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| | ==Crystal structure of Burkholderia pseudomallei KatG N240D variant== | | ==Crystal structure of Burkholderia pseudomallei KatG N240D variant== |
| - | <StructureSection load='5syv' size='340' side='right' caption='[[5syv]], [[Resolution|resolution]] 1.75Å' scene=''> | + | <StructureSection load='5syv' size='340' side='right'caption='[[5syv]], [[Resolution|resolution]] 1.75Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5syv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Burp1 Burp1]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4qzl 4qzl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SYV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5SYV FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5syv]] 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=4qzl 4qzl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SYV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5SYV FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <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]] 1.75Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TOX:1-HYDROPEROXY-L-TRYPTOPHAN'>TOX</scene></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <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>, <scene name='pdbligand=TOX:1-HYDROPEROXY-L-TRYPTOPHAN'>TOX</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">katG, BURPS1710b_3366 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320372 BURP1])</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=5syv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5syv OCA], [https://pdbe.org/5syv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5syv RCSB], [https://www.ebi.ac.uk/pdbsum/5syv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5syv ProSAT]</span></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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5syv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5syv OCA], [http://pdbe.org/5syv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5syv RCSB], [http://www.ebi.ac.uk/pdbsum/5syv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5syv 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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| | </div> | | </div> |
| | <div class="pdbe-citations 5syv" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 5syv" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Catalase 3D structures|Catalase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Burp1]] | + | [[Category: Burkholderia pseudomallei 1710b]] |
| - | [[Category: Catalase peroxidase]] | + | [[Category: Large Structures]] |
| - | [[Category: Loewen, P C]] | + | [[Category: Loewen PC]] |
| - | [[Category: Catalase-peroxidase]]
| + | |
| - | [[Category: Katg]]
| + | |
| - | [[Category: N240d variant]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
5syv is a 2 chain structure with sequence from Burkholderia pseudomallei 1710b. This structure supersedes the now removed PDB entry 4qzl. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.75Å |
| 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
The unusual Met-Tyr-Trp adduct composed of cross-linked side chains along with an associated mobile Arg is essential for catalase activity in catalase-peroxidases. In addition, acidic residues in the entrance channel, in particular an Asp and a Glu approximately 7 and approximately 15 A, respectively, from the heme, significantly enhance catalase activity. The mechanism by which these channel carboxylates influence catalase activity is the focus of this work. Seventeen new variants with fewer and additional acidic residues have been constructed and characterized structurally and for enzymatic activity, revealing that their effect on activity is roughly inversely proportional to their distance from the heme and adduct, suggesting that the electrostatic potential of the heme cavity may be affected. A discrete group of protonable residues are contained within a 15 A sphere surrounding the heme iron, and a computational analysis reveals that the pKa of the distal His112, alone, is modulated within the pH range of catalase activity by the remote acidic residues in a pattern consistent with its protonated form having a key role in the catalase reaction cycle. The electrostatic potential also impacts the catalatic reaction through its influence on the charged status of the Met-Tyr-Trp adduct.
The Catalase Activity of Catalase-Peroxidases Is Modulated by Changes in the pKa of the Distal Histidine.,Machuqueiro M, Victor B, Switala J, Villanueva J, Rovira C, Fita I, Loewen PC Biochemistry. 2017 Apr 20. doi: 10.1021/acs.biochem.6b01276. PMID:28409923[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Machuqueiro M, Victor B, Switala J, Villanueva J, Rovira C, Fita I, Loewen PC. The Catalase Activity of Catalase-Peroxidases Is Modulated by Changes in the pKa of the Distal Histidine. Biochemistry. 2017 Apr 20. doi: 10.1021/acs.biochem.6b01276. PMID:28409923 doi:http://dx.doi.org/10.1021/acs.biochem.6b01276
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