3ixf: Difference between revisions
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==Crystal Structure of Dehaloperoxidase B at 1.58 and Structural Characterization of the AB Dimer from Amphitrite ornata== | |||
<StructureSection load='3ixf' size='340' side='right'caption='[[3ixf]], [[Resolution|resolution]] 1.58Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3ixf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IXF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IXF 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]] 1.58Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=3ixf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ixf OCA], [https://pdbe.org/3ixf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ixf RCSB], [https://www.ebi.ac.uk/pdbsum/3ixf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ixf ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q9NAV7_9ANNE Q9NAV7_9ANNE] | |||
== 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/ix/3ixf_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=3ixf ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
As members of the globin superfamily, dehaloperoxidase (DHP) isoenzymes A and B from the marine annelid Amphitrite ornata possess hemoglobin function, but they also exhibit a biologically relevant peroxidase activity that is capable of converting 2,4,6-trihalophenols to the corresponding 2,6-dihaloquinones in the presence of hydrogen peroxide. Here, a comprehensive structural study of recombinant DHP B, both by itself and cocrystallized with isoenzyme A, using X-ray diffraction is presented. The structure of DHP B refined to 1.58 A resolution exhibits the same distal histidine (His55) conformational flexibility as that observed in isoenzyme A, as well as additional changes to the distal and proximal hydrogen-bonding networks. Furthermore, preliminary characterization of the DHP AB heterodimer is presented, which exhibits differences in the AB interface that are not observed in the A-only or B-only homodimers. These structural investigations of DHP B provide insights that may relate to the mechanistic details of the H(2)O(2)-dependent oxidative dehalogenation reaction catalyzed by dehaloperoxidase, present a clearer description of the function of specific residues in DHP at the molecular level and lead to a better understanding of the paradigms of globin structure-function relationships. | |||
Structure of dehaloperoxidase B at 1.58 A resolution and structural characterization of the AB dimer from Amphitrite ornata.,de Serrano V, D'Antonio J, Franzen S, Ghiladi RA Acta Crystallogr D Biol Crystallogr. 2010 May;66(Pt 5):529-38. Epub 2010, Apr 21. PMID:20445228<ref>PMID:20445228</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3ixf" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Dehaloperoxidase|Dehaloperoxidase]] | *[[Dehaloperoxidase 3D structures|Dehaloperoxidase 3D structures]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
</StructureSection> | |||
[[Category: Amphitrite ornata]] | [[Category: Amphitrite ornata]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: D'Antonio J]] | ||
[[Category: | [[Category: Franzen S]] | ||
[[Category: | [[Category: Ghiladi RA]] | ||
[[Category: Thompson | [[Category: Thompson MK]] | ||
[[Category: | [[Category: De Serrano VS]] | ||
Latest revision as of 10:59, 6 September 2023
Crystal Structure of Dehaloperoxidase B at 1.58 and Structural Characterization of the AB Dimer from Amphitrite ornataCrystal Structure of Dehaloperoxidase B at 1.58 and Structural Characterization of the AB Dimer from Amphitrite ornata
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedAs members of the globin superfamily, dehaloperoxidase (DHP) isoenzymes A and B from the marine annelid Amphitrite ornata possess hemoglobin function, but they also exhibit a biologically relevant peroxidase activity that is capable of converting 2,4,6-trihalophenols to the corresponding 2,6-dihaloquinones in the presence of hydrogen peroxide. Here, a comprehensive structural study of recombinant DHP B, both by itself and cocrystallized with isoenzyme A, using X-ray diffraction is presented. The structure of DHP B refined to 1.58 A resolution exhibits the same distal histidine (His55) conformational flexibility as that observed in isoenzyme A, as well as additional changes to the distal and proximal hydrogen-bonding networks. Furthermore, preliminary characterization of the DHP AB heterodimer is presented, which exhibits differences in the AB interface that are not observed in the A-only or B-only homodimers. These structural investigations of DHP B provide insights that may relate to the mechanistic details of the H(2)O(2)-dependent oxidative dehalogenation reaction catalyzed by dehaloperoxidase, present a clearer description of the function of specific residues in DHP at the molecular level and lead to a better understanding of the paradigms of globin structure-function relationships. Structure of dehaloperoxidase B at 1.58 A resolution and structural characterization of the AB dimer from Amphitrite ornata.,de Serrano V, D'Antonio J, Franzen S, Ghiladi RA Acta Crystallogr D Biol Crystallogr. 2010 May;66(Pt 5):529-38. Epub 2010, Apr 21. PMID:20445228[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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