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 CBS domain protein/ACT domain protein (TM0892) from Thermotoga maritima at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 1vr9 Target Id 282761
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1243,TM0892, 84890, 90109 Molecular Weight 22891.12 Da.
    Residues 201 Isoelectric Point 4.81
    Sequence mkvkkwvtqdfpmveesatvreclhrmrqyqtnecivkdreghfrgvvnkedlldldldssvfnkvslp dffvheednithalllflehqepylpvvdeemrlkgavslhdflealiealamdvpgirfsvlledkpg elrkvvdalalsninilsvittrsgdgkrevlikvdavdegtliklfeslgikiesiekeegf
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.70 Rfree 0.26992
    Matthews' coefficent 2.64 Rfactor 0.24563
    Waters 242 Solvent Content 53.45

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    Ligand Information


    Google Scholar output for 1vr9
    1. The Buccaneer software for automated model building. 1. Tracing protein chains
    K Cowtan - Acta Crystallographica Section D: Biological , 2006 - scripts.iucr.org
    2. Structure of a CBS-domain pair from the regulatory 1 subunit of human AMPK in complex with AMP and ZMP
    P Day, A Sharff, L Parra, A Cleasby - Section D: Biological , 2007 - scripts.iucr.org
    3. Biochemical and Structural Characterization of a Novel Family of Cystathionine [beta]-Synthase Domain Proteins Fused to a Zn Ribbon-Like Domain
    M Proudfoot, SA Sanders, A Singer, R Zhang - Journal of molecular , 2008 - Elsevier
    4. Structure of the Bateman2 domain of yeast Snf4: dimeric association and relevance for AMP binding
    MJ Rudolph, GA Amodeo, SH Iram, SP Hong, G Pirino - Structure, 2007 - Elsevier
    5. Binding of S-methyl-5'-thioadenosine and S-adenosyl-L-methionine to protein MJ0100 triggers an open-to-closed conformational change in its CBS motif pair
    M Lucas, JA Encinar, EA Arribas, I Oyenarte - Journal of molecular , 2010 - Elsevier
    6. Structures and functional implications of an AMP-binding cystathionine _-synthase domain protein from a hyperthermophilic archaeon
    NP King, TM Lee, MR Sawaya, D Cascio - Journal of molecular , 2008 - Elsevier
    7. The structure and unusual protein chemistry of hypoxic response protein 1, a latency antigen and highly expressed member of the DosR regulon in Mycobacterium
    ML Sharpe, C Gao, SL Kendall, EN Baker - Journal of molecular , 2008 - Elsevier
    H Tuominen - 2011 - doria.fi
    9. Functional studies on bacterial nucleotide-regulated inorganic pyrophosphatases
    J Jmsn - 2011 - doria.fi
    10. Refinement of All-atom Backbone Prediction of Proteins
    HY Chang - 2008 - etd.lib.nsysu.edu.tw

    Protein Summary

    The TM0892 gene from Thermotoga maritima encodes the NP_228700 protein containing a cystathionine beta-synthase (CBS) domain pair at the N-terminus (PF00571, COG0517) and an ACT domain (PF01842) at the C-terminus. The genetic neighborhood of TM0892 suggests a high degree of confidence in a functional association with 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (EC, undecaprenyl-diphosphatase (EC, 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC, glycogen synthase (EC and galactose-1-phosphate uridylyltransferase (EC suggesting a role for TM0892 in energy metabolism.


    The TM0892 structure, 1vr9, adopts a CBS-domain fold and shows strong structural similarity (main-chain rmsd of 1.7 Å over 112 residues and a sequence identity of 21%; Dali Zscr=15) with a hypoxic response protein from Mycobacterium tuberculosis (PDB ids: 1y5h, 1xkf) that has been suggested to modulate the host's immune response (Sharpee 2008). The closest homolog (28% seq.id.) with high structural similarity (Z=15) is the T. thermophilus Mg ion transporter 2yvy. Similar results were obtained for the yeast ortholog of the gamma subunit of AMP-activated protein kinase (PDB ids: 2nyc, 2nye; Z=14) (Rudolph 2007, Amodeo 2007), a CBS domain from Pyrobaculum aerophilum complexed with AMP (PDB id: 2rif; Z=15) (King 2008), Nitrosomonas europaea (PDB id: 2rc3; Z=13) (Dong 2007), a putative acetoin utilization protein from Vibrio cholerae (PDB id: 2o16; Z=14), uncharacterized CBS domains from Methanococcus jannaschii (PDB id: 2p9m; Z=15), Geobacillus kaustophilus (PDB id: 2emq; Z=14) and Sulfolobus tokadaii (PDB id: 2ef7; Z=15) (Ragunathan 2008), as well as the cytoplasmic domain of human chloride transporter channels (PDB ids: 2ja3, Z=10; 2d4z, Z=10) (Meyer 2006, Meyer 2007).

    The structures of two additional T. maritima CBS domains have been described, one encoding an inosine-5'-monophosphate dehydrogenase (gene TM1347, PDB id: 1vrd), the other a distant IMPDH homolog (gene TM0935, PDB id: 1o50) (Miller 2004). Other CBS domains solved by the PSI include the cytoplasmic domain of a magnesium transporter from Enterococcus faecalis (PDB id: 2oux), CBS domains from Methanobacterium thermoautotrophicum (PDB id: 1pbj) and Bacillus subtilis (PDB id: 1yav) and a CBS domain fused with a zinc-ribbon like domain from Thermoplasma acidophilum (PDB id: 1pvm) (Proudfoot 2008).


    CBS domains usually come in tandem repeats forming either dimers or tetramers and are found in cytosolic and membrane proteins performing different functions (metabolic enzymes, kinases, and channels). Depending on the protein in which they occur, CBS domains have been proposed to affect multimerization and sorting of proteins, channel gating, and ligand binding. CBS domains can bind adenosine-containing ligands such ATP, AMP, or S-adenosylmethionine leading to the proposal that they function as sensors of intracellular metabolites (Ignoul 2005). Several human hereditary diseases (homocystinuria (Jhee 2005), retinitis pigmentosa (Hedstrom 2008), hypertrophic cardiomyopathy, congenital myotonia (Fialho 2007) and others) can be caused by mutations in the CBS domains of, respectively, cystathionine-beta-synthase, inosine 5'-monophosphate dehydrogenase, AMP kinase, and chloride channels.

    Ligand Summary





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