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| | ==Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant== | | ==Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant== |
| - | <StructureSection load='3rzz' size='340' side='right' caption='[[3rzz]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='3rzz' size='340' side='right'caption='[[3rzz]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3rzz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_viridochromogenes Streptomyces viridochromogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RZZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RZZ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3rzz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_viridochromogenes Streptomyces viridochromogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RZZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RZZ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</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]] 2.2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3gbf|3gbf]], [[3g7d|3g7d]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">phpD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1938 Streptomyces viridochromogenes])</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=3rzz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rzz OCA], [https://pdbe.org/3rzz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rzz RCSB], [https://www.ebi.ac.uk/pdbsum/3rzz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rzz 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=3rzz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rzz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rzz RCSB], [http://www.ebi.ac.uk/pdbsum/3rzz PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/Q5IW40_STRVR Q5IW40_STRVR]] Non-heme-dependent dioxygenase that catalyzes the conversion of 2-hydroxyethylphosphonate (HEP) to hydroxymethylphosphonate (HMP) in the biosynthesis of phosphinothricin tripeptide (PTT). PTT contains the unusual amino acid phosphinothricin attached to 2 alanine residues. Synthetic phosphinothricin (glufosinate) is a key component of commercial herbicides.<ref>PMID:17632514</ref> <ref>PMID:19839620</ref> <ref>PMID:21381767</ref> <ref>PMID:19516340</ref> <ref>PMID:21711001</ref> | + | [https://www.uniprot.org/uniprot/HEPD_STRVT HEPD_STRVT] Non-heme-dependent dioxygenase that catalyzes the conversion of 2-hydroxyethylphosphonate (HEP) to hydroxymethylphosphonate (HMP) in the biosynthesis of phosphinothricin tripeptide (PTT). PTT contains the unusual amino acid phosphinothricin attached to 2 alanine residues. Synthetic phosphinothricin (glufosinate) is a key component of commercial herbicides.<ref>PMID:17632514</ref> <ref>PMID:19516340</ref> <ref>PMID:19839620</ref> <ref>PMID:21381767</ref> <ref>PMID:21711001</ref> |
| - | <div style="background-color:#fffaf0;">
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| - | == Publication Abstract from PubMed ==
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| - | HEPD belongs to the superfamily of 2-His-1-carboxylate non-heme iron-dependent dioxygenases. It converts 2-hydroxyethylphosphonate (2-HEP) to hydroxymethylphosphonate (HMP) and formate. Previously postulated mechanisms for the reaction catalyzed by HEPD cannot explain its conversion of 1-HEP to acetylphosphate. Alternative mechanisms that involve either phosphite or methylphosphonate as intermediates, which potentially explain all experimental studies including isotope labeling experiments and use of substrate analogues, were investigated. The results of these studies reveal that these alternative mechanisms are not correct. Site-directed mutagenesis studies of Lys16, Arg90, and Tyr98 support roles of these residues in binding of 2-HEP. Mutation of Lys16 to Ala resulted in an inactive enzyme, whereas mutation of Arg90 to Ala or Tyr98 to Phe greatly decreased k(cat)/K(m,2-HEP). Furthermore, the latter mutants could not be saturated in O(2). These results suggest that proper binding of 2-HEP is important for O(2) activation and that the enzyme uses a compulsory binding order with 2-HEP binding before O(2). The Y98F mutant produces methylphosphonate as a minor side product providing indirect support for the proposal that the last step during catalysis involves a ferric hydroxide reacting with a methylphosphonate radical.
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| - | Mechanism and Substrate Recognition of 2-Hydroxyethylphosphonate Dioxygenase.,Peck SC, Cooke HA, Cicchillo RM, Malova P, Hammerschmidt F, Nair SK, van der Donk WA Biochemistry. 2011 Jul 8. PMID:21711001<ref>PMID:21711001</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | ==See Also== |
| - | </div>
| + | *[[Dioxygenase 3D structures|Dioxygenase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[Category: Streptomyces viridochromogenes]] | | [[Category: Streptomyces viridochromogenes]] |
| - | [[Category: Cooke, H A]] | + | [[Category: Cooke HA]] |
| - | [[Category: Biosynthetic protein]]
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| - | [[Category: Cupin]]
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| - | [[Category: Oxidoreductase]]
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| Structural highlights
Function
HEPD_STRVT Non-heme-dependent dioxygenase that catalyzes the conversion of 2-hydroxyethylphosphonate (HEP) to hydroxymethylphosphonate (HMP) in the biosynthesis of phosphinothricin tripeptide (PTT). PTT contains the unusual amino acid phosphinothricin attached to 2 alanine residues. Synthetic phosphinothricin (glufosinate) is a key component of commercial herbicides.[1] [2] [3] [4] [5]
See Also
References
- ↑ Blodgett JA, Thomas PM, Li G, Velasquez JE, van der Donk WA, Kelleher NL, Metcalf WW. Unusual transformations in the biosynthesis of the antibiotic phosphinothricin tripeptide. Nat Chem Biol. 2007 Aug;3(8):480-5. Epub 2007 Jul 15. PMID:17632514 doi:http://dx.doi.org/10.1038/nchembio.2007.9
- ↑ Cicchillo RM, Zhang H, Blodgett JA, Whitteck JT, Li G, Nair SK, van der Donk WA, Metcalf WW. An unusual carbon-carbon bond cleavage reaction during phosphinothricin biosynthesis. Nature. 2009 Jun 11;459(7248):871-4. PMID:19516340 doi:10.1038/nature07972
- ↑ Whitteck JT, Cicchillo RM, van der Donk WA. Hydroperoxylation by hydroxyethylphosphonate dioxygenase. J Am Chem Soc. 2009 Nov 11;131(44):16225-32. doi: 10.1021/ja906238r. PMID:19839620 doi:http://dx.doi.org/10.1021/ja906238r
- ↑ Whitteck JT, Malova P, Peck SC, Cicchillo RM, Hammerschmidt F, van der Donk WA. On the stereochemistry of 2-hydroxyethylphosphonate dioxygenase. J Am Chem Soc. 2011 Mar 30;133(12):4236-9. doi: 10.1021/ja1113326. Epub 2011 Mar , 7. PMID:21381767 doi:http://dx.doi.org/10.1021/ja1113326
- ↑ Peck SC, Cooke HA, Cicchillo RM, Malova P, Hammerschmidt F, Nair SK, van der Donk WA. Mechanism and Substrate Recognition of 2-Hydroxyethylphosphonate Dioxygenase. Biochemistry. 2011 Jul 8. PMID:21711001 doi:10.1021/bi200804r
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