1p4n

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of Weissella viridescens FemX:UDP-MurNAc-pentapeptide complex

Structural highlights

1p4n is a 2 chain structure with sequence from Staphylococcus aureus and Weissella viridescens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9Å
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:4248527, PubMed:12679335, PubMed:15901708, PubMed:23744707). 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]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Members of the FemABX protein family are novel therapeutic targets, as they are involved in the synthesis of the bacterial cell wall. They catalyze the addition of amino acid(s) on the peptidoglycan precursor using aminoacylated tRNA as a substrate. We report here the high-resolution structure of Weissella viridescens L-alanine transferase FemX and its complex with the UDP-MurNAc-pentapeptide. This is the first structure example of a FemABX family member that does not possess a coiled-coil domain. FemX consists of two structurally equivalent domains, separated by a cleft containing the binding site of the UDP-MurNAc-pentapeptide and a long channel that traverses one of the two domains. Our structural studies bring new insights into the evolution of the FemABX and the related GNAT superfamilies, shed light on the recognition site of the aminoacylated tRNA in Fem proteins, and allowed manual docking of the acceptor end of the alanyl-tRNAAla.

Crystal structures of Weissella viridescens FemX and its complex with UDP-MurNAc-pentapeptide: insights into FemABX family substrates recognition.,Biarrotte-Sorin S, Maillard AP, Delettre J, Sougakoff W, Arthur M, Mayer C Structure. 2004 Feb;12(2):257-67. PMID:14962386^[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
↑ Biarrotte-Sorin S, Maillard AP, Delettre J, Sougakoff W, Arthur M, Mayer C. Crystal structures of Weissella viridescens FemX and its complex with UDP-MurNAc-pentapeptide: insights into FemABX family substrates recognition. Structure. 2004 Feb;12(2):257-67. PMID:14962386 doi:10.1016/j.str.2004.01.006

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1p4n"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Weissella viridescens FemX:UDP-MurNAc-pentapeptide complex==
-<StructureSection load='1p4n' size='340' side='right' caption='[[1p4n]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='1p4n' size='340' side='right'caption='[[1p4n]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1p4n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus] and [http://en.wikipedia.org/wiki/Weissella_viridescens Weissella viridescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P4N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1P4N FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1p4n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus] and [https://en.wikipedia.org/wiki/Weissella_viridescens Weissella viridescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P4N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P4N FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><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]] 1.9&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FGA:GAMMA-D-GLUTAMIC+ACID'>FGA</scene>, <scene name='pdbligand=UMA:URIDINE-5-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE'>UMA</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UMA:URIDINE-5-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE'>UMA</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ne9|1ne9]]</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=1p4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p4n OCA], [https://pdbe.org/1p4n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p4n RCSB], [https://www.ebi.ac.uk/pdbsum/1p4n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p4n ProSAT]</span></td></tr>
-<tr><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 Weissella viridescens])</td></tr>
+</table>
-<tr><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>
+== Function ==
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1p4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p4n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1p4n RCSB], [http://www.ebi.ac.uk/pdbsum/1p4n PDBsum]</span></td></tr>
+[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:4248527, PubMed:12679335, PubMed:15901708, PubMed:23744707). 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>
-<table>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p4/1p4n_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p4/1p4n_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1p4n ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 26: @@
 Crystal structures of Weissella viridescens FemX and its complex with UDP-MurNAc-pentapeptide: insights into FemABX family substrates recognition.,Biarrotte-Sorin S, Maillard AP, Delettre J, Sougakoff W, Arthur M, Mayer C Structure. 2004 Feb;12(2):257-67. PMID:14962386<ref>PMID:14962386</ref>
-From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1p4n" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Staphylococcus aureus]]
 [[Category: Weissella viridescens]]
-[[Category: Arthur, M.]]
+[[Category: Arthur M]]
-[[Category: Biarrotte-Sorin, S.]]
+[[Category: Biarrotte-Sorin S]]
-[[Category: Delettre, J.]]
+[[Category: Delettre J]]
-[[Category: Maillard, A.]]
+[[Category: Maillard A]]
-[[Category: Mayer, C.]]
+[[Category: Mayer C]]
-[[Category: Sougakoff, W.]]
+[[Category: Sougakoff W]]
-[[Category: Femx]]
-[[Category: Transferase-transferase substrate complex]]

1p4n

From Proteopedia

Current revision

Crystal Structure of Weissella viridescens FemX:UDP-MurNAc-pentapeptide complex

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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