6c8t: Difference between revisions
New page: '''Unreleased structure''' The entry 6c8t is ON HOLD Authors: Han, L., Silvaggi, N.R. Description: The structure of MppP soaked with the substrate L-Arg [[Category: Unreleased Structur... |
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The | ==The structure of MppP soaked with the substrate L-Arg== | ||
<StructureSection load='6c8t' size='340' side='right'caption='[[6c8t]], [[Resolution|resolution]] 2.20Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6c8t]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_wadayamensis Streptomyces wadayamensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C8T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6C8T 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]] 2.2Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EQJ:(E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-arginine'>EQJ</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</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=6c8t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c8t OCA], [https://pdbe.org/6c8t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6c8t RCSB], [https://www.ebi.ac.uk/pdbsum/6c8t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6c8t ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A0X1KHF5_9ACTN A0A0X1KHF5_9ACTN] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The PLP-dependent l-arginine hydroxylase/deaminase MppP from Streptomyces wadayamensis (SwMppP) is involved in the biosynthesis of l-enduracididine, a nonproteinogenic amino acid found in several nonribosomally produced peptide antibiotics. SwMppP uses only PLP and molecular oxygen to catalyze a 4-electron oxidation of l-arginine to form a mixture of 2-oxo-4(S)-hydroxy-5-guanidinovaleric acid and 2-oxo-5-guanidinovaleric acid. Steady-state kinetics analysis in the presence and absence of catalase shows that one molecule of peroxide is formed for every molecule of dioxygen consumed in the reaction. Moreover, for each molecule of 2-oxo-4(S)-hydroxy-5-guanidinovaleric acid produced, two molecules of dioxygen are consumed, suggesting that both the 4-hydroxy and 2-keto groups are derived from water. This was confirmed by running the reactions using either ([18])O2 or H2([18])O and analyzing the products by ESI-MS. Incorporation of ([18])O was only observed when the reaction was performed in H2([18])O. Crystal structures of SwMppP with l-arginine, 2-oxo-4(S)-hydroxy-5-guanidinovaleric acid, or 2-oxo-5-guanidinovaleric acid bound were determined at resolutions of 2.2, 1.9. and 1.8 A, respectively. The structural data show that the N-terminal portion of the protein is disordered unless substrate or product is bound in the active site, in which case it forms a well-ordered helix that covers the catalytic center. This observation suggested that the N-terminal helix may have a role in substrate binding and/or catalysis. Our structural and kinetic characterizations of N-terminal variants show that the N-terminus is critical for catalysis. In light of this new information, we have refined our previously proposed mechanism of the SwMppP-catalyzed oxidation of l-arginine. | |||
Streptomyces wadayamensis MppP is a PLP-Dependent Oxidase, Not an Oxygenase.,Han L, Vuksanovic N, Oehm SA, Fenske TG, Schwabacher AW, Silvaggi NR Biochemistry. 2018 Mar 6. doi: 10.1021/acs.biochem.8b00130. PMID:29473729<ref>PMID:29473729</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 6c8t" style="background-color:#fffaf0;"></div> | ||
[[Category: Han | |||
==See Also== | |||
*[[Hydroxylases 3D structures|Hydroxylases 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Streptomyces wadayamensis]] | |||
[[Category: Han L]] | |||
[[Category: Silvaggi NR]] | |||