View source for 8vkd


==Crystal structure of dehaloperoxidase A in complex with substrate 4-nitrocatechol==
<StructureSection load='8vkd' size='340' side='right'caption='[[8vkd]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[8vkd]] 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=8VKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8VKD 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]] 1.4&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4NC:4-NITROCATECHOL'>4NC</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=8vkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8vkd OCA], [https://pdbe.org/8vkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8vkd RCSB], [https://www.ebi.ac.uk/pdbsum/8vkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8vkd ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q9NAV8_9ANNE Q9NAV8_9ANNE] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Dehalperoxidase (DHP) has diverse catalytic activities depending on the substrate binding conformation, pH, and dynamics in the distal pocket above the heme. According to our hypothesis, the molecular structure of the substrate and binding orientation in DHP guide enzymatic function. Enzyme kinetic studies have shown that the catalytic activity of DHP B is significantly higher than that of DHP A despite 96% sequence homology. There are more than 30 substrate-bound structures with DHP B, each providing insight into the nature of enzymatic binding at the active site. By contrast, the only X-ray crystallographic structures of small molecules in a complex with DHP A are phenols. This study is focused on investigating substrate binding in DHP A to compare with DHP B structures. Fifteen substrates were selected that were known to bind to DHP B in the crystal to test whether soaking substrates into DHP A would yield similar structures. Five of these substrates yielded X-ray crystal structures of substrate-bound DHP A, namely, 2,4-dichlorophenol (1.48 A, PDB: 8EJN), 2,4-dibromophenol (1.52 A, PDB: 8VSK), 4-nitrophenol (2.03 A, PDB: 8VKC), 4-nitrocatechol (1.40 A, PDB: 8VKD), and 4-bromo-o-cresol (1.64 A, PDB: 8VZR). For the remaining substrates that bind to DHP B, such as cresols, 5-bromoindole, benzimidazole, 4,4-biphenol, 4.4-ethylidenebisphenol, 2,4-dimethoxyphenol, and guaiacol, the electron density maps in DHP A are not sufficient to determine the presence of the substrates, much less their orientation. In our hands, only phenols, 4-Br-o-cresol, and 4-nitrocatechol can be soaked into crystalline DHP A. None of the larger substrates were observed to bind. A minimum of seven hanging drops were selected for soaking with more than 50 crystals screened for each substrate. The five high-quality examples of direct comparison of modes of binding in DHP A and B for the same substrate provide further support for the hypothesis that the substrate-binding conformation determines the enzyme function of DHP.

Structural Comparison of Substrate Binding Sites in Dehaloperoxidase A and B.,Aktar MS, de Serrano V, Ghiladi RA, Franzen S Biochemistry. 2024 Jul 16;63(14):1761-1773. doi: 10.1021/acs.biochem.4c00179. , Epub 2024 Jul 3. PMID:38959050<ref>PMID:38959050</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 8vkd" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Amphitrite ornata]]
[[Category: Large Structures]]
[[Category: Aktar MS]]
[[Category: Franzen S]]
[[Category: Ghiladi RA]]
[[Category: De Serrano VS]]