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2wbp

From Proteopedia

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Current revision

Crystal structure of VioC in complex with Fe(II), (2S,3S)- hydroxyarginine, and succinate

Structural highlights

2wbp 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 1.16Å
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]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The nonheme iron oxygenase VioC from Streptomyces vinaceus catalyzes Fe(II)-dependent and alpha-ketoglutarate-dependent Cbeta-hydroxylation of L-arginine during the biosynthesis of the tuberactinomycin antibiotic viomycin. Crystal structures of VioC were determined in complexes with the cofactor Fe(II), the substrate L-arginine, the product (2S,3S)-hydroxyarginine and the coproduct succinate at 1.1-1.3 A resolution. The overall structure reveals a beta-helix core fold with two additional helical subdomains that are common to nonheme iron oxygenases of the clavaminic acid synthase-like superfamily. In contrast to other clavaminic acid synthase-like oxygenases, which catalyze the formation of threo diastereomers, VioC produces the erythro diastereomer of Cbeta-hydroxylated L-arginine. This unexpected stereospecificity is caused by conformational control of the bound substrate, which enforces a gauche(-) conformer for chi(1) instead of the trans conformers observed for the asparagine oxygenase AsnO and other members of the clavaminic acid synthase-like superfamily. Additionally, the substrate specificity of VioC was investigated. The side chain of the L-arginine substrate projects outwards from the active site by undergoing interactions mainly with the C-terminal helical subdomain. Accordingly, VioC exerts broadened substrate specificity by accepting the analogs L-homoarginine and L-canavanine for Cbeta-hydroxylation.

Structural basis for the erythro-stereospecificity of the L-arginine oxygenase VioC in viomycin biosynthesis.,Helmetag V, Samel SA, Thomas MG, Marahiel MA, Essen LO FEBS J. 2009 Jul;276(13):3669-82. Epub 2009 May 26. PMID:19490124^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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
↑ 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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2wbp"

@@ Line 3: / Line 3: @@
 <StructureSection load='2wbp' size='340' side='right'caption='[[2wbp]], [[Resolution|resolution]] 1.16&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2wbp]] is a 1 chain structure with sequence from [https://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=2WBP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WBP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2wbp]] 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=2WBP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WBP FirstGlance]. <br>
-</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=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.16&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2wbo|2wbo]], [[2wbq|2wbq]]</div></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=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=ZZU:(2S,3S)-3-HYDROXYARGININE'>ZZU</scene></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=2wbp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wbp OCA], [https://pdbe.org/2wbp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wbp RCSB], [https://www.ebi.ac.uk/pdbsum/2wbp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wbp ProSAT]</span></td></tr>
 </table>
+== Function ==
+[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>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 34: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: As 4 1305]]
 [[Category: Large Structures]]
-[[Category: Essen, L O]]
+[[Category: Streptomyces vinaceus]]
-[[Category: Helmetag, V]]
+[[Category: Essen L-O]]
-[[Category: Marahiel, M A]]
+[[Category: Helmetag V]]
-[[Category: Samel, S A]]
+[[Category: Marahiel MA]]
-[[Category: Thomas, M G]]
+[[Category: Samel SA]]
-[[Category: Alpha-ketoglutarate]]
+[[Category: Thomas MG]]
-[[Category: Cbeta-hydroxylation]]
-[[Category: Nrp]]
-[[Category: Oxidoreductase]]
-[[Category: Viomycin]]

2wbp

From Proteopedia

Current revision

Crystal structure of VioC in complex with Fe(II), (2S,3S)- hydroxyarginine, and succinate

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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