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| | ==Crystal structure of D141E variant of B. pseudomallei KatG== | | ==Crystal structure of D141E variant of B. pseudomallei KatG== |
| - | <StructureSection load='5sx1' size='340' side='right' caption='[[5sx1]], [[Resolution|resolution]] 1.80Å' scene=''> | + | <StructureSection load='5sx1' size='340' side='right'caption='[[5sx1]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5sx1]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2dv1 2dv1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SX1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5SX1 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5sx1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_pseudomallei_1710b Burkholderia pseudomallei 1710b]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2dv1 2dv1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SX1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5SX1 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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]] 1.8Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5l02|5l02]], [[5l05|5l05]], [[5sw4|5sw4]], [[5sw5|5sw5]], [[5sw6|5sw6]], [[5sx0|5sx0]], [[5sx2|5sx2]], [[5sx3|5sx3]], [[5sx6|5sx6]], [[5sx7|5sx7]], [[5sxq|5sxq]], [[5sxr|5sxr]], [[5sxs|5sxs]], [[5sxt|5sxt]], [[5sxx|5sxx]], [[5syh|5syh]], [[5syi|5syi]], [[5syj|5syj]], [[5syk|5syk]], [[5syl|5syl]], [[5syu|5syu]], [[5syv|5syv]], [[5syw|5syw]], [[5syx|5syx]], [[5syy|5syy]]</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=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catalase_peroxidase Catalase peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.21 1.11.1.21] </span></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=5sx1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5sx1 OCA], [https://pdbe.org/5sx1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5sx1 RCSB], [https://www.ebi.ac.uk/pdbsum/5sx1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5sx1 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5sx1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5sx1 OCA], [http://pdbe.org/5sx1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5sx1 RCSB], [http://www.ebi.ac.uk/pdbsum/5sx1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5sx1 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/KATG_BURP1 KATG_BURP1]] Bifunctional enzyme with both catalase and broad-spectrum peroxidase activity. | + | [https://www.uniprot.org/uniprot/KATG_BURP1 KATG_BURP1] Bifunctional enzyme with both catalase and broad-spectrum peroxidase activity. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[Catalase|Catalase]] | + | *[[Catalase 3D structures|Catalase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Catalase peroxidase]] | + | [[Category: Burkholderia pseudomallei 1710b]] |
| - | [[Category: Loewen, P C]] | + | [[Category: Large Structures]] |
| - | [[Category: Catalase-peroxidase]] | + | [[Category: Loewen PC]] |
| - | [[Category: Katg]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
5sx1 is a 2 chain structure with sequence from Burkholderia pseudomallei 1710b. This structure supersedes the now removed PDB entry 2dv1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.8Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
KATG_BURP1 Bifunctional enzyme with both catalase and broad-spectrum peroxidase activity.
Publication Abstract from PubMed
Five residues in the multifunctional catalase-peroxidase KatG of Burkholderia pesudomallei are essential for catalase, but not peroxidase, activity. Asp141 is the only one of these catalase-specific residues not related with the covalent adduct found in KatGs that when replaced with a nonacidic residue reduces catalase activity to 5% of native levels. Replacing the nearby catalytic residue Arg108 causes a reduction in catalase activity to 35% of native levels, whereas a variant with both Asp141 and Arg108 replaced exhibits near normal catalase activity (82% of native), suggesting a synergism in the roles of the two residues in support of catalase activity in the enzyme. Among the Asp141 variants, D141E is unique in retaining normal catalase activity but with modified kinetics, suggesting more favorable compound I formation and less favorable compound I reduction. The crystal structure of the D141E variant has been determined at 1.8-A resolution, revealing that the carboxylate of Glu141 is moved only slightly compared with Asp141, but retains its hydrogen bond interaction with the main chain nitrogen of Ile237. In contrast, the low temperature ferric Electron Paramagnetic Resonance spectra of the D141A, R108A, and R108A/D141A variants are consistent with modifications of the water matrix and/or the relative positioning of the distal residue side chains. Such changes explain the reduction in catalase activity in all but the double variant R108A/D141A. Two pathways of hydrogen bonded solvent lead from the entrance channel into the heme active site, one running between Asp141 and Arg108 and the second between Asp141 and the main chain atoms of residues 237-239. It is proposed that binding of substrate H(2)O(2) to Asp141 and Arg108 controls H(2)O(2) access to the heme active site, thereby modulating the catalase reaction.
Two alternative substrate paths for compound I formation and reduction in catalase-peroxidase KatG from Burkholderia pseudomallei.,Deemagarn T, Wiseman B, Carpena X, Ivancich A, Fita I, Loewen PC Proteins. 2007 Jan 1;66(1):219-28. PMID:17063492[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Deemagarn T, Wiseman B, Carpena X, Ivancich A, Fita I, Loewen PC. Two alternative substrate paths for compound I formation and reduction in catalase-peroxidase KatG from Burkholderia pseudomallei. Proteins. 2007 Jan 1;66(1):219-28. PMID:17063492 doi:http://dx.doi.org/10.1002/prot.21209
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