7f3v
From Proteopedia
(Difference between revisions)
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==Crystal structure of YfiH with C107A mutation in complex with endogenous UDP-MurNAc== | ==Crystal structure of YfiH with C107A mutation in complex with endogenous UDP-MurNAc== | ||
| - | <StructureSection load='7f3v' size='340' side='right'caption='[[7f3v]]' scene=''> | + | <StructureSection load='7f3v' size='340' side='right'caption='[[7f3v]], [[Resolution|resolution]] 1.47Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7F3V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F3V FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7f3v]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7F3V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F3V FirstGlance]. <br> |
| - | </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=7f3v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f3v OCA], [https://pdbe.org/7f3v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f3v RCSB], [https://www.ebi.ac.uk/pdbsum/7f3v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f3v ProSAT]</span></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPZ:(2R)-2-{[(2R,3R,4R,5S,6R)-3-(ACETYLAMINO)-2-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-5-HYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-4-YL]OXY}PROPANOIC+ACID'>EPZ</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr> |
| + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Adenosine_deaminase Adenosine deaminase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.4 3.5.4.4] </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=7f3v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f3v OCA], [https://pdbe.org/7f3v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f3v RCSB], [https://www.ebi.ac.uk/pdbsum/7f3v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f3v ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [[https://www.uniprot.org/uniprot/PURNU_ECOLI PURNU_ECOLI]] Purine nucleoside enzyme that catalyzes the phosphorolysis of adenosine and inosine nucleosides, yielding D-ribose 1-phosphate and the respective free bases, adenine and hypoxanthine (PubMed:31978345). Also catalyzes the phosphorolysis of S-methyl-5'-thioadenosine into adenine and S-methyl-5-thio-alpha-D-ribose 1-phosphate (PubMed:31978345). Also has adenosine deaminase activity (PubMed:31978345). May also act as a polyphenol oxidase: able to oxidize syringaldazine and 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) in vitro (PubMed:16740638).<ref>PMID:16740638</ref> <ref>PMID:31978345</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Bacterial cells are encased in peptidoglycan (PG), a polymer of disaccharide N-acetylglucosamine (GlcNAc) and N-acetyl-muramic acid (MurNAc) cross-linked by peptide stems. PG is synthesized in the cytoplasm as UDP-MurNAc-peptide precursors, of which the amino acid composition of the peptide is unique, with l-Ala added at the first position in most bacteria but with l-Ser or Gly in some bacteria. YfiH is a PG-editing factor whose absence causes misincorporation of l-Ser instead of l-Ala into peptide stems, but its mechanistic function is unknown. Here, we report the crystal structures of substrate-bound and product-bound YfiH, showing that YfiH is a cytoplasmic amidase that controls the incorporation of the correct amino acid to the nucleotide precursors by preferentially cleaving the nucleotide precursor by-product UDP-MurNAc-l-Ser. This work reveals an editing mechanism in the cytoplasmic steps of peptidoglycan biosynthesis. IMPORTANCE YfiH is a peptidoglycan (PG)-editing factor required for the maintenance of specific amino acid compositions of the stem peptides. However, the activity of YfiH has not been deciphered, and the editing mechanism involving YfiH has remained a mystery. Through X-ray crystallographic and biochemical analyses, we demonstrate that YfiH is a hydrolase with a previously unknown activity specific for the UDP-MurNAc-monopeptide, one of the nucleotide precursors from the cytoplasmic steps of the PG biosynthesis pathway. YfiH selectively hydrolyzes UDP-MurNAc-Ser, an incorrect by-product of the biosynthesis reaction, to ensure that only the correct PG precursor, UDP-MurNAc-Ala, is incorporated. Therefore, this work reveals coupled synthetic and editing reactions in the cytoplasmic steps of PG biosynthesis. | ||
| + | |||
| + | Structural Basis for the Peptidoglycan-Editing Activity of YfiH.,Lee MS, Hsieh KY, Kuo CI, Lee SH, Garde S, Reddy M, Chang CI mBio. 2022 Feb 15:e0364621. doi: 10.1128/mbio.03646-21. PMID:35164571<ref>PMID:35164571</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7f3v" style="background-color:#fffaf0;"></div> | ||
| + | |||
| + | ==See Also== | ||
| + | *[[Purine nucleoside phosphorylase 3D structures|Purine nucleoside phosphorylase 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Adenosine deaminase]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Chang | + | [[Category: Chang, C I]] |
| - | [[Category: Hsieh | + | [[Category: Hsieh, K Y]] |
| - | [[Category: Lee | + | [[Category: Lee, M S]] |
| + | [[Category: Amidase]] | ||
| + | [[Category: Duf152]] | ||
| + | [[Category: Hydrolase]] | ||
Revision as of 07:26, 2 March 2022
Crystal structure of YfiH with C107A mutation in complex with endogenous UDP-MurNAc
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