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1vk3

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

    Title Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 A resolution. Proteins 63 1106-1111 2006
    Site JCSG
    PDB Id 1vk3 Target Id 283111
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1272,TM1246 Molecular Weight 65965.23 Da.
    Residues 603 Isoelectric Point 5.38
    Sequence mklrylnilkeklgreptfvelqafsvmwsehcgyshtkkyirrlpktgfegnagvvnlddyysvafki eshnhpsaiepyngaatgvggiirdvlamgarptaifdslhmsriidgiiegiadygnsigvptvggel risslyahnplvnvlaagvvrndmlvdskasrpgqvivifggatgrdgihgasfasedltgdkatklsi qvgdpfaekmlieaflemveeglvegaqdlgaggvlsatselvakgnlgaivhldrvplrepdmepwei lisesqermavvtspqkasrileiarkhllfgdvvaevieepvyrvmyrndlvmevpvqllanapeedi veytpgkipefkrvefeevnarevfeqydhmvgtdtvvppgfgaavmrikrdggyslvthsradlalqd tywgtliavlesvrktlsvgaeplaitncvnygdpdvdpvglsammtalknacefsgvpvasgnaslyn tyqgkpipptlvvgmlgkvnpqkvakpkpskvfavgwndfelerekelwrairklseegafilsssqll trthvetfreyglkievklpevrpahqmvlvfsertpvvdvpvkeigtlsr
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.15 Rfree 0.25423
    Matthews' coefficent 2.14 Rfactor 0.18645
    Waters 221 Solvent Content 41.95

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1vk3
    1. The Buccaneer software for automated model building. 1. Tracing protein chains
    K Cowtan - Acta Crystallographica Section D: Biological , 2006 - scripts.iucr.org
     
    2. Complexed structures of formylglycinamide ribonucleotide amidotransferase from Thermotoga maritima describe a novel ATP binding protein superfamily
    M Morar, R Anand, AA Hoskins, JA Stubbe - Biochemistry, 2006 - ACS Publications
     
    3. Structural Studies of Thiamin Monophosphate Kinase in Complex with Substrates and Products,
    KM McCulloch, C Kinsland, TP Begley, SE Ealick - Biochemistry, 2008 - ACS Publications
     
    4. High-throughput protein production for X-ray crystallography and use of size exclusion chromatography to validate or refute computational biological unit predictions
    D McMullan, JM Canaves, K Quijano - Journal of structural and , 2005 - Springer
     
    5. A fold-recognition approach to loop modeling
    C Levefelt, D Lundh - Journal of molecular modeling, 2006 - Springer
     
    6. Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 resolution
    II Mathews, S Krishna - Proteins: Structure, , 2006 - Wiley Online Library
     
    7. Formylglycinamide Ribonucleotide Amidotransferase from Thermotoga maritima: Structural Insights into Complex Formation
    M Morar, AA Hoskins, JA Stubbe, SE Ealick - Biochemistry, 2008 - ACS Publications
     
    8. A novel structural motif and structural trees for proteins containing it
    AM Kargatov, AV Efimov - Biochemistry (Moscow), 2010 - Springer
     

    Protein Summary

    The TM1246 gene (smPurL) from Thermotoga maritima encodes a phospho-ribosyl-formylglycinamidine synthase II (FGAM; EC 6.3.5.3; COG0046), a purine biosynthesis enzyme.

    In Gram-positive bacteria, archaebacteria, and Gram-negative T. maritima TM1246 (PurL, designated here as smPurL) forms a complex with PurS and PurQ. In eukaryotes, proteobacteria and other Gram-negative bacteria PurL is a part of multidomain protein formed by gene fusion between synthase and glutamine amidotransferase (PubMed:12049665 and PDB structures: 1t3t, 1cli, 1vqv).

    Several genes predicted (http://string.embl.de) to have functional associations with TM1246 are in the same genomic neighborhood (i.e.: TM1245, TM1251, TM1248, TM1247, TM1243, TM1250, TM1249, TM0446, TM0447, and TM1095).

    The structure of TM1246 monomer comprises 4 ?+? domains, where domains 1 and 3 has Bacillus chorismate mutase-like fold (SCOP sunid 55297). Domain 2 and 4 of TM1246 have duplicated PurM C-terminal domain-like fold (SCOP sunid 56041). 

    The five highly conserved residues located in C-terminal half of PurL from Salmonella typhimurium (PDB id 1t3t) are involved in interactions with the ADP moiety and the Mg2+ ions but (except Glu718 of PDB structure 1t3t) those residues are not conserved in TM1246 (PubMed:16544324).



    Ligand Summary



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