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The Open Protein Structure Annotation Network
PDB Keyword
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1vpv

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

    Title Crystal structure of UPF0230 protein TM1468 (TM1468) from Thermotoga maritima at 2.45 A resolution. To be published
    Site JCSG
    PDB Id 1vpv Target Id 283326
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1291,TM1468, 429685 Molecular Weight 32572.90 Da.
    Residues 288 Isoelectric Point 5.86
    Sequence mkvkilvdstadvpfswmekydidsiplyvvwedgrsepderepeeimnfykrireagsvpktsqpsve dfkkrylkykeedydvvlvltlssklsgtynsavlaskevdipvyvvdtllasgaiplparvaremlen gatieevlkkldermknkdfkaifyvsnfdylvkggrvskfqgfvgnllkirvclhiengelipyrkvr gdkkaiealieklredtpegsklrvigvhadneagvvellntlrksyevvdeiispmgkvitthvgpgt vgfgievlerkr
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.45 Rfree 0.25188
    Matthews' coefficent 2.42 Rfactor 0.17987
    Waters 107 Solvent Content 48.83

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1vpv
    1. Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families
    K Ellrott, L Jaroszewski, W Li, JC Wooley - PLoS computational , 2010 - dx.plos.org
     
    2. Structure of a fatty acid-binding protein from Bacillus subtilis determined by sulfur-SAD phasing using in-house chromium radiation
    J Nan, Y Zhou, C Yang, E Brostromer - Section D: Biological , 2009 - scripts.iucr.org
     

    Protein Summary

    The gene TM1468 from Thermotoga maritima encodes a putative fatty-acid binding domain protein (NP_229268), from a well-conserved among bacteria DegV family PF02645 COG1307. STRING genome context analysis provides a reliable hit (score 0.98) based on neighbourhood, gene fusion, and co-ocurrence with the uncharacterized protein TM1772. 

    SCOP classifies 1vpv in the alpha/beta class, DAK1/DegV-like superfamily, DegV-like family. DALI top hits are with the DegV family proteins PDB:2dt8 (Z=35), PDB:3fys (Z=33), the APC36103 protein PDB:1pzx (Z=32) and the SPY1493 protien PDB:2g7z (Z=32). Weaker hits are observed with the dihydroxyacetone kinases PDB:3ct4 and PDB:2iu4 (Z=16).

    The structure of TM1468 protein had been previously solved in a different crystal form and resolution (1MGP). Both solved structures of the TM1468 protein contain co-crystallized palmitic acid, which is consistent with its putative fatty-acid binding function. The TM1468 structure is in a closed conformation, which is probably induced by palmitate binding.

    The fold type of the TM1468 is similar to that of lipoate-protein ligase A from E.coli 1X2G (SufE/NifU fold.)  Lipoate-protein ligase A (LplA) catalyzes the formation of lipoyl-AMP from lipoate and ATP and then transfers the lipoyl moiety to a specific lysine residue on the acyltransferase subunit of α-ketoacid dehydrogenase complexes and on H-protein of the glycine cleavage system.  

    Ligand Summary



    References

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