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| | <StructureSection load='6ymh' size='340' side='right'caption='[[6ymh]], [[Resolution|resolution]] 2.42Å' scene=''> | | <StructureSection load='6ymh' size='340' side='right'caption='[[6ymh]], [[Resolution|resolution]] 2.42Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6ymh]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YMH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YMH FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6ymh]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YMH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YMH FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.417Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6ylz|6ylz]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pdxH, b1638, JW1630 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pyridoxal_5'-phosphate_synthase Pyridoxal 5'-phosphate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.5 1.4.3.5] </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=6ymh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ymh OCA], [https://pdbe.org/6ymh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ymh RCSB], [https://www.ebi.ac.uk/pdbsum/6ymh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ymh 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=6ymh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ymh OCA], [https://pdbe.org/6ymh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ymh RCSB], [https://www.ebi.ac.uk/pdbsum/6ymh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ymh ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/PDXH_ECOLI PDXH_ECOLI]] Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP).[HAMAP-Rule:MF_01629]
| + | [https://www.uniprot.org/uniprot/PDXH_ECOLI PDXH_ECOLI] Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP).[HAMAP-Rule:MF_01629] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6ymh" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6ymh" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Pyridoxine 5'-phosphate oxidase|Pyridoxine 5'-phosphate oxidase]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli K-12]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Pyridoxal 5'-phosphate synthase]]
| + | [[Category: Barile A]] |
| - | [[Category: Barile, A]] | + | [[Category: Battista T]] |
| - | [[Category: Battista, T]] | + | [[Category: Fiorillo A]] |
| - | [[Category: Fiorillo, A]] | + | [[Category: Ilari A]] |
| - | [[Category: Ilari, A]] | + | [[Category: Sularea M]] |
| - | [[Category: Sularea, M]] | + | [[Category: Tramonti A]] |
| - | [[Category: Tramonti, A]] | + | |
| - | [[Category: Flavoprotein]]
| + | |
| - | [[Category: Oxidase]]
| + | |
| - | [[Category: Pyridoxal 5'-phosphate]]
| + | |
| - | [[Category: Vitamine b6 metabolism]]
| + | |
| Structural highlights
Function
PDXH_ECOLI Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP).[HAMAP-Rule:MF_01629]
Publication Abstract from PubMed
Pyridoxal 5'-phosphate (PLP), the catalytically active form of vitamin B6, plays a pivotal role in metabolism as an enzyme cofactor. PLP is a very reactive molecule and can be very toxic unless its intracellular concentration is finely regulated. In Escherichia coli, PLP formation is catalyzed by pyridoxine 5'-phosphate oxidase (PNPO), a homodimeric FMN-dependent enzyme that is responsible for the last step of PLP biosynthesis and is also involved in the PLP salvage pathway. We have recently observed that E. coli PNPO undergoes an allosteric feedback inhibition by PLP, caused by a strong allosteric coupling between PLP binding at the allosteric site and substrate binding at the active site. Here we report the crystallographic identification of the PLP allosteric site, located at the interface between the enzyme subunits and mainly circumscribed by three arginine residues (Arg23, Arg24, and Arg215) that form an "arginine cage" and efficiently trap PLP. The crystal structure of the PNPO-PLP complex, characterized by a marked structural asymmetry, presents only one PLP molecule bound at the allosteric site of one monomer and sheds light on the allosteric inhibition mechanism that makes the enzyme-substrate-PLP ternary complex catalytically incompetent. Site-directed mutagenesis studies focused on the arginine cage validate the identity of the allosteric site and provide an effective means to modulate the allosteric properties of the enzyme, from the loosening of the allosteric coupling (in the R23L/R24L and R23L/R215L variants) to the complete loss of allosteric properties (in the R23L/R24L/R21L variant).
Identification and characterization of the pyridoxal 5'-phosphate allosteric site in Escherichia coli pyridoxine 5'-phosphate oxidase.,Barile A, Battista T, Fiorillo A, di Salvo ML, Malatesta F, Tramonti A, Ilari A, Contestabile R J Biol Chem. 2021 Jan-Jun;296:100795. doi: 10.1016/j.jbc.2021.100795. Epub 2021, May 18. PMID:34019876[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Barile A, Battista T, Fiorillo A, di Salvo ML, Malatesta F, Tramonti A, Ilari A, Contestabile R. Identification and characterization of the pyridoxal 5'-phosphate allosteric site in Escherichia coli pyridoxine 5'-phosphate oxidase. J Biol Chem. 2021 Jan-Jun;296:100795. doi: 10.1016/j.jbc.2021.100795. Epub 2021, May 18. PMID:34019876 doi:http://dx.doi.org/10.1016/j.jbc.2021.100795
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