The Open Protein Structure Annotation Network
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    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title Crystal structure of aminomethyltransferase (T protein; tetrahydrofolate-dependent) of glycine cleavage system (np417381) from Escherichia coli k12 at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 1vlo Target Id 358290
    Molecular Characteristics
    Source Escherichia coli k12
    Alias Ids TPS1387,NP_417381.1 Molecular Weight 40144.62 Da.
    Residues 364 Isoelectric Point 5.36
    Sequence maqqtplyeqhtlcgarmvdfhgwmmplhygsqidehhavrtdagmfdvshmtivdlrgsrtreflryl landvakltksgkalysgmlnasggviddlivyyftedffrlvvnsatrekdlswitqhaepfgieitv rddlsmiavqgpnaqakaatlfndaqrqavegmkpffgvqagdlfiattgytgeagyeialpnekaadf wralveagvkpcglgardtlrleagmnlygqemdetisplaanmgwtiawepadrdfigrealevqreh gteklvglvmtekgvlrnelpvrftdaqgnqhegiitsgtfsptlgysialarvpegigetaivqirnr empvkvtkpvfvrngkava
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.70 Rfree 0.19514
    Matthews' coefficent 1.93 Rfactor 0.15872
    Waters 419 Solvent Content 35.81

    Ligand Information


    Google Scholar output for 1vlo
    1. The Buccaneer software for automated model building. 1. Tracing protein chains
    K Cowtan - Acta Crystallographica Section D: Biological , 2006 - scripts.iucr.org
    2. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
    3. Domain definition and target classification for CASP6
    M Tress, CH Tai, G Wang, I Ezkurdia - PROTEINS: , 2005 - Wiley Online Library
    4. Fast and accurate algorithms for protein side-chain packing
    J Xu, B Berger - Journal of the ACM (JACM), 2006 - dl.acm.org
    5. Crystal structure of human T-protein of glycine cleavage system at 2.0 resolution and its implication for understanding non-ketotic hyperglycinemia
    K Okamura-Ikeda, H Hosaka, M Yoshimura - Journal of molecular , 2005 - Elsevier
    6. Stochastic pairwise alignments and scoring methods for comparative protein structure modeling
    AC Marko, K Stafford, T Wymore - Journal of chemical information , 2007 - ACS Publications
    7. Prediction of protein domain boundaries from statistics of appearance of amino acid residues
    OV Galzitskaya, NV Dovidchenko, MY Lobanov - Molecular Biology, 2006 - Springer
    8. Protein structure prediction based on the sliced lattice model
    CC Wang, CB Yang, HY Ann - 2008 Conference on , 2005 - etd.lib.nsysu.edu.tw
    9. Crystal structure of aminomethyltransferase in complex with dihydrolipoyl-H-protein of the glycine cleavage system
    K Okamura-Ikeda, H Hosaka, N Maita - Journal of Biological , 2010 - ASBMB
    10. Prediction of Protein Backbone Based on the Sliced Lattice Model
    CC Wang, CB Yang, HY Ann, HY Chang - 2008 - csie.npu.edu.tw
    11. Solution Structure of LCI, A Novel Antimicrobial Peptide from Bacillus subtilis
    W Gong, J Wang, Z Chen, B Xia, G Lu - Biochemistry, 2011 - ACS Publications

    Protein Summary

    The gene NP_417381.1 from Escherichia coli encodes the enzyme of aminomethyltransferase (T protein, tetrahydrofolate-dependent PF01571) of glycine cleavage system COG0404 EC:  The protein belongs to the class of alpha and beta proteins (a+b) and reveals folate binding domain fold type SCOP103025, similar to N,N-aminomethyltransferase. The glycine cleavage system catalyzes the oxidative decarboxylation of glycine in bacteria and in mitochondria of animals and plants. Its deficiency in human causes nonketotic hyperglycinemia, an inborn error of glycine metabolism. T-protein, one of the four components of the glycine cleavage system, is a tetrahydrofolate dependent aminomethyltransferase. It catalyzes the transfer of the methylene carbon unit to tetrahydrofolate from the methylamine group covalently attached to the lipoamide arm of H-protein [Ref]. The structure of the human enzyme as well as those from Thermotoga maritima and Pyrococcus horikoshii have been solved and discussed previously [Ref][Ref][Ref].

    Ligand Summary





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