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==X-ray crystal structure of VioC bound to vanadyl ion, L-homoarginine, and succinate==
==X-ray crystal structure of VioC bound to vanadyl ion, L-homoarginine, and succinate==
<StructureSection load='6db2' size='340' side='right' caption='[[6db2]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
<StructureSection load='6db2' size='340' side='right'caption='[[6db2]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6db2]] 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=6DB2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DB2 FirstGlance]. <br>
<table><tr><td colspan='2'>[[6db2]] 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=6DB2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DB2 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HRG:L-HOMOARGININE'>HRG</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=VVO:oxovanadium(2+)'>VVO</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]] 1.7&#8491;</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HRG:L-HOMOARGININE'>HRG</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=VVO:oxovanadium(2+)'>VVO</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=6db2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6db2 OCA], [http://pdbe.org/6db2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6db2 RCSB], [http://www.ebi.ac.uk/pdbsum/6db2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6db2 ProSAT]</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=6db2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6db2 OCA], [https://pdbe.org/6db2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6db2 RCSB], [https://www.ebi.ac.uk/pdbsum/6db2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6db2 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;">
== Publication Abstract from PubMed ==
Hydroxylation of aliphatic carbons by non-heme Fe(IV)-oxo (ferryl) complexes proceeds by hydrogen-atom (H*) transfer (HAT) to the ferryl and subsequent coupling between the carbon radical and Fe(III)-coordinated oxygen (termed rebound). Enzymes that use H*-abstracting ferryl complexes for other transformations must either suppress rebound or further process hydroxylated intermediates. For olefin-installing C-C desaturations, it has been proposed that a second HAT to the Fe(III)-OH complex from the carbon alpha to the radical preempts rebound. Deuterium ((2)H) at the second site should slow this step, potentially making rebound competitive. Desaturations mediated by two related L-arginine-modifying iron(II)- and 2-(oxo)glutarate-dependent (Fe/2OG) oxygenases behave oppositely in this key test, implicating different mechanisms. NapI, the L-Arg 4,5-desaturase from the naphthyridinomycin biosynthetic pathway, abstracts H* first from C5 but hydroxylates this site (leading to guanidine release) to the same modest extent whether C4 harbors (1)H or (2)H. By contrast, an unexpected 3,4-desaturation of L-homoarginine (L-hArg) by VioC, the L-Arg 3-hydroxylase from the viomycin biosynthetic pathway, is markedly disfavored relative to C4 hydroxylation when C3 (the second hydrogen donor) harbors (2)H. Anchimeric assistance by N6 permits removal of the C4-H as a proton in the NapI reaction, but, with no such assistance possible in the VioC desaturation, a second HAT step (from C3) is required. The close proximity (&lt;/= 3.5 A) of both L-hArg carbons to the (hydr)oxo group in an x-ray crystal structure of VioC harboring a vanadium-based ferryl mimic supports and rationalizes the sequential-HAT mechanism. The results suggest that, although the sequential-HAT mechanism is feasible, its geometric requirements may ensure competing hydroxylation, thus explaining why nearly all natural substrates for Fe/2OG desaturases have alpha-heteroatoms.


Two Distinct Mechanisms for C-C Desaturation by Iron(II)- and 2-(Oxo)glutarate-Dependent Oxygenases: Importance of alpha-Heteroatom Assistance.,Dunham NP, Chang WC, Mitchell AJ, Martinie RJ, Zhang B, Bergman JA, Rajakovich LJ, Wang B, Silakov A, Krebs C, Boal AK, Bollinger JM Jr J Am Chem Soc. 2018 Apr 30. doi: 10.1021/jacs.8b01933. PMID:29708749<ref>PMID:29708749</ref>
==See Also==
 
*[[Hydroxylases 3D structures|Hydroxylases 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6db2" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Oxidoreductase]]
[[Category: Large Structures]]
[[Category: Streptomyces vinaceus]]
[[Category: Streptomyces vinaceus]]
[[Category: Boal, A K]]
[[Category: Boal AK]]
[[Category: Dunham, N P]]
[[Category: Dunham NP]]
[[Category: Mitchell, A J]]
[[Category: Mitchell AJ]]
[[Category: Desaturase]]
[[Category: Desaturation]]
[[Category: Hydroxylase]]
[[Category: Hydroxylation]]
[[Category: Metalloenzyme]]
[[Category: Oxygenase]]
[[Category: Viomycin]]

Latest revision as of 17:33, 13 March 2024

X-ray crystal structure of VioC bound to vanadyl ion, L-homoarginine, and succinateX-ray crystal structure of VioC bound to vanadyl ion, L-homoarginine, and succinate

Structural highlights

6db2 is a 1 chain structure with sequence from Streptomyces vinaceus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.7Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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]

See Also

References

  1. ↑ 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
  2. ↑ 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
  3. ↑ 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

6db2, resolution 1.70Å

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