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PDBsum entry 1p4n

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protein ligands metals links
Transferase/transferase substrate PDB id
1p4n
Jmol
Contents
Protein chain
335 a.a. *
Ligands
UMA-FGA-LYS-DAL-
DAL
GOL ×2
Metals
_MG ×3
Waters ×466
* Residue conservation analysis
PDB id:
1p4n
Name: Transferase/transferase substrate
Title: Crystal structure of weissella viridescens femx:udp-murnac- pentapeptide complex
Structure: Femx. Chain: a. Engineered: yes. Udp-murnac-pentapeptide. Chain: b
Source: Weissella viridescens. Organism_taxid: 1629. Gene: femx. Expressed in: escherichia coli. Expression_system_taxid: 562. Staphylococcus aureus. Organism_taxid: 1280
Biol. unit: Dimer (from PQS)
Resolution:
1.90Å     R-factor:   0.172     R-free:   0.207
Authors: S.Biarrotte-Sorin,A.Maillard,J.Delettre,W.Sougakoff,M.Arthur
Key ref:
S.Biarrotte-Sorin et al. (2004). Crystal structures of Weissella viridescens FemX and its complex with UDP-MurNAc-pentapeptide: insights into FemABX family substrates recognition. Structure, 12, 257-267. PubMed id: 14962386 DOI: 10.1016/S0969-2126(04)00009-7
Date:
23-Apr-03     Release date:   10-Feb-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9EY50  (Q9EY50_LACVI) -  FemX
Seq:
Struc:
336 a.a.
335 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     peptidoglycan biosynthetic process   1 term 
  Biochemical function     transferase activity, transferring amino-acyl groups     1 term  

 

 
DOI no: 10.1016/S0969-2126(04)00009-7 Structure 12:257-267 (2004)
PubMed id: 14962386  
 
 
Crystal structures of Weissella viridescens FemX and its complex with UDP-MurNAc-pentapeptide: insights into FemABX family substrates recognition.
S.Biarrotte-Sorin, A.P.Maillard, J.Delettré, W.Sougakoff, M.Arthur, C.Mayer.
 
  ABSTRACT  
 
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.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Weissella viridescens FemX Structure and Its Complex with UDP-MurNAc-Pentapeptide(A) FemX is a 38 kDa enzyme constituted by two domains, separated by a cleft: domain 1 represented in blue (residues 1-145 and 317-335) and domain 2 in magenta (residues 146-316). The two domains have a similar fold (rms deviation of 2.0 for the 73 Ca atoms in common).(B) Crossed-eye stereo view of the binary complex formed by FemX and the UDP-MurNAc-pentapeptide. Complexation of FemX does not lead to structural rearrangements in the protein (rms deviation of 0.2 ). The UDP-MurNAc-pentapeptide, shown in green, lies in the cleft between the two domains and mostly contacts domain 1.(C) Crossed-eye stereo ribbon plot of FemX (red) is shown optimally superimposed with S. aureus FemA (yellow, Protein Data Bank code 1LRZ, 2.1 resolution). The overall structures are similar (rms deviation of 2.8 for the 309 Ca atoms in common). The major structural difference is the absence in FemX of the coiled-coil region constituted by two helices inserted in FemA domain 2. The figure was prepared using PyMOL (DeLano, 2002).
 
  The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 257-267) copyright 2004.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20416511 B.T.Circello, A.C.Eliot, J.H.Lee, W.A.van der Donk, and W.W.Metcalf (2010).
Molecular cloning and heterologous expression of the dehydrophos biosynthetic gene cluster.
  Chem Biol, 17, 402-411.  
19903480 R.Banerjee, S.Chen, K.Dare, M.Gilreath, M.Praetorius-Ibba, M.Raina, N.M.Reynolds, T.Rogers, H.Roy, S.S.Yadavalli, and M.Ibba (2010).
tRNAs: cellular barcodes for amino acids.
  FEBS Lett, 584, 387-395.  
19151092 M.Fonvielle, M.Chemama, R.Villet, M.Lecerf, A.Bouhss, J.M.Valéry, M.Ethève-Quelquejeu, and M.Arthur (2009).
Aminoacyl-tRNA recognition by the FemXWv transferase for bacterial cell wall synthesis.
  Nucleic Acids Res, 37, 1589-1601.  
18081839 A.Bouhss, A.E.Trunkfield, T.D.Bugg, and D.Mengin-Lecreulx (2008).
The biosynthesis of peptidoglycan lipid-linked intermediates.
  FEMS Microbiol Rev, 32, 208-233.  
18842590 G.De Pascale, A.J.Lloyd, J.A.Schouten, A.M.Gilbey, D.I.Roper, C.G.Dowson, and T.D.Bugg (2008).
Kinetic Characterization of Lipid II-Ala:Alanyl-tRNA Ligase (MurN) from Streptococcus pneumoniae using Semisynthetic Aminoacyl-lipid II Substrates.
  J Biol Chem, 283, 34571-34579.  
18266857 J.L.Mainardi, R.Villet, T.D.Bugg, C.Mayer, and M.Arthur (2008).
Evolution of peptidoglycan biosynthesis under the selective pressure of antibiotics in Gram-positive bacteria.
  FEMS Microbiol Rev, 32, 386-408.  
18194336 W.Vollmer, D.Blanot, and M.A.de Pedro (2008).
Peptidoglycan structure and architecture.
  FEMS Microbiol Rev, 32, 149-167.  
18063720 J.van Heijenoort (2007).
Lipid intermediates in the biosynthesis of bacterial peptidoglycan.
  Microbiol Mol Biol Rev, 71, 620-635.  
17891155 K.Watanabe, Y.Toh, K.Suto, Y.Shimizu, N.Oka, T.Wada, and K.Tomita (2007).
Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase.
  Nature, 449, 867-871.
PDB codes: 2z3k 2z3l 2z3m 2z3n 2z3o 2z3p
17932062 R.Villet, M.Fonvielle, P.Busca, M.Chemama, A.P.Maillard, J.E.Hugonnet, L.Dubost, A.Marie, N.Josseaume, S.Mesnage, C.Mayer, J.M.Valéry, M.Ethève-Quelquejeu, and M.Arthur (2007).
Idiosyncratic features in tRNAs participating in bacterial cell wall synthesis.
  Nucleic Acids Res, 35, 6870-6883.  
17242373 X.Dong, M.Kato-Murayama, T.Muramatsu, H.Mori, M.Shirouzu, Y.Bessho, and S.Yokoyama (2007).
The crystal structure of leucyl/phenylalanyl-tRNA-protein transferase from Escherichia coli.
  Protein Sci, 16, 528-534.
PDB code: 2cxa
17110926 K.Suto, Y.Shimizu, K.Watanabe, T.Ueda, S.Fukai, O.Nureki, and K.Tomita (2006).
Crystal structures of leucyl/phenylalanyl-tRNA-protein transferase and its complex with an aminoacyl-tRNA analog.
  EMBO J, 25, 5942-5950.
PDB codes: 2dps 2dpt
16855251 M.N.Hung, E.Rangarajan, C.Munger, G.Nadeau, T.Sulea, and A.Matte (2006).
Crystal structure of TDP-fucosamine acetyltransferase (WecD) from Escherichia coli, an enzyme required for enterobacterial common antigen synthesis.
  J Bacteriol, 188, 5606-5617.
PDB codes: 2fs5 2ft0
16826240 R.Rai, A.Mushegian, K.Makarova, and A.Kashina (2006).
Molecular dissection of arginyltransferases guided by similarity to bacterial peptidoglycan synthases.
  EMBO Rep, 7, 800-805.  
15901708 A.P.Maillard, S.Biarrotte-Sorin, R.Villet, S.Mesnage, A.Bouhss, W.Sougakoff, C.Mayer, and M.Arthur (2005).
Structure-based site-directed mutagenesis of the UDP-MurNAc-pentapeptide-binding cavity of the FemX alanyl transferase from Weissella viridescens.
  J Bacteriol, 187, 3833-3838.
PDB codes: 1xe4 1xf8 1xix
  16511014 S.Biarrotte-Sorin, and C.Mayer (2005).
Cloning, purification, crystallization and preliminary crystallographic analysis of a hypothetical acetyltransferase from Pyrococcus furiosus.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 269-270.  
15158255 G.Mallorquí-Fernández, A.Marrero, S.García-Piquè, R.García-Castellanos, and F.X.Gomis-Rüth (2004).
Staphylococcal methicillin resistance: fine focus on folds and functions.
  FEMS Microbiol Lett, 235, 1-8.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.