5x3d

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Current revision (10:17, 27 March 2024) (edit) (undo)
 
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<StructureSection load='5x3d' size='340' side='right'caption='[[5x3d]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
<StructureSection load='5x3d' size='340' side='right'caption='[[5x3d]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5x3d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X3D OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5X3D FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5x3d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_wedmorensis Streptomyces wedmorensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X3D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X3D FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7XL:[[(2R,3S,4R,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-(2-hydroxyethyl)phosphinic+acid'>7XL</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.93&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5x3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x3d OCA], [http://pdbe.org/5x3d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x3d RCSB], [http://www.ebi.ac.uk/pdbsum/5x3d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x3d ProSAT]</span></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7XL:[[(2R,3S,4R,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-(2-hydroxyethyl)phosphinic+acid'>7XL</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5x3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x3d OCA], [https://pdbe.org/5x3d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x3d RCSB], [https://www.ebi.ac.uk/pdbsum/5x3d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x3d ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/FOM1_STRWE FOM1_STRWE] Bifunctional enzyme that catalyzes two steps during fosfomycin biosynthesis (PubMed:28727444). It catalyzes the conversion of phosphoenolpyruvate (PEP) to phosphonopyruvate (PnPy), the first step of the pathway. It also catalyzes the cytidylylation of the 2-hydroxyethylphosphonate (HEP) intermediate to produce cytidylyl-2-hydroxyethylphosphonate (HEP-CMP), the fourth step of the pathway (PubMed:28727444).<ref>PMID:28727444</ref>
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Fosfomycin is a wide-spectrum phosphonate antibiotic that is used clinically to treat cystitis, tympanitis, etc. Its biosynthesis starts with the formation of a carbon-phosphorus bond catalyzed by the phosphoenolpyruvate phosphomutase Fom1. We identified an additional cytidylyltransferase (CyTase) domain at the Fom1 N-terminus in addition to the phosphoenolpyruvate phosphomutase domain at the Fom1 C-terminus. Here, we demonstrate that Fom1 is bifunctional and that the Fom1 CyTase domain catalyzes the cytidylylation of the 2-hydroxyethylphosphonate (HEP) intermediate to produce cytidylyl-HEP. On the basis of this new function of Fom1, we propose a revised fosfomycin biosynthetic pathway that involves the transient CMP-conjugated intermediate. The identification of a biosynthetic mechanism via such transient cytidylylation of a biosynthetic intermediate fundamentally advances the understanding of phosphonate biosynthesis in nature. The crystal structure of the cytidylyl-HEP-bound CyTase domain provides a basis for the substrate specificity and reveals unique catalytic elements not found in other members of the CyTase family.
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Fosfomycin Biosynthesis via Transient Cytidylylation of 2-Hydroxyethylphosphonate by the Bifunctional Fom1 Enzyme.,Cho SH, Kim SY, Tomita T, Shiraishi T, Park JS, Sato S, Kudo F, Eguchi T, Funa N, Nishiyama M, Kuzuyama T ACS Chem Biol. 2017 Aug 18;12(8):2209-2215. doi: 10.1021/acschembio.7b00419. Epub, 2017 Jul 20. PMID:28727444<ref>PMID:28727444</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5x3d" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Cho, S H]]
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[[Category: Streptomyces wedmorensis]]
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[[Category: Kuzuyama, T]]
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[[Category: Cho SH]]
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[[Category: Nishiyama, M]]
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[[Category: Kuzuyama T]]
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[[Category: Tomita, T]]
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[[Category: Nishiyama M]]
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[[Category: Cytidylyltransferase]]
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[[Category: Tomita T]]
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[[Category: Fosfomycin biosynthesis]]
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[[Category: Nucleotidyltransferase]]
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[[Category: Transferase]]
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Current revision

Crystal structure of HEP-CMP-bound form of cytidylyltransferase (CyTase) domain of Fom1 from Streptomyces wedmorensis

PDB ID 5x3d

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