6daw: Difference between revisions

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<StructureSection load='6daw' size='340' side='right'caption='[[6daw]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
<StructureSection load='6daw' size='340' side='right'caption='[[6daw]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6daw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_15842 Atcc 15842]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DAW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DAW FirstGlance]. <br>
<table><tr><td colspan='2'>[[6daw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_lusitanus Streptomyces lusitanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DAW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DAW FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</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]] 2.1&#8491;</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=6daw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6daw OCA], [http://pdbe.org/6daw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6daw RCSB], [http://www.ebi.ac.uk/pdbsum/6daw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6daw ProSAT]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</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=6daw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6daw OCA], [https://pdbe.org/6daw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6daw RCSB], [https://www.ebi.ac.uk/pdbsum/6daw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6daw ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/S4TL40_9ACTN S4TL40_9ACTN]
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 6daw" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 15842]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Boal, A K]]
[[Category: Streptomyces lusitanus]]
[[Category: Dunham, N P]]
[[Category: Boal AK]]
[[Category: Mitchell, A J]]
[[Category: Dunham NP]]
[[Category: Biosynthesis]]
[[Category: Mitchell AJ]]
[[Category: Desaturase]]
[[Category: Desaturation]]
[[Category: Metalloenzyme]]
[[Category: Natural product]]
[[Category: Oxidoreductase]]
[[Category: Oxygenase]]

Latest revision as of 17:33, 13 March 2024

X-ray crystal structure of NapI L-arginine desaturase bound to Fe(II), L-arginine, and acetateX-ray crystal structure of NapI L-arginine desaturase bound to Fe(II), L-arginine, and acetate

Structural highlights

6daw is a 2 chain structure with sequence from Streptomyces lusitanus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.1Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

S4TL40_9ACTN

See Also

6daw, resolution 2.10Å

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