2ymm: Difference between revisions
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== | ==Sulfate bound L-haloacid dehalogenase from a Rhodobacteraceae family bacterium== | ||
[[2ymm]] is a 4 chain structure with sequence from [ | <StructureSection load='2ymm' size='340' side='right'caption='[[2ymm]], [[Resolution|resolution]] 1.64Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2ymm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodobacteraceae Rhodobacteraceae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YMM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YMM 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]] 1.64Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=2ymm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ymm OCA], [https://pdbe.org/2ymm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ymm RCSB], [https://www.ebi.ac.uk/pdbsum/2ymm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ymm ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/R4GRT2_9RHOB R4GRT2_9RHOB] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The putative l-haloacid dehalogenase gene (DehRhb) from a marine Rhodobacteraceae family was cloned and overexpressed in Escherichia coli. The DehRhb protein was shown to be an l-haloacid dehalogenase with highest activity towards brominated substrates with short carbon chains (</= C3). The optimal temperature for enzyme activity was 55 degrees C, and the Vmax and Km were 1.75 mum.min(-1) .mg(-1) of protein and 6.72 mm, respectively, when using monobromoacetic acid as a substrate. DehRhb showed moderate thermal stability, with a melting temperature of 67 degrees C. The enzyme demonstrated high tolerance to solvents, as shown by thermal shift experiments and solvent incubation assays. The DehRhb protein was crystallized and structures of the native, reaction intermediate and substrate-bound forms were determined. The active site of DehRhb had significant differences from previously studied l-haloacid dehalogenases. The asparagine and arginine residues shown to be essential for catalytic activity in other l-haloacid dehalogenases are not present in DehRhb. The histidine residue which replaces the asparagine residue in DehRhb was coordinated by a conformationally strained glutamate residue that replaces a conserved glycine. The His/Glu dyad is positioned for deprotonation of the catalytic water which attacks the ester bond in the reaction intermediate. The catalytic water in DehRhb is shifted by ~ 1.5 A from its position in other l-haloacid dehalogenases. A similar His/Glu or Asp dyad is known to activate the catalytic water in haloalkane dehalogenases. The DehRhb enzyme represents a novel member within the l-haloacid dehalogenase family and it has potential to be used as a commercial biocatalyst. DATABASE: The coordinates and structure factors of the crystal structures have been deposited in the Protein Data Bank with the codes 2yml, 2ymm, 2ymp, 2ymq and 2yn4. Nucleotide sequence data has been deposited in the GenBank database under the accession number JX868516. | |||
Marine Rhodobacteraceae l-haloacid dehalogenase contains a novel His/Glu dyad that could activate the catalytic water.,Novak HR, Sayer C, Isupov MN, Paszkiewicz K, Gotz D, Mearns Spragg A, Littlechild JA FEBS J. 2013 Apr;280(7):1664-80. doi: 10.1111/febs.12177. Epub 2013 Mar 8. PMID:23384397<ref>PMID:23384397</ref> | |||
<ref | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2ymm" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Dehalogenase 3D structures|Dehalogenase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Rhodobacteraceae]] | [[Category: Rhodobacteraceae]] | ||
[[Category: Gotz | [[Category: Gotz D]] | ||
[[Category: Isupov | [[Category: Isupov MN]] | ||
[[Category: Littlechild | [[Category: Littlechild JA]] | ||
[[Category: Novak | [[Category: Novak HR]] | ||
[[Category: Paszkiewicz | [[Category: Paszkiewicz K]] | ||
[[Category: Sayer | [[Category: Sayer C]] | ||
[[Category: Spragg | [[Category: Spragg AM]] | ||
Latest revision as of 13:55, 20 December 2023
Sulfate bound L-haloacid dehalogenase from a Rhodobacteraceae family bacteriumSulfate bound L-haloacid dehalogenase from a Rhodobacteraceae family bacterium
Structural highlights
FunctionPublication Abstract from PubMedThe putative l-haloacid dehalogenase gene (DehRhb) from a marine Rhodobacteraceae family was cloned and overexpressed in Escherichia coli. The DehRhb protein was shown to be an l-haloacid dehalogenase with highest activity towards brominated substrates with short carbon chains (</= C3). The optimal temperature for enzyme activity was 55 degrees C, and the Vmax and Km were 1.75 mum.min(-1) .mg(-1) of protein and 6.72 mm, respectively, when using monobromoacetic acid as a substrate. DehRhb showed moderate thermal stability, with a melting temperature of 67 degrees C. The enzyme demonstrated high tolerance to solvents, as shown by thermal shift experiments and solvent incubation assays. The DehRhb protein was crystallized and structures of the native, reaction intermediate and substrate-bound forms were determined. The active site of DehRhb had significant differences from previously studied l-haloacid dehalogenases. The asparagine and arginine residues shown to be essential for catalytic activity in other l-haloacid dehalogenases are not present in DehRhb. The histidine residue which replaces the asparagine residue in DehRhb was coordinated by a conformationally strained glutamate residue that replaces a conserved glycine. The His/Glu dyad is positioned for deprotonation of the catalytic water which attacks the ester bond in the reaction intermediate. The catalytic water in DehRhb is shifted by ~ 1.5 A from its position in other l-haloacid dehalogenases. A similar His/Glu or Asp dyad is known to activate the catalytic water in haloalkane dehalogenases. The DehRhb enzyme represents a novel member within the l-haloacid dehalogenase family and it has potential to be used as a commercial biocatalyst. DATABASE: The coordinates and structure factors of the crystal structures have been deposited in the Protein Data Bank with the codes 2yml, 2ymm, 2ymp, 2ymq and 2yn4. Nucleotide sequence data has been deposited in the GenBank database under the accession number JX868516. Marine Rhodobacteraceae l-haloacid dehalogenase contains a novel His/Glu dyad that could activate the catalytic water.,Novak HR, Sayer C, Isupov MN, Paszkiewicz K, Gotz D, Mearns Spragg A, Littlechild JA FEBS J. 2013 Apr;280(7):1664-80. doi: 10.1111/febs.12177. Epub 2013 Mar 8. PMID:23384397[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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