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| | ==Crystal structure of Weissella viridescens FemXVv non-ribosomal amino acid transferase in complex with a peptidyl-RNA conjugate== | | ==Crystal structure of Weissella viridescens FemXVv non-ribosomal amino acid transferase in complex with a peptidyl-RNA conjugate== |
| - | <StructureSection load='4ii9' size='340' side='right' caption='[[4ii9]], [[Resolution|resolution]] 1.66Å' scene=''> | + | <StructureSection load='4ii9' size='340' side='right'caption='[[4ii9]], [[Resolution|resolution]] 1.66Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4ii9]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"lactobacillus_viridescens_subsp._minor"_kandler_and_albo-elnaga_1966 "lactobacillus viridescens subsp. minor" kandler and albo-elnaga 1966]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4II9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4II9 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4ii9]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Weissella_viridescens Weissella viridescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4II9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4II9 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MUB:N-ACETYLMURAMIC+ACID'>MUB</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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]] 1.66Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=A9Z:2-DEOXY-2-(4-ETHYL-1H-1,2,3-TRIAZOL-1-YL)ADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A9Z</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FGA:GAMMA-D-GLUTAMIC+ACID'>FGA</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A9Z:2-DEOXY-2-(4-ETHYL-1H-1,2,3-TRIAZOL-1-YL)ADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A9Z</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FGA:GAMMA-D-GLUTAMIC+ACID'>FGA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MUB:N-ACETYLMURAMIC+ACID'>MUB</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ne9|1ne9]], [[1p4n|1p4n]], [[1xe4|1xe4]], [[1xf8|1xf8]], [[1xix|1xix]], [[3gkr|3gkr]]</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=4ii9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ii9 OCA], [https://pdbe.org/4ii9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ii9 RCSB], [https://www.ebi.ac.uk/pdbsum/4ii9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ii9 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">femX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1629 "Lactobacillus viridescens subsp. minor" Kandler and Albo-Elnaga 1966])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-N-acetylmuramoylpentapeptide-lysine_N(6)-alanyltransferase UDP-N-acetylmuramoylpentapeptide-lysine N(6)-alanyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.10 2.3.2.10] </span></td></tr> | + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ii9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ii9 OCA], [http://pdbe.org/4ii9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ii9 RCSB], [http://www.ebi.ac.uk/pdbsum/4ii9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ii9 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/FEMX_WEIVI FEMX_WEIVI] Involved in the synthesis of the bacterial cell wall. Catalyzes the addition of alanine into the interchain peptide bridge of peptidoglycan precursor using aminoacyl-tRNA(Ala) as amino acid donor. This alanine is added to the epsilon-amino group of the L-lysine of the peptidoglycan UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-L-lysyl-D-alanyl-D-alanine, in a ribosome-independent mechanism (PubMed:11083873, PubMed:12679335, PubMed:15901708, PubMed:23744707, PubMed:4248527). Specific for UDP-N-acetyl-muramoyl-pentapeptide. Has no activity toward UDP-N-acetyl-muramoyl-tetrapeptide or UDP-N-acetyl-muramoyl-tripeptide (PubMed:15901708). Also acts on L-seryl-tRNA(Ser) (PubMed:4248527).<ref>PMID:11083873</ref> <ref>PMID:12679335</ref> <ref>PMID:15901708</ref> <ref>PMID:23744707</ref> <ref>PMID:4248527</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Lactobacillus viridescens subsp. minor kandler and albo-elnaga 1966]] | + | [[Category: Large Structures]] |
| - | [[Category: Arthur, M]] | + | [[Category: Weissella viridescens]] |
| - | [[Category: Etheve-Quelquejeu, M]] | + | [[Category: Arthur M]] |
| - | [[Category: Fonvielle, M]] | + | [[Category: Etheve-Quelquejeu M]] |
| - | [[Category: Sierra-Gallay, I Li de la]] | + | [[Category: Fonvielle M]] |
| - | [[Category: Tilbeurgh, H van]] | + | [[Category: Li de la Sierra-Gallay I]] |
| - | [[Category: Femx]]
| + | [[Category: Van Tilbeurgh H]] |
| - | [[Category: Peptidoglycan]]
| + | |
| - | [[Category: Peptidyl-rna conjugate complex]]
| + | |
| - | [[Category: Transferase]]
| + | |
| - | [[Category: Transferase-peptide-rna complex]]
| + | |
| Structural highlights
4ii9 is a 3 chain structure with sequence from Weissella viridescens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.66Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
FEMX_WEIVI Involved in the synthesis of the bacterial cell wall. Catalyzes the addition of alanine into the interchain peptide bridge of peptidoglycan precursor using aminoacyl-tRNA(Ala) as amino acid donor. This alanine is added to the epsilon-amino group of the L-lysine of the peptidoglycan UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-L-lysyl-D-alanyl-D-alanine, in a ribosome-independent mechanism (PubMed:11083873, PubMed:12679335, PubMed:15901708, PubMed:23744707, PubMed:4248527). Specific for UDP-N-acetyl-muramoyl-pentapeptide. Has no activity toward UDP-N-acetyl-muramoyl-tetrapeptide or UDP-N-acetyl-muramoyl-tripeptide (PubMed:15901708). Also acts on L-seryl-tRNA(Ser) (PubMed:4248527).[1] [2] [3] [4] [5]
Publication Abstract from PubMed
To gain insight into the catalytic mechanism of non-ribosomal amino acid transferases, peptidyl-RNA conjugates were synthesized for co-crystallization with FemXWv of Weissella viridescens, which transfers L-Ala from Ala-tRNAAla to the peptidoglycan precursor UDP-MurNAc-pentapeptide. The structure of the resulting complex and mutational studies revealed the mechanism by which FemXWv binds its substrates for substrate-assisted catalysis and stabilization of the tetrahedral intermediate.
The Structure of FemX in Complex with a Peptidyl-RNA Conjugate: Mechanism of Aminoacyl Transfer from Ala-tRNA to Peptidoglycan Precursors.,Fonvielle M, Li de La Sierra-Gallay I, El-Sagheer AH, Lecerf M, Patin D, Mellal D, Mayer C, Blanot D, Gale N, Brown T, van Tilbeurgh H, Etheve-Quelquejeu M, Arthur M Angew Chem Int Ed Engl. 2013 Jun 6. doi: 10.1002/anie.201301411. PMID:23744707[6]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Hegde SS, Shrader TE. FemABX family members are novel nonribosomal peptidyltransferases and important pathogen-specific drug targets. J Biol Chem. 2001 Mar 9;276(10):6998-7003. Epub 2000 Nov 16. PMID:11083873 doi:http://dx.doi.org/10.1074/jbc.M008591200
- ↑ Hegde SS, Blanchard JS. Kinetic and mechanistic characterization of recombinant Lactobacillus viridescens FemX (UDP-N-acetylmuramoyl pentapeptide-lysine N6-alanyltransferase). J Biol Chem. 2003 Jun 20;278(25):22861-7. doi: 10.1074/jbc.M301565200. Epub 2003 , Apr 4. PMID:12679335 doi:http://dx.doi.org/10.1074/jbc.M301565200
- ↑ Maillard AP, Biarrotte-Sorin S, Villet R, Mesnage S, Bouhss A, Sougakoff W, Mayer C, Arthur M. Structure-based site-directed mutagenesis of the UDP-MurNAc-pentapeptide-binding cavity of the FemX alanyl transferase from Weissella viridescens. J Bacteriol. 2005 Jun;187(11):3833-8. PMID:15901708 doi:http://dx.doi.org/187/11/3833
- ↑ Fonvielle M, Li de La Sierra-Gallay I, El-Sagheer AH, Lecerf M, Patin D, Mellal D, Mayer C, Blanot D, Gale N, Brown T, van Tilbeurgh H, Etheve-Quelquejeu M, Arthur M. The Structure of FemX in Complex with a Peptidyl-RNA Conjugate: Mechanism of Aminoacyl Transfer from Ala-tRNA to Peptidoglycan Precursors. Angew Chem Int Ed Engl. 2013 Jun 6. doi: 10.1002/anie.201301411. PMID:23744707 doi:10.1002/anie.201301411
- ↑ Plapp R, Strominger JL. Biosynthesis of the peptidoglycan of bacterial cell walls. 18. Purification and properties of L-alanyl transfer ribonucleic acid-uridine diphosphate-N-acetylmuramyl-pentapeptide transferase from Lactobacillus viridescens. J Biol Chem. 1970 Jul 25;245(14):3675-82. PMID:4248527
- ↑ Fonvielle M, Li de La Sierra-Gallay I, El-Sagheer AH, Lecerf M, Patin D, Mellal D, Mayer C, Blanot D, Gale N, Brown T, van Tilbeurgh H, Etheve-Quelquejeu M, Arthur M. The Structure of FemX in Complex with a Peptidyl-RNA Conjugate: Mechanism of Aminoacyl Transfer from Ala-tRNA to Peptidoglycan Precursors. Angew Chem Int Ed Engl. 2013 Jun 6. doi: 10.1002/anie.201301411. PMID:23744707 doi:10.1002/anie.201301411
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