|
|
| Line 3: |
Line 3: |
| | <StructureSection load='5kah' size='340' side='right'caption='[[5kah]], [[Resolution|resolution]] 2.78Å' scene=''> | | <StructureSection load='5kah' size='340' side='right'caption='[[5kah]], [[Resolution|resolution]] 2.78Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5kah]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptomyces_toyocaensis"_nishimura_et_al. "streptomyces toyocaensis" nishimura et al.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KAH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KAH FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5kah]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_toyocaensis Streptomyces toyocaensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KAH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KAH FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=YE1:[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL+(3R)-4-({3-[(2-{[(3,5-DIHYDROXYPHENYL)ACETYL]AMINO}ETHYL)AMINO]-3-OXOPROPYL}AMINO)-3-HYDROXY-2,2-DIMETHYL-4-OXOBUTYL+DIHYDROGEN+DIPHOSPHATE'>YE1</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]] 2.779Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5kag|5kag]], [[5kaj|5kaj]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=YE1:[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL+(3R)-4-({3-[(2-{[(3,5-DIHYDROXYPHENYL)ACETYL]AMINO}ETHYL)AMINO]-3-OXOPROPYL}AMINO)-3-HYDROXY-2,2-DIMETHYL-4-OXOBUTYL+DIHYDROGEN+DIPHOSPHATE'>YE1</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BU52_01220 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=55952 "Streptomyces toyocaensis" Nishimura et al.])</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=5kah FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kah OCA], [https://pdbe.org/5kah PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kah RCSB], [https://www.ebi.ac.uk/pdbsum/5kah PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kah 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/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.80 1.13.11.80] </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=5kah FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kah OCA], [http://pdbe.org/5kah PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kah RCSB], [http://www.ebi.ac.uk/pdbsum/5kah PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kah ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DPGC_STRTO DPGC_STRTO]] Involved in the biosynthesis of the nonproteinogenic amino acid monomer (S)-3,5-dihydroxyphenylglycine (Dpg) responsible of the production of vancomycin and teicoplanin antibiotics. Catalyzes the unusual conversion 3,5-dihydroxyphenylacetyl-CoA (DPA-CoA) to 3,5-dihydroxyphenylglyoxylate. DpgC performed a net four-electron oxidation of the benzylic carbon of DPA-CoA and the hydrolysis of the thioester bond to generate free CoA (PubMed:18004875, PubMed:17507985). DpgC has the ability to process a diverse range of substituted phenylacetyl-CoA substrates (PubMed:18004875).<ref>PMID:17507985</ref> <ref>PMID:18004875</ref> | + | [https://www.uniprot.org/uniprot/DPGC_STRTO DPGC_STRTO] Involved in the biosynthesis of the nonproteinogenic amino acid monomer (S)-3,5-dihydroxyphenylglycine (Dpg) responsible of the production of vancomycin and teicoplanin antibiotics. Catalyzes the unusual conversion 3,5-dihydroxyphenylacetyl-CoA (DPA-CoA) to 3,5-dihydroxyphenylglyoxylate. DpgC performed a net four-electron oxidation of the benzylic carbon of DPA-CoA and the hydrolysis of the thioester bond to generate free CoA (PubMed:18004875, PubMed:17507985). DpgC has the ability to process a diverse range of substituted phenylacetyl-CoA substrates (PubMed:18004875).<ref>PMID:17507985</ref> <ref>PMID:18004875</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 25: |
Line 23: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Streptomyces toyocaensis nishimura et al]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Oxidoreductase]] | + | [[Category: Streptomyces toyocaensis]] |
| - | [[Category: Bruner, S D]] | + | [[Category: Bruner SD]] |
| - | [[Category: Condurso, H L]] | + | [[Category: Condurso HL]] |
| - | [[Category: Fielding, E N]] | + | [[Category: Fielding EN]] |
| - | [[Category: Li, K]] | + | [[Category: Li K]] |
| - | [[Category: Dioxygenase]]
| + | |
| - | [[Category: Dpgc]]
| + | |
| Structural highlights
Function
DPGC_STRTO Involved in the biosynthesis of the nonproteinogenic amino acid monomer (S)-3,5-dihydroxyphenylglycine (Dpg) responsible of the production of vancomycin and teicoplanin antibiotics. Catalyzes the unusual conversion 3,5-dihydroxyphenylacetyl-CoA (DPA-CoA) to 3,5-dihydroxyphenylglyoxylate. DpgC performed a net four-electron oxidation of the benzylic carbon of DPA-CoA and the hydrolysis of the thioester bond to generate free CoA (PubMed:18004875, PubMed:17507985). DpgC has the ability to process a diverse range of substituted phenylacetyl-CoA substrates (PubMed:18004875).[1] [2]
Publication Abstract from PubMed
The enzyme DpgC is included in the small family of cofactor-independent dioxygenases. The chemistry of DpgC is uncommon as the protein binds and utilizes dioxygen without the aid of a metal or organic cofactor. Previous structural and biochemical studies identified the substrate-binding mode and the components of the active site that are important in the catalytic mechanism. In addition, the results delineated a putative binding pocket and migration pathway for the co-substrate dioxygen. Here, structural biology is utilized, along with site-directed mutagenesis, to probe the assigned dioxygen-binding pocket. The key residues implicated in dioxygen trafficking were studied to probe the process of binding, activation and chemistry. The results support the proposed chemistry and provide insight into the general mechanism of dioxygen binding and activation.
Probing the structural basis of oxygen binding in a cofactor-independent dioxygenase.,Li K, Fielding EN, Condurso HL, Bruner SD Acta Crystallogr D Struct Biol. 2017 Jul 1;73(Pt 7):573-580. doi:, 10.1107/S2059798317007045. Epub 2017 Jun 30. PMID:28695857[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Widboom PF, Fielding EN, Liu Y, Bruner SD. Structural basis for cofactor-independent dioxygenation in vancomycin biosynthesis. Nature. 2007 May 17;447(7142):342-5. PMID:17507985 doi:http://dx.doi.org/10.1038/nature05702
- ↑ Fielding EN, Widboom PF, Bruner SD. Substrate recognition and catalysis by the cofactor-independent dioxygenase DpgC. Biochemistry. 2007 Dec 11;46(49):13994-4000. Epub 2007 Nov 16. PMID:18004875 doi:10.1021/bi701148b
- ↑ Li K, Fielding EN, Condurso HL, Bruner SD. Probing the structural basis of oxygen binding in a cofactor-independent dioxygenase. Acta Crystallogr D Struct Biol. 2017 Jul 1;73(Pt 7):573-580. doi:, 10.1107/S2059798317007045. Epub 2017 Jun 30. PMID:28695857 doi:http://dx.doi.org/10.1107/S2059798317007045
|
