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The Open Protein Structure Annotation Network
PDB Keyword
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4ntl

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

    Title Crystal structure of a lipoprotein, YaeC family (EF3198) from Enterococcus faecalis V583 at 1.80 A resolution. To be published
    Site JCSG
    PDB Id 4ntl Target Id 420195
    Molecular Characteristics
    Source Enterococcus faecalis v583
    Alias Ids TPS82727,NP_816800.1 Molecular Weight 27347.57 Da.
    Residues 246 Isoelectric Point 5.00
    Sequence dqkedkeitvavqlesskdileiakkeaekkgykinimevsdnvayndavqhdeadanfaqhqpfmemf nkekkadlvavqpiyyfaggfyskeyqdakdlpenakvgipsdptnegralailnangviklkegvgfn gtvadvvenpknitfesidllnlakaydekdiamvfcypaylepaglttkdailledkeaskhyalqvv trkgekdsekikvlkeamttkevaeyikknskganipaf
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.80 Rfree 0.2126
    Matthews' coefficent 3.08 Rfactor 0.1790
    Waters 284 Solvent Content 60.12

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Target ID 420195 can be classified into the Lipoprotein_9 (PF03180) Pfam family but it is also a member of a clan containg 22 additional Pfam familes (Pfam Clan PBP CL0177). Members of this clan include a diverse set of periplamic binding proteins that usually close around a bound ligand. This architecture is found in transcriptional regulators, such as the lac repressors. In addition serveral eukaryotic receptors sometimes show extracellular domains homologus tro PBP and these receptors include glutamate/glycine-gated ion channels.

    Shown below is a ribbons representation of the monomeric structure of target id 420195 color coded with the N-terminal end in blue and the C-terminal end in red.

    SP17422AA_monomer.png

     

     

     

     

     

    The protein consists of two structural domains. The larger of the structural domains (marine blue) is composed of discontinuous segnents of the protein sequence. The two domains are colored in marine blue and green. The larger domnain (marine blue) is composed of residues 31-113 and 225-572, and the second domain green is composed of residues 114-224.

     

    SP17422AA_domain_assignment.png

     

     

     

     

     


    A search of the PDB using DALI, shows that target id 420195 has structural similarity to the following hits.

     

    PDB ID DALI Z-Score rmsd (Ang) length of alignment number of residues in hit structure sequence identity (%) Description
    4k3f 29.2 2.9 237 241 37 Crystal structure of a putative TonB-dependent receptor (PA5505) from Pseudomonas aeruginosa PAO1 at 1.60 A resolution
    1xs5 28.6 2.8 236 240 32 The Crystal Structure of Lipoprotein Tp32 from Treponema pallidum [Ref]
    4ib2 28.5 3.0 238 244 38 Crystal structure of a putative lipoprotein (RUMGNA_00858) from Ruminococcus gnavus ATCC 29149 at 1.76 A resolution
    4got 28.1 2.9 240 248 36 Crystal structure of a putative methionine-binding lipoprotein (BSU32730) from Bacillus subtilis subsp. subtilis str. 168 at 1.95 A resolution
    3tqw 27.8 2.8 233 236 30 Structure of a ABC transporter, periplasmic substrate-binding protein from Coxiella burnetii
    4ef2 27.1 3.2 239 244 32 Crystal structure of a pheromone cOB1 precursor/lipoprotein, YaeC family (EF2496) from Enterococcus faecalis V583 at 2.10 A resolution
    1p99 26.4 3.1 237 255 25 1.7A crystal structure of protein PG110 from Staphylococcus aureus[Ref]
    3k2d 26.2 3.0 229 238 31 Crystal structure of Immunogenic lipoprotein A from Vibrio vulnificus [Ref]
    3gxa 25.6 3.0 235 240 27 Crystal structure of GNA1946[Ref]
    3up9 25.4 3.5 235 240 27 Crystal structure of a putative lipoprotein (ACTODO_00931) from Actinomyces odontolyticus ATCC 17982 at 2.35 A resolution

    Five of these hits include PDB ID 4k3f, 4ib2, 4got, and 4ef2, which are JCSG structures. Perhaps the most significant difference between target id 420195 is that whereas the four other JCSG homologs contain a free Met/Mse amino acid ligand bound at the interface between the two domains, target id 420195 does not show a bound Met/Mse ligand. Instead of a Mse/Met, there is an EDO bound instead. This indicates that target id 420195 binds a different exogeneous ligand than the other JCSG homologs.

    Ligand Summary

    Reviews

    References

     

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