The Open Protein Structure Annotation Network
PDB Keyword


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

    Title Crystal structure of hypothetical protein (TM1225) from Thermotoga maritima at 2.10 A resolution. To be published
    Site JCSG
    PDB Id 1vkd Target Id 283090
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1270,TM1225, _0065.000420_, 84757 Molecular Weight 37256.32 Da.
    Residues 326 Isoelectric Point 5.66
    Sequence mkvftekipnipweerpegytgpvwrysknpiigrnpvpkgarvfnsavvpyngefvgvfridhkntrp flhfgrskdginweiepeeiqwvdvngepfqpsyaydprvvkiedtyyitfctddhgptigvgmtkdfk tfvrlpnayvpfnrngvlfprkingkyvmlnrpsdnghtpfgdiflsespdmihwgnhrfvlgrssynw wenlkigagpypietsegwlliyhgvtltcngyvysfgaalldlddpskvlyrsryylltpeeeyetvg fvpnvvfpcaalcdadtgrvaiyygaadthvalafgyideivdfvkrnsm
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 6
    Resolution (Å) 2.10 Rfree 0.20404
    Matthews' coefficent 2.36 Rfactor 0.16203
    Waters 954 Solvent Content 47.48

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    Ligand Information


    Google Scholar output for 1vkd
    1. The Buccaneer software for automated model building. 1. Tracing protein chains
    K Cowtan - Acta Crystallographica Section D: Biological , 2006 - scripts.iucr.org
    2. Protein function prediction using local 3D templates
    RA Laskowski, JD Watson, JM Thornton - Journal of Molecular Biology, 2005 - Elsevier
    3. 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
    4. Structure-based design of an urokinase-type plasminogen activator receptorderived peptide inhibiting cell migration and lung metastasis
    MV Carriero, I Longanesi-Cattani, K Bifulco - Molecular cancer , 2009 - AACR
    5. 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
    6. New microbial mannan catabolic pathway that involves a novel mannosylglucose phosphorylase
    T Senoura, S Ito, H Taguchi, M Higa, S Hamada - Biochemical and , 2011 - Elsevier
    7. Furanosidase superfamily: Search of homologues
    DG Naumoff - Molecular Biology, 2012 - Springer
    8. Re-Annotation of Two Hyperthermophilic Archaea Pyrococcus abyssi GE5 and Pyrococcus furiosus DSM 3638
    J Gao, J Wang - Current microbiology, 2012 - Springer
    9. Papaya glutamine cyclotransferase shows a singular five-fold b-propeller architecture that suggests a novel reaction mechanism
    S Garca-Pique, GE Petersen, C Lauritzen, J Pedersen - Biol. Chem, 2006 - ibmb.csic.es
    10. A network-based representation of protein fold space
    S Bliven - 2011 - acsweb.ucsd.edu
    11. Mathematical Modeling and Screening of Ligand Binding Sites in Protein using the Tetrahedral Motif Method and Double-Centroid Representation
    VM Reyes - 2012 - ritdml.rit.edu

    Protein Summary

    The gene TM1225 from Thermotoga maritima encodes the NP_229030 protein from the DUF377 group (PF04041). The protein belongs to the glycosyl hydrolases 43 superfamily COG2152. The genomic neighborhood of TM1225 shows the presence (score 0.8) of a transcriptional regulator XylR-related (TM1224).

    SCOP classifies 1vkd in the all beta class, 5-bladed beta propeller fold, arabinase/levansucrase/invertase superfamily, TM1225-like family. 1vkd shows structural similarity (Dali Z=22) to many beta-xylosidases like 3cpn, 1yrz, 2exh, or 3c2u.

    Glycosyl hydrolases are a big and widespread family of enzymes that hydrolyse the glycosidic bonds between carbohydrates or between a carbohydrate and an aglycone moiety. On the basis of sequence and structural similarity, the glycoside hydrolase family belongs to the beta-fructosidase (furanosidase) family of glycosyl hydrolases [Ref].  The enzyme, most probably, acts on a furanoside residue (fructose, arabinose and ribose).

    Ligand Summary





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