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| | <StructureSection load='6y12' size='340' side='right'caption='[[6y12]], [[Resolution|resolution]] 1.70Å' scene=''> | | <StructureSection load='6y12' size='340' side='right'caption='[[6y12]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6y12]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/As_4.1305 As 4.1305]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y12 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Y12 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6y12]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_vinaceus Streptomyces vinaceus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y12 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y12 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=ZZU:(2S,3S)-3-HYDROXYARGININE'>ZZU</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]] 1.7Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6alr|6alr]], [[2wbo|2wbo]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=ZZU:(2S,3S)-3-HYDROXYARGININE'>ZZU</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">vioC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1960 AS 4.1305])</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=6y12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y12 OCA], [https://pdbe.org/6y12 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y12 RCSB], [https://www.ebi.ac.uk/pdbsum/6y12 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y12 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=1.14.11.41 1.14.11.41] </span></td></tr> | + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6y12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y12 OCA], [http://pdbe.org/6y12 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6y12 RCSB], [http://www.ebi.ac.uk/pdbsum/6y12 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6y12 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/ARGHX_STRVI ARGHX_STRVI]] Involved in the biosynthesis of capreomycidine, an unusual amino acid used by non-ribosomal peptide synthases (NRPS) to make the tuberactinomycin class of peptide antibiotics such as viomycin and capreomycin. Catalyzes the stereospecific hydroxylation of the C3 of (2S)-arginine to generate (3S)-hydroxy-(2S)-arginine. Usually clavaminic acid synthase-like oxygenases catalyze the formation of threo diastereomers, however VioC produces the erythro diastereomer of beta-carbon-hydroxylated L-arginine. It exerts a broad substrate specificity by accepting the analogs L-homoarginine and L-canavanine for the beta-carbon hydroxylation.<ref>PMID:15368580</ref> <ref>PMID:15368582</ref> <ref>PMID:19490124</ref> | + | [https://www.uniprot.org/uniprot/ARGHX_STRVI ARGHX_STRVI] Involved in the biosynthesis of capreomycidine, an unusual amino acid used by non-ribosomal peptide synthases (NRPS) to make the tuberactinomycin class of peptide antibiotics such as viomycin and capreomycin. Catalyzes the stereospecific hydroxylation of the C3 of (2S)-arginine to generate (3S)-hydroxy-(2S)-arginine. Usually clavaminic acid synthase-like oxygenases catalyze the formation of threo diastereomers, however VioC produces the erythro diastereomer of beta-carbon-hydroxylated L-arginine. It exerts a broad substrate specificity by accepting the analogs L-homoarginine and L-canavanine for the beta-carbon hydroxylation.<ref>PMID:15368580</ref> <ref>PMID:15368582</ref> <ref>PMID:19490124</ref> |
| | <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 6y12" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6y12" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Hydroxylases 3D structures|Hydroxylases 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: As 4 1305]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Oxidoreductase]] | + | [[Category: Streptomyces vinaceus]] |
| - | [[Category: Aller, P]] | + | [[Category: Aller P]] |
| - | [[Category: Axford, D]] | + | [[Category: Axford D]] |
| - | [[Category: Beale, J H]] | + | [[Category: Beale JH]] |
| - | [[Category: Butryn, A]] | + | [[Category: Butryn A]] |
| - | [[Category: Dirr, A S]] | + | [[Category: Dirr AS]] |
| - | [[Category: Kamps, J J.A G]] | + | [[Category: Kamps JJAG]] |
| - | [[Category: Lang, P A]] | + | [[Category: Lang PA]] |
| - | [[Category: Leissing, T M]] | + | [[Category: Leissing TM]] |
| - | [[Category: McDonough, M A]] | + | [[Category: McDonough MA]] |
| - | [[Category: Orville, A M]] | + | [[Category: Orville AM]] |
| - | [[Category: Owen, R]] | + | [[Category: Owen R]] |
| - | [[Category: Rabe, P]] | + | [[Category: Rabe P]] |
| - | [[Category: Schofield, C J]] | + | [[Category: Schofield CJ]] |
| - | [[Category: Arginine hydroxylase]]
| + | |
| - | [[Category: Iron dependent oxygenase]]
| + | |
| Structural highlights
Function
ARGHX_STRVI Involved in the biosynthesis of capreomycidine, an unusual amino acid used by non-ribosomal peptide synthases (NRPS) to make the tuberactinomycin class of peptide antibiotics such as viomycin and capreomycin. Catalyzes the stereospecific hydroxylation of the C3 of (2S)-arginine to generate (3S)-hydroxy-(2S)-arginine. Usually clavaminic acid synthase-like oxygenases catalyze the formation of threo diastereomers, however VioC produces the erythro diastereomer of beta-carbon-hydroxylated L-arginine. It exerts a broad substrate specificity by accepting the analogs L-homoarginine and L-canavanine for the beta-carbon hydroxylation.[1] [2] [3]
Publication Abstract from PubMed
Cryogenic X-ray diffraction is a powerful tool for crystallographic studies on enzymes including oxygenases and oxidases. Amongst the benefits that cryo-conditions (usually employing a nitro-gen cryo-stream at 100 K) enable, is data collection of di-oxy-gen-sensitive samples. Although not strictly anaerobic, at low temperatures the vitreous ice conditions severely restrict O2 diffusion into and/or through the protein crystal. Cryo-conditions limit chemical reactivity, including reactions that require significant conformational changes. By contrast, data collection at room temperature imposes fewer restrictions on diffusion and reactivity; room-temperature serial methods are thus becoming common at synchrotrons and XFELs. However, maintaining an anaerobic environment for di-oxy-gen-dependent enzymes has not been explored for serial room-temperature data collection at synchrotron light sources. This work describes a methodology that employs an adaptation of the 'sheet-on-sheet' sample mount, which is suitable for the low-dose room-temperature data collection of anaerobic samples at synchrotron light sources. The method is characterized by easy sample preparation in an anaerobic glovebox, gentle handling of crystals, low sample consumption and preservation of a localized anaerobic environment over the timescale of the experiment (<5 min). The utility of the method is highlighted by studies with three X-ray-radiation-sensitive Fe(II)-containing model enzymes: the 2-oxoglutarate-dependent l-arginine hy-droxy-lase VioC and the DNA repair enzyme AlkB, as well as the oxidase isopenicillin N synthase (IPNS), which is involved in the biosynthesis of all penicillin and cephalosporin antibiotics.
Anaerobic fixed-target serial crystallography.,Rabe P, Beale JH, Butryn A, Aller P, Dirr A, Lang PA, Axford DN, Carr SB, Leissing TM, McDonough MA, Davy B, Ebrahim A, Orlans J, Storm SLS, Orville AM, Schofield CJ, Owen RL IUCrJ. 2020 Aug 21;7(Pt 5):901-912. doi: 10.1107/S2052252520010374. eCollection, 2020 Sep 1. PMID:32939282[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Yin X, Zabriskie TM. VioC is a non-heme iron, alpha-ketoglutarate-dependent oxygenase that catalyzes the formation of 3S-hydroxy-L-arginine during viomycin biosynthesis. Chembiochem. 2004 Sep 6;5(9):1274-7. PMID:15368580 doi:http://dx.doi.org/10.1002/cbic.200400082
- ↑ Ju J, Ozanick SG, Shen B, Thomas MG. Conversion of (2S)-arginine to (2S,3R)-capreomycidine by VioC and VioD from the viomycin biosynthetic pathway of Streptomyces sp. strain ATCC11861. Chembiochem. 2004 Sep 6;5(9):1281-5. PMID:15368582 doi:http://dx.doi.org/10.1002/cbic.200400136
- ↑ Helmetag V, Samel SA, Thomas MG, Marahiel MA, Essen LO. Structural basis for the erythro-stereospecificity of the L-arginine oxygenase VioC in viomycin biosynthesis. FEBS J. 2009 Jul;276(13):3669-82. Epub 2009 May 26. PMID:19490124 doi:10.1111/j.1742-4658.2009.07085.x
- ↑ Rabe P, Beale JH, Butryn A, Aller P, Dirr A, Lang PA, Axford DN, Carr SB, Leissing TM, McDonough MA, Davy B, Ebrahim A, Orlans J, Storm SLS, Orville AM, Schofield CJ, Owen RL. Anaerobic fixed-target serial crystallography. IUCrJ. 2020 Aug 21;7(Pt 5):901-912. doi: 10.1107/S2052252520010374. eCollection, 2020 Sep 1. PMID:32939282 doi:http://dx.doi.org/10.1107/S2052252520010374
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