6xam: Difference between revisions

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<StructureSection load='6xam' size='340' side='right'caption='[[6xam]], [[Resolution|resolution]] 1.48&Aring;' scene=''>
<StructureSection load='6xam' size='340' side='right'caption='[[6xam]], [[Resolution|resolution]] 1.48&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6xam]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_sp._NRRL_F-5053 Streptomyces sp. NRRL F-5053]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XAM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XAM FirstGlance]. <br>
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XAM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XAM FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.481&#8491;</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]] 1.481&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=WMA:(3S,6S)-3-ethyl-6-[(1H-indol-3-yl)methyl]piperazine-2,5-dione'>WMA</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=WMA:(3S,6S)-3-ethyl-6-[(1H-indol-3-yl)methyl]piperazine-2,5-dione'>WMA</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=6xam FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xam OCA], [https://pdbe.org/6xam PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xam RCSB], [https://www.ebi.ac.uk/pdbsum/6xam PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xam 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=6xam FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xam OCA], [https://pdbe.org/6xam PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xam RCSB], [https://www.ebi.ac.uk/pdbsum/6xam PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xam ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The dimeric diketopiperazine (DKPs) alkaloids are a diverse family of natural products (NPs) whose unique structural architectures and biological activities have inspired the development of new synthetic methodologies to access these molecules. However, catalyst-controlled methods that enable the selective formation of constitutional and stereoisomeric dimers from a single monomer are lacking. To resolve this long-standing synthetic challenge, we sought to characterize the biosynthetic enzymes that assemble these NPs for application in biocatalytic syntheses. Genome mining enabled identification of the cytochrome P450, NzeB (Streptomyces sp. NRRL F-5053), which catalyzes both intermolecular carbon-carbon (C-C) and carbon-nitrogen (C-N) bond formation. To identify the molecular basis for the flexible site-selectivity, stereoselectivity, and chemoselectivity of NzeB, we obtained high-resolution crystal structures (1.5 A) of the protein in complex with native and non-native substrates. This, to our knowledge, represents the first crystal structure of an oxidase catalyzing direct, intermolecular C-H amination. Site-directed mutagenesis was utilized to assess the role individual active-site residues play in guiding selective DKP dimerization. Finally, computational approaches were employed to evaluate plausible mechanisms regarding NzeB function and its ability to catalyze both C-C and C-N bond formation. These results provide a structural and computational rationale for the catalytic versatility of NzeB, as well as new insights into variables that control selectivity of CYP450 diketopiperazine dimerases.
Structure and Function of NzeB, a Versatile C-C and C-N Bond-Forming Diketopiperazine Dimerase.,Shende VV, Khatri Y, Newmister SA, Sanders JN, Lindovska P, Yu F, Doyon TJ, Kim J, Houk KN, Movassaghi M, Sherman DH J Am Chem Soc. 2020 Oct 14;142(41):17413-17424. doi: 10.1021/jacs.0c06312. Epub, 2020 Sep 30. PMID:32786740<ref>PMID:32786740</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6xam" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Streptomyces sp. NRRL F-5053]]
[[Category: Doyon TJ]]
[[Category: Doyon TJ]]
[[Category: Houk KN]]
[[Category: Houk KN]]

Latest revision as of 13:41, 23 October 2024

Crystal structure of NzeB in complex with cyclo-(L-Trp-L-homoalanine)Crystal structure of NzeB in complex with cyclo-(L-Trp-L-homoalanine)

Structural highlights

Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.481Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

6xam, resolution 1.48Å

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OCA
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