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The Open Protein Structure Annotation Network
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1vk2

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

    Title Crystal structure of Uracil-DNA glycosylase (TM0511) from Thermotoga maritima at 1.90 A resolution. To be published
    Site JCSG
    PDB Id 1vk2 Target Id 359753
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1430,TM0511, 396382 Molecular Weight 21499.79 Da.
    Residues 192 Isoelectric Point 8.60
    Sequence mytreelmeivservkkctacplhlnrtnvvvgegnldtrivfvgegpgeeedktgrpfvgragmllte llresgirredvyicnvvkcrppnnrtptpeeqaacghfllaqieiinpdvivalgatalsffvdgkkv sitkvrgnpidwlggkkviptfhpsyllrnrsnelrrivlediekaksfikkeg
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.90 Rfree 0.20573
    Matthews' coefficent 2.65 Rfactor 0.17743
    Waters 114 Solvent Content 53.13

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    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1vk2
    1. The Buccaneer software for automated model building. 1. Tracing protein chains
    K Cowtan - Acta Crystallographica Section D: Biological , 2006 - scripts.iucr.org
     
    2. Prediction of protein structure from ideal forms
    WR Taylor, GJ Bartlett, V Chelliah - Proteins: Structure, , 2008 - Wiley Online Library
     
    3. 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
     
    4. Functional site prediction selects correct protein models
    V Chelliah, WR Taylor - BMC bioinformatics, 2008 - biomedcentral.com
     
    5. Purification, crystallization and preliminary X-ray analysis of uracil-DNA glycosylase from Sulfolobus tokodaii strain 7
    A Kawai, S Higuchi, M Tsunoda - Section F: Structural , 2012 - scripts.iucr.org
     
    6. Re-Annotation of Two Hyperthermophilic Archaea Pyrococcus abyssi GE5 and Pyrococcus furiosus DSM 3638
    J Gao, J Wang - Current microbiology, 2012 - Springer
     

    Protein Summary

    The gene TM0511 from Thermotoga maritima encodes the enzyme uracil-DNA glycosylase (UDG)PFAM:PF03167 EC:3.2.2.15 COG0692.  The protein belongs to the class of alpha and beta (a+b) proteins and reveals uracil-DNA glycosylase-like fold SCOP52140.  The function of uracil-DNA glycosylase is to prevent mutagenesis by eliminating uracil from DNA molecules by cleaving the N-glycosylic bond and initiating the base-excision repair (BER) pathway.   The hydrolytic deamination of cytosine to uracil is one of the most frequent DNA-damaging events in all cells.  Thus, UDG is an essential enzyme for maintaining the integrity of genomic information, and its orthologs exist ubiquitously among prokaryotes and eukaryotes and even in some DNA viruses (e.g. herpes and poxviruses).  The presence of [4Fe-4S] iron-sulfur cluster associates the enzyme with the family 4 UDG (not all UDGs contain iron-sulfur clusters).  The structure of similar UDG enzyme from Thermus Thermophilus has been solved PDB:1UI0 .

    Ligand Summary



    References

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