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6mp9

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==X-ray crystal structure of VioC bound to Fe(II), 2-oxo-5-guanidinopentanoic acid, and succinate==
==X-ray crystal structure of VioC bound to Fe(II), 2-oxo-5-guanidinopentanoic acid, and succinate==
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<StructureSection load='6mp9' size='340' side='right' caption='[[6mp9]], [[Resolution|resolution]] 1.89&Aring;' scene=''>
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<StructureSection load='6mp9' size='340' side='right'caption='[[6mp9]], [[Resolution|resolution]] 1.89&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6mp9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_vinaceus Streptomyces vinaceus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MP9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MP9 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6mp9]] 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=6MP9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MP9 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=JX7:5-carbamimidamido-2-oxopentanoic+acid'>JX7</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.89&#8491;</td></tr>
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<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>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=JX7:5-carbamimidamido-2-oxopentanoic+acid'>JX7</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene></td></tr>
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<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=6mp9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mp9 OCA], [http://pdbe.org/6mp9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mp9 RCSB], [http://www.ebi.ac.uk/pdbsum/6mp9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mp9 ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6mp9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mp9 OCA], [https://pdbe.org/6mp9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mp9 RCSB], [https://www.ebi.ac.uk/pdbsum/6mp9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mp9 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[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>
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[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>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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When challenged with substrate analogues, iron(II)- and 2-(oxo)glutarate-dependent (Fe/2OG) oxygenases can promote transformations different from those they enact upon their native substrates. We show here that the Fe/2OG enzyme, VioC, which is natively an l-arginine 3-hydroxylase, catalyzes an efficient oxidative deamination of its substrate enantiomer, d-Arg. The reactant complex with d-Arg retains all interactions between enzyme and substrate functional groups, but the required structural adjustments and opposite configuration of C2 position this carbon more optimally than C3 to donate hydrogen (H(*)) to the ferryl intermediate. The simplest possible mechanism, C2 hydroxylation followed by elimination of ammonia, is inconsistent with the demonstrated solvent origin of the ketone oxygen in the product. Rather, the reaction proceeds via a hydrolytically labile C2-iminium intermediate, demonstrated by its reductive trapping in solution with NaB(2)H4 to produce racemic [(2)H]Arg. Of two alternative pathways to the iminium species, C2 hydroxylation followed by dehydration versus direct desaturation, the latter possibility appears to be more likely, because the former mechanism would be expected to result in detectable incorporation of (18)O from (18)O2. The direct desaturation of a C-N bond implied by this analysis is analogous to that recently posited for the reaction of the l-Arg 4,5-desaturase, NapI, thus lending credence to the prior mechanistic proposal. Such a pathway could also potentially be operant in a subset of reactions catalyzed by Fe/2OG N-demethylases, which have instead been purported to enact C-N bond cleavage by methyl hydroxylation and elimination of formaldehyde.
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alpha-Amine Desaturation of d-Arginine by the Iron(II)- and 2-(Oxo)glutarate-Dependent l-Arginine 3-Hydroxylase, VioC.,Dunham NP, Mitchell AJ, Del Rio Pantoja JM, Krebs C, Bollinger JM Jr, Boal AK Biochemistry. 2018 Nov 20;57(46):6479-6488. doi: 10.1021/acs.biochem.8b00901., Epub 2018 Nov 7. PMID:30403469<ref>PMID:30403469</ref>
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==See Also==
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*[[Hydroxylases 3D structures|Hydroxylases 3D structures]]
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6mp9" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Oxidoreductase]]
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[[Category: Large Structures]]
[[Category: Streptomyces vinaceus]]
[[Category: Streptomyces vinaceus]]
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[[Category: Boal, A K]]
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[[Category: Boal AK]]
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[[Category: Dunham, N P]]
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[[Category: Dunham NP]]
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[[Category: Deaminase]]
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[[Category: Deamination]]
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[[Category: Hydroxylase]]
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[[Category: Hydroxylation]]
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[[Category: Metalloenzyme]]
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[[Category: Oxygenase]]
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[[Category: Viomycin]]
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Current revision

X-ray crystal structure of VioC bound to Fe(II), 2-oxo-5-guanidinopentanoic acid, and succinate

PDB ID 6mp9

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