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The Open Protein Structure Annotation Network
PDB Keyword
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3clo

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

    Title Crystal structure of putative transcriptional regulator containing a LuxR DNA binding domain (NP_811094.1) from Bacteroides thetaiotaomicron VPI-5482 at 2.04 A resolution. To be published
    Site JCSG
    PDB Id 3clo Target Id 383272
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS1770,NP_811094.1, 88499 Molecular Weight 29573.30 Da.
    Residues 257 Isoelectric Point 5.87
    Sequence mdvlqkeidevyathptahealdngiveqhqqfvrsltevnggcavisdlsnrksyvtvhpwanflglt peeaalsvidsmdedciyrrihpedlvekrlmeykffqktfsmspgerlkyrgrcrlrmmnekgvyqyi dnlvqimqntpagnvwlifclyslsadqrpeqgiyatitqmergevetlslseehrnilserekeilrc irkglsskeiaatlyisvntvnrhrqnileklsvgnsieacraaelmkll
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 3
    Resolution (Å) 2.04 Rfree 0.217
    Matthews' coefficent 3.64 Rfactor 0.187
    Waters 494 Solvent Content 66.25

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3clo
    1. Increased detection in Australia and Singapore of a novel influenza A (H1N1) 2009 variant with reduced oseltamivir and zanamivir sensitivity due to a S247N
    AC Hurt, RT Lee, SK Leang, L Cui, Y Deng - Euro , 2011 - eurosurveillance.eu
     
    2. Homology modeling, docking, and molecular dynamics reveal HR1039 as a potent inhibitor of 2009 A (H1N1) influenza neuraminidase
    YT Wang, C Chan, ZY Su, CL Chen - Biophysical chemistry, 2010 - Elsevier
     
    3. MODELAGEM MOLECULAR NO ENSINO DE QUMICA FARMACUTICA
    CH Andrade, GHG Trossini, EI Ferreira - Revista Eletrnica de , 2010 - revistas.ufg.br
     
    4. Mutations I117V and I117M and Oseltamivir Sensitivity of Pandemic (H1N1) 2009 Viruses
    AC Hurt, SK Leang, DJ Speers, IG Barr - Emerging infectious , 2012 - flu.org.cn
     
    5. Combining molecular simulation techniques to predict the binding modes of oseltamivir, zanamivir and natural herb products with the neuramindase of the H1N1
    YT Wang, C Chan - Bioinformatics and Biomedical Technology , 2010 - ieeexplore.ieee.org
     

    Protein Summary

    NP_811094.1 contains two domains (1-197, 198-257). The C-terminal domain contains a LuxR DNA binding domain and  has well defined structural homologs (rmsd<1 and seq id ~30), the N-terminal domain seems to be novel. There are no known structures which are highly homologous to the N-terminal domain.

    This protein is likely to function as a dimer. The two DNA binding domains of NP_811094.1 are placed in an interesting fashion. By superimposing the LuxR domains of this proteins and NarL-C/DNA complex, two strands of dsDNA can be approximately positioned onto NP_811094.1. Thus it appears that this protein severly bends the dsDNA or that it has to bind to separate strands of dsDNA.


    Fig 1. NP_811094.1 with modeled dsDNA

    This protein is likely to function as transcription regulator. The N-terminal domain can bind small molecule substrate. There are very few known sequence homologs for the N-terminal domain. It is thus not easy to infer whether it is the substrate binding site.



    Fig 2. Sequence conservation on NP_811094.1 dimer surface. cyan-least conserved, magenta-most conserved residues.

    Ligand Summary



    References

    Reviews

    References

     

    No references found.

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