6alr: Difference between revisions

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New page: ==VioC L-arginine hydroxylase bound to the vanadyl ion, L-arginine, and succinate== <StructureSection load='6alr' size='340' side='right' caption='6alr, resolution 1.55...
 
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==VioC L-arginine hydroxylase bound to the vanadyl ion, L-arginine, and succinate==
==VioC L-arginine hydroxylase bound to the vanadyl ion, L-arginine, and succinate==
<StructureSection load='6alr' size='340' side='right' caption='[[6alr]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
<StructureSection load='6alr' size='340' side='right'caption='[[6alr]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6alr]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ALR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ALR FirstGlance]. <br>
<table><tr><td colspan='2'>[[6alr]] 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=6ALR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ALR FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARG:ARGININE'>ARG</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]] 1.55&#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=ARG:ARGININE'>ARG</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=6alr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6alr OCA], [http://pdbe.org/6alr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6alr RCSB], [http://www.ebi.ac.uk/pdbsum/6alr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6alr 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=6alr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6alr OCA], [https://pdbe.org/6alr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6alr RCSB], [https://www.ebi.ac.uk/pdbsum/6alr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6alr 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 ==
Iron(II)- and 2-(oxo)-glutarate-dependent oxygenases catalyze diverse oxidative transformations that are often initiated by abstraction of hydrogen from carbon by iron(IV)-oxo (ferryl) complexes. Control of the relative orientation of the substrate C-H and ferryl Fe-O bonds, primarily by direction of the oxo group into one of two cis-related coordination sites (termed inline and offline), may be generally important for control of the reaction outcome. Neither the ferryl complexes nor their fleeting precursors have been crystallographically characterized, hindering direct experimental validation of the offline hypothesis and elucidation of the means by which the protein might dictate an alternative oxo position. Comparison of high-resolution x-ray crystal structures of the substrate complex, an Fe(II)-peroxysuccinate ferryl precursor, and a vanadium(IV)-oxo mimic of the ferryl intermediate in the L-arginine 3-hydroxylase, VioC, reveals coordinated motions of active site residues that appear to control the intermediate geometries to determine reaction outcome.


Visualizing the reaction cycle in an iron(II)- and 2-(oxo)-glutarate-dependent hydroxylase.,Mitchell AJ, Dunham NP, Martinie RJ, Bergman JA, Pollock CJ, Hu K, Allen BD, Chang WC, Silakov A, Bollinger JM Jr, Krebs C, Boal AK J Am Chem Soc. 2017 Aug 20. doi: 10.1021/jacs.7b07374. PMID:28823155<ref>PMID:28823155</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 6alr" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Oxidoreductase]]
[[Category: Large Structures]]
[[Category: Bergman, J A]]
[[Category: Streptomyces vinaceus]]
[[Category: Boal, A K]]
[[Category: Bergman JA]]
[[Category: Dunham, N P]]
[[Category: Boal AK]]
[[Category: Mitchell, A J]]
[[Category: Dunham NP]]
[[Category: 2-oxo-glutarate]]
[[Category: Mitchell AJ]]
[[Category: Hydroxylase]]
[[Category: Vanadyl ion]]

Latest revision as of 17:17, 13 March 2024

VioC L-arginine hydroxylase bound to the vanadyl ion, L-arginine, and succinateVioC L-arginine hydroxylase bound to the vanadyl ion, L-arginine, and succinate

Structural highlights

6alr 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 1.55Å
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

6alr, resolution 1.55Å

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