9iz3: Difference between revisions
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The | ==Crystal structure of phosphonopyruvate decarboxylase RhiEF from Bacillus subtilis ATCC6633== | ||
<StructureSection load='9iz3' size='340' side='right'caption='[[9iz3]], [[Resolution|resolution]] 2.46Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[9iz3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._spizizenii_ATCC_6633_=_JCM_2499 Bacillus subtilis subsp. spizizenii ATCC 6633 = JCM 2499]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9IZ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9IZ3 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]] 2.46Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=9iz3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9iz3 OCA], [https://pdbe.org/9iz3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9iz3 RCSB], [https://www.ebi.ac.uk/pdbsum/9iz3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9iz3 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/D4HRI2_BACSC D4HRI2_BACSC] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The RhiE and RhiF proteins work together as RhiEF and function as a thiamine pyrophosphate (TPP)-dependent phosphonopyruvate decarboxylase to produce phosphonoacetaldehyde in the rhizocticin biosynthesis pathway. In this study, we determined the crystal structure of the RhiEF complexed with TPP and Mg(2+). RhiEF forms a dimer of heterodimers, and the cofactor TPP is bound at the heterotetrameric subunit interface. Structural analysis of RhiEF revealed that the RhiE and RhiF moieties correspond to the pyrimidine-binding (PYR) and pyrophosphate-binding (PP) domains commonly found in TPP-dependent enzymes, respectively, as predicted by amino acid sequence alignment analysis. In contrast to other TPP-dependent enzymes with known structures, RhiEF has no domains other than the PYR and PP domains. Furthermore, structure-based evolutionary and sequence-based phylogenetic analyses have suggested that heteromultimeric enzymes such as RhiEF are ancestral types. These results indicate that RhiEF is one of the smallest and most ancient TPP-dependent decarboxylases. Based on the structural comparisons of RhiEF with other TPP-dependent decarboxylases, we identified the amino acid residues responsible for the catalytic mechanism of TPP-dependent decarboxylation in RhiEF. | |||
Structural Analysis of Phosphonopyruvate Decarboxylase RhiEF: First Insights into an Ancestral Heterooligomeric Thiamine Pyrophosphate-Dependent Decarboxylase.,Nakamura A, Shiina A, Fukaya T, Seki Y, Momiyama M, Kojima S Biochemistry. 2024 Dec 17;63(24):3250-3260. doi: 10.1021/acs.biochem.4c00559. , Epub 2024 Nov 25. PMID:39586109<ref>PMID:39586109</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 9iz3" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Bacillus subtilis subsp. spizizenii ATCC 6633 = JCM 2499]] | |||
[[Category: Large Structures]] | |||
[[Category: Kojima S]] | |||
[[Category: Nakamura A]] | |||
