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1kq4

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

    Title Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc.Natl.Acad.Sci.USA 99 11664-11669 2002
    Site JCSG
    PDB Id 1kq4 Target Id 282322
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1206,TM0449, 84968 Molecular Weight 26002.69 Da.
    Residues 220 Isoelectric Point 7.83
    Sequence mkidildkgfvelvdvmgndlsavraarvsfdmglkdeerdrhlieylmkhghetpfehivftfhvkap ifvarqwfrhriasynelsgrysklsyefyipsperlegykttippervtekiseivdkayrtylelie sgvprevarivlplnlytrffwtvnarslmnflnlradshaqweiqqyalaiarifkekcpwtfeaflk yaykgdilkevqv
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.25 Rfree 0.24
    Matthews' coefficent 2.02 Rfactor 0.192
    Waters 274 Solvent Content 39.00

    Pathway

    Reactions found in Metabolic Reconstruction for TM0449

    Name: thymidylate synthase (FAD dependent)
    Metabolic Subsystem: Pyrimidine Metabolism
    Reaction: : dump + h + mlthf + nadph --> dtmp + nadp + thf

     

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1kq4
    1. Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline
    SA Lesley, P Kuhn, A Godzik - Proceedings of the , 2002 - National Acad Sciences
     
    2. Crystal structure of thy1, a thymidylate synthase complementing protein from Thermotoga maritima at 2.25 resolution
    P Kuhn, SA Lesley, II Mathews - Proteins: Structure, , 2002 - Wiley Online Library
     
    3. Genetic evidence for a novel thymidylate synthase in the halophilic archaeon Halobacterium salinarum and in Campylobacter jejuni
    M Giladi, G Bitan_Banin, M Mevarech - FEMS microbiology , 2002 - Wiley Online Library
     
    4. Prediction of active sites for protein structures from computed chemical properties
    J Ko, LF Murga, Y Wei, MJ Ondrechen - Bioinformatics, 2005 - Oxford Univ Press
     
    5. DNA building block reinvented
    AG Murzin - Science, 2002 - sciencemag.org
     
    6. What we have learned about prokaryotes from structural genomics
    D Frishman - Omics A Journal of Integrative Biology, 2003 - online.liebertpub.com
     
    7. 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
     
    8. Developments in structural genomics: protein purification and function interpretation
    CZ Zhou, YX Chen - Current Genomics, 2004 - ingentaconnect.com
     
    9. Static and dynamic characteristics of protein contact networks
    S Khor - Arxiv preprint arXiv:1011.2222, 2010 - arxiv.org
     
    10. Folate_Dependent Thymidylate_Forming Enzymes
    H Myllykallio, S Skouloubris, H Grosjean, U Liebl - 2009 - fly-bay.net
     

    Protein Summary

    Gene TM0449 from Thermotoga maritima encodes a flavin-dependent Thymidylate Synthase Thy1 (ThyX)  (EC.2.1.1.148; 5,10-methylenetetrahydrofolate,FADH2:dUMP C-methyltransferase) that belongs to Pfam02511 and are similar to proteins from COG1351. Thy1 (ThyX) enzymes are mainly limited to microbial and viral genomes that lack ThyA and are an important drug target as they occur in several pathogens like e.g.: Helicobacter pylori, Chlamydia trachomatis or Mycobacterium tuberculosis but are absent in humans (PubMed:12029065, 16730023). 

     

    When the structure of Thy1 from Thermotoga maritima solved by JCSG was published in 2002, it was correctly proposed that Thy1 is capable of both methyl transfer and reduction of substrate or a cofactor (PubMed:12211025). The flavin-dependent thymidylate synthesis was described in details in a series of papers (PubMed:12029065, 16730023, 15123820, 15591067, 16707489). Despite enormous amount of research data gathered since the first reports about Thy1 function (PubMed:12029065) and structure (PubMed:12211025) new interesting properties of this enzymes, like RNA-binding (PubMed:16176183) are being discovered.
    Thy1 (TM0449) from Thermotoga maritima is a tetramer composed of identical 220-residue subunits with a unique ?+? fold (SCOP fold id: 69795) where each monomer consist of: antiparallel 5-stranded ?-sheet (order 12354), a long ?-helix, and six ?-helices on one side of the sheet (Figure 1) (PubMed:12211025). The interface between subunits of Thy1 tetramer is formed by a partial stacking of the ?-sheets and two long helices, where a large active site pocket with four channels running along the molecular interfaces is formed (PubMed:12211025).

    Ligand Summary



    References

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