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| | ==Structure of Sorghum peroxidase== | | ==Structure of Sorghum peroxidase== |
| - | <StructureSection load='5aog' size='340' side='right' caption='[[5aog]], [[Resolution|resolution]] 1.27Å' scene=''> | + | <StructureSection load='5aog' size='340' side='right'caption='[[5aog]], [[Resolution|resolution]] 1.27Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5aog]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sorghum_bicolor Sorghum bicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AOG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AOG FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5aog]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sorghum_bicolor Sorghum bicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AOG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AOG FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IAC:1H-INDOL-3-YLACETIC+ACID'>IAC</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</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]] 1.27Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxidase Peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.7 1.11.1.7] </span></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IAC:1H-INDOL-3-YLACETIC+ACID'>IAC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></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=5aog FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5aog OCA], [http://pdbe.org/5aog PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5aog RCSB], [http://www.ebi.ac.uk/pdbsum/5aog PDBsum]</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=5aog FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5aog OCA], [https://pdbe.org/5aog PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5aog RCSB], [https://www.ebi.ac.uk/pdbsum/5aog PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5aog ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PER1_SORBI PER1_SORBI]] Removal of H(2)O(2), oxidation of toxic reductants, biosynthesis and degradation of lignin, suberization, auxin catabolism, response to environmental stresses such as wounding, pathogen attack and oxidative stress. These functions might be dependent on each isozyme/isoform in each plant tissue. Has a high preference for hydroxycinnamates as substrates. Substrate preference is ferulic acid > p-coumaric acid > N-acetyl tyrosine methyl ester > N-acetyl-tyrosine > tyrosine > catechol > Gly-Tyr-Gly. May be involved in the formation of diferulate linkages in the plant cell wall.[PROSITE-ProRule:PRU00297]<ref>PMID:16650004</ref> | + | [https://www.uniprot.org/uniprot/PER1_SORBI PER1_SORBI] Removal of H(2)O(2), oxidation of toxic reductants, biosynthesis and degradation of lignin, suberization, auxin catabolism, response to environmental stresses such as wounding, pathogen attack and oxidative stress. These functions might be dependent on each isozyme/isoform in each plant tissue. Has a high preference for hydroxycinnamates as substrates. Substrate preference is ferulic acid > p-coumaric acid > N-acetyl tyrosine methyl ester > N-acetyl-tyrosine > tyrosine > catechol > Gly-Tyr-Gly. May be involved in the formation of diferulate linkages in the plant cell wall.[PROSITE-ProRule:PRU00297]<ref>PMID:16650004</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Peroxidase]] | + | [[Category: Large Structures]] |
| | [[Category: Sorghum bicolor]] | | [[Category: Sorghum bicolor]] |
| - | [[Category: Agirre, J]] | + | [[Category: Agirre J]] |
| - | [[Category: Basran, J]] | + | [[Category: Basran J]] |
| - | [[Category: Efimov, I]] | + | [[Category: Efimov I]] |
| - | [[Category: Kwon, H]] | + | [[Category: Kwon H]] |
| - | [[Category: Moody, P C.E]] | + | [[Category: Moody PCE]] |
| - | [[Category: Nnamchi, C I]] | + | [[Category: Nnamchi CI]] |
| - | [[Category: Parkin, G]] | + | [[Category: Parkin G]] |
| - | [[Category: Raven, E L]] | + | [[Category: Raven EL]] |
| - | [[Category: Glycoslylation]]
| + | |
| - | [[Category: Heme peroxidase]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Plant peroxidase]]
| + | |
| - | [[Category: Sorghum]]
| + | |
| Structural highlights
5aog is a 1 chain structure with sequence from Sorghum bicolor. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.27Å |
| Ligands: | , , , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
PER1_SORBI Removal of H(2)O(2), oxidation of toxic reductants, biosynthesis and degradation of lignin, suberization, auxin catabolism, response to environmental stresses such as wounding, pathogen attack and oxidative stress. These functions might be dependent on each isozyme/isoform in each plant tissue. Has a high preference for hydroxycinnamates as substrates. Substrate preference is ferulic acid > p-coumaric acid > N-acetyl tyrosine methyl ester > N-acetyl-tyrosine > tyrosine > catechol > Gly-Tyr-Gly. May be involved in the formation of diferulate linkages in the plant cell wall.[PROSITE-ProRule:PRU00297][1]
Publication Abstract from PubMed
A cationic class III peroxidase from Sorghum bicolor was purified to homogeneity. The enzyme contains a high-spin heme, as evidenced by UV-visible spectroscopy and EPR. Steady state oxidation of guaiacol was demonstrated and the enzyme was shown to have higher activity in the presence of calcium ions. A FeIII/FeII reduction potential of -266 mV vs NHE was determined. Stopped-flow experiments with H2O2 showed formation of a typical peroxidase Compound I species, which converts to Compound II in the presence of calcium. A crystal structure of the enzyme is reported, the first for a sorghum peroxidase. The structure reveals an active site that is analogous to those for other class I heme peroxidase, and a substrate binding site (assigned as arising from binding of indole-3-acetic acid) at the gamma-heme edge. Metal binding sites are observed in the structure on the distal (assigned as a Na+ ion) and proximal (assigned as a Ca2+) sides of the heme, which is consistent with the Ca2+-dependence of the steady state and pre-steady state kinetics. It is probably the case that the structural integrity (and, thus, the catalytic activity) of the sorghum enzyme is dependent on metal ion incorporation at these positions.
Structural and spectroscopic characterisation of a heme peroxidase from sorghum.,Nnamchi CI, Parkin G, Efimov I, Basran J, Kwon H, Svistunenko DA, Agirre J, Okolo BN, Moneke A, Nwanguma BC, Moody PC, Raven EL J Biol Inorg Chem. 2015 Dec 14. PMID:26666777[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Dicko MH, Gruppen H, Hilhorst R, Voragen AG, van Berkel WJ. Biochemical characterization of the major sorghum grain peroxidase. FEBS J. 2006 May;273(10):2293-307. PMID:16650004 doi:http://dx.doi.org/EJB5243
- ↑ Nnamchi CI, Parkin G, Efimov I, Basran J, Kwon H, Svistunenko DA, Agirre J, Okolo BN, Moneke A, Nwanguma BC, Moody PC, Raven EL. Structural and spectroscopic characterisation of a heme peroxidase from sorghum. J Biol Inorg Chem. 2015 Dec 14. PMID:26666777 doi:http://dx.doi.org/10.1007/s00775-015-1313-z
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