6alm

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(Difference between revisions)

Revision as of 10:03, 1 January 2020

VioC L-arginine hydroxylase bound to Fe(II), L-arginine, and 2-OXO-GLUTARIC ACID

Structural highlights

6alm is a 1 chain structure with sequence from As 4.1305. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Gene:	vioC (AS 4.1305)
Activity:	Oxidoreductase, with EC number 1.14.11.41
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]

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^[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
↑ 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. Visualizing the reaction cycle in an iron(II)- and 2-(oxo)-glutarate-dependent hydroxylase. J Am Chem Soc. 2017 Aug 20. doi: 10.1021/jacs.7b07374. PMID:28823155 doi:http://dx.doi.org/10.1021/jacs.7b07374

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6alm"

@@ Line 1: / Line 1: @@
 ==VioC L-arginine hydroxylase bound to Fe(II), L-arginine, and 2-OXO-GLUTARIC ACID==
-<StructureSection load='6alm' size='340' side='right' caption='[[6alm]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+<StructureSection load='6alm' size='340' side='right'caption='[[6alm]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6alm]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ALM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ALM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6alm]] 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=6ALM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ALM FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</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='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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6alm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6alm OCA], [http://pdbe.org/6alm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6alm RCSB], [http://www.ebi.ac.uk/pdbsum/6alm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6alm ProSAT]</span></td></tr>
@@ Line 19: / Line 20: @@
 </div>
 <div class="pdbe-citations 6alm" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Hydroxylases 3D structures|Hydroxylases 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: As 4 1305]]
+[[Category: Large Structures]]
 [[Category: Oxidoreductase]]
 [[Category: Boal, A K]]

6alm

From Proteopedia

Revision as of 10:03, 1 January 2020

VioC L-arginine hydroxylase bound to Fe(II), L-arginine, and 2-OXO-GLUTARIC ACID

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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