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1vrb

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

    Title Crystal structure of Putative asparaginyl hydroxylase (2636534) from Bacillus subtilis at 2.60 A resolution. To be published
    Site JCSG
    PDB Id 1vrb Target Id 354163
    Molecular Characteristics
    Source Bacillus subtilis subsp. subtilis str. 168
    Alias Ids TPS1324,2636534, 2.60.120.10 Molecular Weight 37456.37 Da.
    Residues 330 Isoelectric Point 4.78
    Sequence msavtesvlesiispvtmsefleeywpvkplvargeverftsipgfekvrtlenvlaiynnpvmvvgda vieesegitdrflvspaealewyekgaalefdftdlfipqvrrwieklkaelrlpagtsskaivyaakn gggfkahfdaytnlifqiqgektwklaknenvsnpmqhydlseapyypddlqsywkgdppkedlpdaei vnltpgtmlylprglwhstksdqatlalnitfgqpawldlmlaalrkklisdnrfrelavnhqslhess kselngylesliqtlsenaetltpeqifqsqdsdfdpyqstqlvfrqlltsykf
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.60 Rfree 0.27227
    Matthews' coefficent 2.26 Rfactor 0.22144
    Waters 22 Solvent Content 45.49

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1vrb
    1. The Buccaneer software for automated model building. 1. Tracing protein chains
    K Cowtan - Acta Crystallographica Section D: Biological , 2006 - scripts.iucr.org
     
    2. Structural studies on 2-oxoglutarate oxygenases and related double-stranded _-helix fold proteins
    IJ Clifton, MA McDonough, D Ehrismann - Journal of inorganic , 2006 - Elsevier
     
    3. Fast and accurate algorithms for protein side-chain packing
    J Xu, B Berger - Journal of the ACM (JACM), 2006 - dl.acm.org
     
    4. Fitting molecular fragments into electron density
    K Cowtan - Acta Crystallographica Section D: Biological , 2007 - scripts.iucr.org
     
    5. Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins
    P Hahn, J Bse, S Edler, A Lengeling - BMC genomics, 2008 - biomedcentral.com
     
    6. Protein structure prediction based on the sliced lattice model
    CC Wang, CB Yang, HY Ann - 2008 Conference on , 2005 - etd.lib.nsysu.edu.tw
     
    7. Prediction of Protein Backbone Based on the Sliced Lattice Model
    CC Wang, CB Yang, HY Ann, HY Chang - 2008 - csie.npu.edu.tw
     

    Protein Summary

    The gene 2636534 from Bacillus subtilis encodes a putative asparaginyl hydroxylase  EC:1.14.11.16 (other names: peptide-aspartate beta-dioxygenase, aspartate beta-hydroxylase), a clavaminate synthases superfamily. The protein contains Cupin 4 superfamily domain PF08007, which includes a large number of hypothetical proteins.  The core of the protein reveals a double-stranded beta-helix (jelly-roll topology) fold type SCOP51181, common for this class of enzymes.  The jelly-roll domain houses conserved amino acid residues involved in Fe2+ binding.  The primary function of asparaginyl hydroxylases is to control the activity of transcription factors in response to changes in the environmental O2 concentration.  In multicellular organisms, under normoxic conditions  the proline and asparagine residues are hydroxylated by prolyl and asparaginyl hydroxylases. These hydroxylations regulate the stability and transcriptional activity of the HIF-1a (hypoxia induced factor) subunit.  It has been shown that hypoxic condition of host cells decreases virulence of certain pathogenic bacterial strains [Ref].  Therefore, it is plausible that pathogenic bacteria utilize asparaginyl hydroxylase to mimic the biochemical state of normoxic condition by keeping host HIF-1 hydroxylated.  In the context of Bacillus subtilis, which is not pathogenic and classified as an obligate aerobe, asparaginyl hydroxylase is probably involved in metabolic regulation.

    Ligand Summary



    References

    Reviews

    References

     

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