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PDBsum entry 1j6u

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protein links
Ligase PDB id
1j6u
Jmol
Contents
Protein chain
430 a.a. *
Waters ×245
* Residue conservation analysis
PDB id:
1j6u
Name: Ligase
Title: Crystal structure of udp-n-acetylmuramate-alanine ligase murc (tm0231) from thermotoga maritima at 2.3 a resolution
Structure: Udp-n-acetylmuramate-alanine ligase murc. Chain: a. Synonym: udp-n-acetylmuramoyl-l-alanine synthetase. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Gene: tm0231. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PQS)
Resolution:
2.30Å     R-factor:   0.234     R-free:   0.279
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref:
G.Spraggon et al. (2004). Crystal structure of an Udp-n-acetylmuramate-alanine ligase MurC (TM0231) from Thermotoga maritima at 2.3 A resolution. Proteins, 55, 1078-1081. PubMed id: 15146505 DOI: 10.1002/prot.20034
Date:
29-Aug-02     Release date:   06-Nov-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9WY73  (MURC_THEMA) -  UDP-N-acetylmuramate--L-alanine ligase
Seq:
Struc:
457 a.a.
430 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.3.2.8  - UDP-N-acetylmuramate--L-alanine ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Peptidoglycan Biosynthesis (Part 1)
      Reaction: ATP + UDP-N-acetylmuramate + L-alanine = ADP + phosphate + UDP-N- acetylmuramoyl-L-alanine
ATP
+ UDP-N-acetylmuramate
+ L-alanine
= ADP
+ phosphate
+ UDP-N- acetylmuramoyl-L-alanine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     cell wall organization   6 terms 
  Biochemical function     nucleotide binding     4 terms  

 

 
    reference    
 
 
DOI no: 10.1002/prot.20034 Proteins 55:1078-1081 (2004)
PubMed id: 15146505  
 
 
Crystal structure of an Udp-n-acetylmuramate-alanine ligase MurC (TM0231) from Thermotoga maritima at 2.3 A resolution.
G.Spraggon, R.Schwarzenbacher, A.Kreusch, C.C.Lee, P.Abdubek, E.Ambing, T.Biorac, L.S.Brinen, J.M.Canaves, J.Cambell, H.J.Chiu, X.Dai, A.M.Deacon, M.DiDonato, M.A.Elsliger, S.Eshagi, R.Floyd, A.Godzik, C.Grittini, S.K.Grzechnik, E.Hampton, L.Jaroszewski, C.Karlak, H.E.Klock, E.Koesema, J.S.Kovarik, P.Kuhn, I.Levin, D.McMullan, T.M.McPhillips, M.D.Miller, A.Morse, K.Moy, J.Ouyang, R.Page, K.Quijano, A.Robb, R.C.Stevens, H.van den Bedem, J.Velasquez, J.Vincent, F.von Delft, X.Wang, B.West, G.Wolf, Q.Xu, K.O.Hodgson, J.Wooley, S.A.Lesley, I.A.Wilson.
 
  ABSTRACT  
 
No abstract given.

 
  Selected figure(s)  
 
Figure 1.
Figure 1. Crystal structure of TM0231. (A) Stereo ribbon diagram of Thermotoga maritima TM0231 color coded from N-terminus (blue) to C-terminus (red) showing the domain organization and the location of the active-site crevice (arrow). elices (H1-H17) and -strands ( 1- 21) are indicated. Figure 1A produced with PYMOL (DeLano Scientific LLC). (B) Diagram showing the secondary structure elements in TM0231 superimposed on its primary sequence. Disordered loop-regions are indicated with a dashed line and -hairpins are depicted in red. Figure 1B adapted from PDBsum (http://www.biochem.ncl.ac.uk/bsm/pdbsum).
Figure 2.
Figure 2. Ribbon diagram of a superposition of TM0231 (cyan) and MurC from Haemophilus influenzae (white; PDB: 1P3D). The substrate UMA (uridine-5 -diphosphate-n-acetylmuramoyl-L-alanine) and the cofactor ANP (phosphoaminophosphonic acid-adenylate esters) bound to MurC from Haemophilus influenzae are depicted in cpk mode.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2004, 55, 1078-1081) copyright 2004.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20361049 J.O.Wrabl, and V.J.Hilser (2010).
Investigating homology between proteins using energetic profiles.
  PLoS Comput Biol, 6, e1000722.  
20024979 T.Tomasić, N.Zidar, A.Kovac, S.Turk, M.Simcic, D.Blanot, M.Müller-Premru, M.Filipic, S.G.Grdadolnik, A.Zega, M.Anderluh, S.Gobec, D.Kikelj, and L.Peterlin Masic (2010).
5-Benzylidenethiazolidin-4-ones as multitarget inhibitors of bacterial Mur ligases.
  ChemMedChem, 5, 286-295.  
19542229 A.Boniface, C.Parquet, M.Arthur, D.Mengin-Lecreulx, and D.Blanot (2009).
The elucidation of the structure of Thermotoga maritima peptidoglycan reveals two novel types of cross-link.
  J Biol Chem, 284, 21856-21862.  
18266853 H.Barreteau, A.Kovac, A.Boniface, M.Sova, S.Gobec, and D.Blanot (2008).
Cytoplasmic steps of peptidoglycan biosynthesis.
  FEMS Microbiol Rev, 32, 168-207.  
17908308 A.Bresell, and B.Persson (2007).
Characterization of oligopeptide patterns in large protein sets.
  BMC Genomics, 8, 346.  
17608695 M.Ishibashi, K.Kurokawa, S.Nishida, K.Ueno, M.Matsuo, and K.Sekimizu (2007).
Isolation of temperature-sensitive mutations in murC of Staphylococcus aureus.
  FEMS Microbiol Lett, 274, 204-209.  
16595662 A.Boniface, A.Bouhss, D.Mengin-Lecreulx, and D.Blanot (2006).
The MurE synthetase from Thermotoga maritima is endowed with an unusual D-lysine adding activity.
  J Biol Chem, 281, 15680-15686.  
17064285 S.B.Conners, E.F.Mongodin, M.R.Johnson, C.I.Montero, K.E.Nelson, and R.M.Kelly (2006).
Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species.
  FEMS Microbiol Rev, 30, 872-905.  
17139082 T.Deva, E.N.Baker, C.J.Squire, and C.A.Smith (2006).
Structure of Escherichia coli UDP-N-acetylmuramoyl:L-alanine ligase (MurC).
  Acta Crystallogr D Biol Crystallogr, 62, 1466-1474.
PDB code: 2f00
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 code is shown on the right.