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1j6u

    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title Crystal structure of an Udp-n-acetylmuramate-alanine ligase MurC (TM0231) from Thermotoga maritima at 2.3 A resolution. Proteins 55 1078-1081 2004
    Site JCSG
    PDB Id 1j6u Target Id 282110
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1194,TM0231, 3.40.1190.10, 89359 Molecular Weight 51868.97 Da.
    Residues 457 Isoelectric Point 5.71
    Sequence mkihfvgiggigmsavalhefsngndvygsnieetertaylrklgipifvphsadnwydpdlviktpav rddnpeivrarmervpienrlhyfrdtlkrekkeefavtgtdgkttttamvahvlkhlrksptvflggi mdslehgnyekgngpvvyeldeseeffsefspnyliitnargdhlenygnsltryrsafekisrntdlv vtfaedeltshlgdvtfgvkkgtytlemrsasraeqkamvekngkrylelklkvpgfhnvlnalavial fdslgydlapvlealeefrgvhrrfsiafhdpetniyviddyahtpdeirnllqtakevfenekivvif qphrysrleredgnfakalqladevvvtevydafeekkngisgkmiwdslkslgkeayfveklpelekv isvsentvflfvgagdiiyssrrfveryqssksspsrvlgsnk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.30 Rfree 0.279
    Matthews' coefficent 5.58 Rfactor 0.234
    Waters 245 Solvent Content 78.82

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    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1j6u
    1. Assessment of homology_based predictions in CASP5
    A Tramontano, V Morea - Proteins: Structure, Function, and , 2003 - Wiley Online Library
     
    2. Development of novel inhibitors targeting intracellular steps of peptidoglycan biosynthesis
    M Kotnik, PS Anderluh, A Prezelj - Current pharmaceutical , 2007 - ingentaconnect.com
     
    3. CASP5 target classification
    LN Kinch, Y Qi, TJP Hubbard - : Structure, Function, and , 2003 - Wiley Online Library
     
    4. Crystal structure of an Udp_n_acetylmuramate_alanine ligase MurC (TM0231) from Thermotoga maritima at 2.3 resolution
    G Spraggon, R Schwarzenbacher - Proteins: Structure, , 2004 - Wiley Online Library
     
    5. Evolutionary trace annotation of protein function in the structural proteome
    S Erdin, RM Ward, E Venner, O Lichtarge - Journal of molecular biology, 2010 - Elsevier
     
    6. A fold-recognition approach to loop modeling
    C Levefelt, D Lundh - Journal of molecular modeling, 2006 - Springer
     
    7. Efficient recognition of protein fold at low sequence identity by conservative application of Psi_BLAST: validation
    FJ Stevens - Journal of Molecular Recognition, 2005 - Wiley Online Library
     
    8. A seqlet-based maximum entropy Markov approach for protein secondary structure prediction
    Q Dong, X Wang, L Lin, Y Guan - Science in China Series C: Life Sciences, 2005 - Springer
     
    9. Peptidoglycan biosynthesis machinery: A rich source of drug targets
    A Gautam, R Vyas, R Tewari - Critical Reviews in , 2011 - ingentaconnect.com
     
    10. Structure and Function of the First Full-Length Murein Peptide Ligase (Mpl) Cell Wall Recycling Protein
    D Das, M Herv, J Feuerhelm, CL Farr, HJ Chiu - PloS one, 2011 - dx.plos.org
     
    11. Purification, crystallization and preliminary X-ray analysis of Escherichia coli UDP-N-acetylmuramoyl: L-alanine ligase (MurC)
    T Deva, KD Pryor, B Leiting, EN Baker - Section D: Biological , 2003 - scripts.iucr.org
     
    12. Comparative modeling of UDP-N-acetylmuramoyl-glycyl-D-glutamate-2, 6-diaminopimelate ligase from Mycobacterium leprae and analysis of its binding features
    A Shanmugam, J Natarajan - Journal of molecular modeling, 2012 - Springer
     
    13. Protein Structure Prediction Using an Augmented Homology Modeling Method: Key Importance of Iterative-Procedures for Obtaining Consistent Quality Models
    S McDonald, S Mylvaganam - Current , 2005 - ingentaconnect.com
     

    Protein Summary

    The TM0231 gene of Thermotoga maritima encodes an UDP-N-acetylmuramate-alanine ligase (MurC; EC 6.3.2.8; COG0773) that is involved in the biosynthesis of the peptidoglycan murein, a major component of the bacterial cell wall (PubMed:15146505). Genes for the peptidoglycan synthesis pathway are also essential for chloroplast division in moss (PubMed:16618924).

    Detailed knowledge of the chemistry and structural features of the murein network is important as the mode of action of the ?-lactam antibiotics, the most important group of antibacterial drugs, and the mechanisms that the bacteria have developed to survive in the presence of these antibiotics, are related to the biosynthesis, three-dimensional structure and morphogenesis of the peptidoglycans.

    There are three domains in the structure of TM0231:
    (a) MurCD N-terminal domain (SCOP sunid:51983) with 3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; incomplete Rossmann-like fold; binds UDP group;
    (b) peptide-binding domain with fold of MurD-like peptide ligases (SCOP sunid 53243) with 3 layers: a/b/a; mixed beta-sheet of 6 strands, order 126345; strand 1 is antiparallel to the rest
    (c) domain with Ribokinase-like fold (SCOP sunid:53612) with core: 3 layers: a/b/a; mixed beta-sheet of 8 strands, order 21345678, strand 7 is antiparallel to the rest; potential superfamily: members of this fold have similar functions but different ATP-binding sites.

    Using FATCAT server structures similar to TM0231 were found  in PDB (i.e.: 1gqqA, 1e0dA, 1e8cA, 1gg4A, 2am1A, 1w78A, 1fgs_, and 1o5zA). There is also significant sequence similarity (analyzed with FFAS03 server) between those structures and TM0231.

    Ligand Summary



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