum/3bxi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bxi 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/bx/3bxi_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=3bxi ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+To the best of our knowledge, this is the first report on the structure of product-inhibited mammalian peroxidase. Lactoperoxidase is a heme containing an enzyme that catalyzes the inactivation of a wide range of microorganisms. In the presence of hydrogen peroxide, it preferentially converts thiocyanate ion into a toxic hypothiocyanate ion. Samples of bovine lactoperoxidase containing thiocyanate (SCN(-)) and hypothiocyanate (OSCN(-)) ions were purified and crystallized. The structure was determined at 2.3-A resolution and refined to R(cryst) and R(free) factors of 0.184 and 0.221, respectively. The determination of structure revealed the presence of an OSCN(-) ion at the distal heme cavity. The presence of OSCN(-) ions in crystal samples was also confirmed by chemical and spectroscopic analysis. The OSCN(-) ion interacts with the heme iron, Gln-105 N(epsilon1), His-109 N(epsilon2), and a water molecule W96. The sulfur atom of the OSCN(-) ion forms a hypervalent bond with a nitrogen atom of the pyrrole ring D of the heme moiety at an S-N distance of 2.8 A. The heme group is covalently bound to the protein through two ester linkages involving carboxylic groups of Glu-258 and Asp-108 and the modified methyl groups of pyrrole rings A and C, respectively. The heme moiety is significantly distorted from planarity, whereas pyrrole rings A, B, C, and D are essentially planar. The iron atom is displaced by approximately 0.2 A from the plane of the heme group toward the proximal site. The substrate channel resembles a long tunnel whose inner walls contain predominantly aromatic residues such as Phe-113, Phe-239, Phe-254, Phe-380, Phe-381, Phe-422, and Pro-424. A phosphorylated Ser-198 was evident at the surface, in the proximity of the calcium-binding channel.
-===Structure of the complex of bovine lactoperoxidase with its catalyzed product hypothiocyanate ion at 2.3A resolution===
+Inhibition of lactoperoxidase by its own catalytic product: crystal structure of the hypothiocyanate-inhibited bovine lactoperoxidase at 2.3-A resolution.,Singh AK, Singh N, Sharma S, Shin K, Takase M, Kaur P, Srinivasan A, Singh TP Biophys J. 2009 Jan;96(2):646-54. PMID:19167310<ref>PMID:19167310</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3bxi" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19167310}}, adds the Publication Abstract to the page
+*[[Lactoperoxidase|Lactoperoxidase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19167310 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19167310}}
+__TOC__
+</StructureSection>
-==About this Structure==
-BXI is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BXI OCA].
-==Reference==
-<ref group="xtra">PMID:19167310</ref><references group="xtra"/>
 [[Category: Bos taurus]]
-[[Category: Peroxidase]]
+[[Category: Large Structures]]
-[[Category: Kaur, P.]]
+[[Category: Kaur P]]
-[[Category: Sharma, S.]]
+[[Category: Sharma S]]
-[[Category: Shin, K.]]
+[[Category: Shin K]]
-[[Category: Singh, A K.]]
+[[Category: Singh AK]]
-[[Category: Singh, N.]]
+[[Category: Singh N]]
-[[Category: Singh, T P.]]
+[[Category: Singh TP]]
-[[Category: Srinivasan, A.]]
+[[Category: Srinivasan A]]
-[[Category: Takase, M.]]
+[[Category: Takase M]]
-[[Category: Antibacterial]]
-[[Category: Antibiotic]]
-[[Category: Antimicrobial]]
-[[Category: Calcium]]
-[[Category: Glycoprotein]]
-[[Category: Heme]]
-[[Category: Hydrogen peroxide]]
-[[Category: Iron]]
-[[Category: Metal-binding]]
-[[Category: Oxidoreductase]]
-[[Category: Peroxidase]]
-[[Category: Secreted]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 25 11:09:40 2009''