7arp: Difference between revisions
No edit summary |
No edit summary |
||
| (One intermediate revision by the same user not shown) | |||
| Line 1: | Line 1: | ||
==Native L-2-haloacid dehalogenase from Zobellia galactanivorans== | ==Native L-2-haloacid dehalogenase from Zobellia galactanivorans== | ||
<StructureSection load='7arp' size='340' side='right'caption='[[7arp]]' scene=''> | <StructureSection load='7arp' size='340' side='right'caption='[[7arp]], [[Resolution|resolution]] 1.78Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ARP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ARP FirstGlance]. <br> | <table><tr><td colspan='2'>[[7arp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Zobellia_galactanivorans Zobellia galactanivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ARP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ARP FirstGlance]. <br> | ||
</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=7arp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7arp OCA], [https://pdbe.org/7arp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7arp RCSB], [https://www.ebi.ac.uk/pdbsum/7arp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7arp ProSAT]</span></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]] 1.78Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</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=7arp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7arp OCA], [https://pdbe.org/7arp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7arp RCSB], [https://www.ebi.ac.uk/pdbsum/7arp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7arp ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/G0L7V6_ZOBGA G0L7V6_ZOBGA] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Haloacid dehalogenases are potentially involved in bioremediation of contaminated environments and few have been biochemically characterized from marine organisms. The L-2-haloacid dehalogenase (L-2-HAD) from the marine Bacteroidetes Zobellia galactanivorans Dsij(T) (ZgHAD) has been shown to catalyze the dehalogenation of C2 and C3 short-chain L-2-haloalkanoic acids. To better understand its catalytic properties, its enzymatic stability, active site and 3D structure were analyzed. ZgHAD demonstrates high stability to solvents and a conserved catalytic activity when heated up to 60 degrees C, its melting temperature being at 65 degrees C. The X-ray structure of the recombinant enzyme was solved by molecular replacement. The enzyme folds as a homodimer and its active site is very similar to DehRhb, the other known L-2-HAD from a marine Rhodobacteraceae. Marked differences are present in the putative substrate entrance sites of the two enzymes. The H179 amino acid potentially involved in the activation of a catalytic water molecule was confirmed as catalytic amino acid through the production of two inactive site-directed mutants. The crystal packing of 13 dimers in the asymmetric unit of an active-site mutant, ZgHAD-H179N, reveals domain movements of the monomeric subunits relative to each other. The involvement of a catalytic His/Glu dyad and substrate binding amino acids was further confirmed by computational docking. All together our results give new insights into the catalytic mechanism of the group of marine L-2-HAD. This article is protected by copyright. All rights reserved. | |||
X-ray structure and mechanism of ZgHAD, a L-2-haloacid dehalogenase from the marine Flavobacterium Zobellia galactanivorans.,Grigorian E, Roret T, Czjzek M, Leblanc C, Delage L Protein Sci. 2022 Dec 10:e4540. doi: 10.1002/pro.4540. PMID:36502283<ref>PMID:36502283</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7arp" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Dehalogenase 3D structures|Dehalogenase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Zobellia galactanivorans]] | |||
[[Category: Czjzek M]] | [[Category: Czjzek M]] | ||
[[Category: Delage L]] | [[Category: Delage L]] | ||
Latest revision as of 15:15, 1 February 2024
Native L-2-haloacid dehalogenase from Zobellia galactanivoransNative L-2-haloacid dehalogenase from Zobellia galactanivorans
Structural highlights
FunctionPublication Abstract from PubMedHaloacid dehalogenases are potentially involved in bioremediation of contaminated environments and few have been biochemically characterized from marine organisms. The L-2-haloacid dehalogenase (L-2-HAD) from the marine Bacteroidetes Zobellia galactanivorans Dsij(T) (ZgHAD) has been shown to catalyze the dehalogenation of C2 and C3 short-chain L-2-haloalkanoic acids. To better understand its catalytic properties, its enzymatic stability, active site and 3D structure were analyzed. ZgHAD demonstrates high stability to solvents and a conserved catalytic activity when heated up to 60 degrees C, its melting temperature being at 65 degrees C. The X-ray structure of the recombinant enzyme was solved by molecular replacement. The enzyme folds as a homodimer and its active site is very similar to DehRhb, the other known L-2-HAD from a marine Rhodobacteraceae. Marked differences are present in the putative substrate entrance sites of the two enzymes. The H179 amino acid potentially involved in the activation of a catalytic water molecule was confirmed as catalytic amino acid through the production of two inactive site-directed mutants. The crystal packing of 13 dimers in the asymmetric unit of an active-site mutant, ZgHAD-H179N, reveals domain movements of the monomeric subunits relative to each other. The involvement of a catalytic His/Glu dyad and substrate binding amino acids was further confirmed by computational docking. All together our results give new insights into the catalytic mechanism of the group of marine L-2-HAD. This article is protected by copyright. All rights reserved. X-ray structure and mechanism of ZgHAD, a L-2-haloacid dehalogenase from the marine Flavobacterium Zobellia galactanivorans.,Grigorian E, Roret T, Czjzek M, Leblanc C, Delage L Protein Sci. 2022 Dec 10:e4540. doi: 10.1002/pro.4540. PMID:36502283[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||