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1o0w

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

    Title Crystal structure of Ribonuclease III (TM1102) from Thermotoga maritima at 2.0 A resolution. To be published
    Site JCSG
    PDB Id 1o0w Target Id 282968
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1261,TM1102, 282139 Molecular Weight 27528.99 Da.
    Residues 240 Isoelectric Point 5.20
    Sequence mneserkiveefqketginfkneellfralchssyaneqnqagrkdvesnekleflgdavlelfvceil ykkypeaevgdlarvksaaaseevlamvsrkmnlgkflflgkgeektggrdrdsiladafeallaaiyl dqgyekikelfeqefefyiekimkgemlfdyktalqeivqsehkvppeyilvrtekndgdrifvvevrv ngktiatgkgrtkkeaekeaariayekllkers
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.00 Rfree 0.23
    Matthews' coefficent 2.23 Rfactor 0.195
    Waters 383 Solvent Content 44.32

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1o0w
    1. A three-dimensional view of the molecular machinery of RNA interference
    M Jinek, JA Doudna - Nature, 2008 - nature.com
     
    2. Assessment of homology_based predictions in CASP5
    A Tramontano, V Morea - Proteins: Structure, Function, and , 2003 - Wiley Online Library
     
    3. Statistical analysis and prediction of proteinprotein interfaces
    AJ Bordner, R Abagyan - Proteins: Structure, Function, and , 2005 - Wiley Online Library
     
    4. Structural insight into the mechanism of double-stranded RNA processing by ribonuclease III
    J Gan, JE Tropea, BP Austin, DS Waugh, X Ji - Cell, 2006 - Elsevier
     
    5. Noncatalytic assembly of ribonuclease III with double-stranded RNA
    J Blaszczyk, J Gan, JE Tropea, DS Waugh, X Ji - Structure, 2004 - Elsevier
     
    6. The continuing story of endoribonuclease III
    D Drider, C Condon - Journal of molecular microbiology and , 2004 - content.karger.com
     
    7. Using property based sequence motifs and 3D modeling to determine structure and functional regions of proteins
    I Ovidiu, O Numan, VS Mathura - Current medicinal , 2004 - ingentaconnect.com
     
    8. An iterative knowledge_based scoring function for proteinprotein recognition
    SY Huang, X Zou - Proteins: Structure, Function, and , 2008 - Wiley Online Library
     
    9. The mechanism of RNase III action: how dicer dices
    X Ji - RNA interference, 2008 - Springer
     
    10. CASP5 target classification
    LN Kinch, Y Qi, TJP Hubbard - : Structure, Function, and , 2003 - Wiley Online Library
     
    11. Characterization of RNA sequence determinants and antideterminants of processing reactivity for a minimal substrate of Escherichia coli ribonuclease III
    AV Pertzev, AW Nicholson - Nucleic acids research, 2006 - Oxford Univ Press
     
    12. Structure of the nuclease domain of ribonuclease III from M. tuberculosis at 2.1
    DL Akey, JM Berger - Protein science, 2005 - Wiley Online Library
     
    13. Homodimeric structure and double-stranded RNA cleavage activity of the C-terminal RNase III domain of human dicer
    D Takeshita, S Zenno, WC Lee, K Nagata - Journal of molecular , 2007 - Elsevier
     
    14. Faster data-collection strategies for structure determination using anomalous dispersion
    A Gonzalez - Acta Crystallographica Section D: Biological , 2003 - scripts.iucr.org
     
    15. Structural basis for non-catalytic and catalytic activities of ribonuclease III
    X Ji - Acta Crystallographica Section D: Biological , 2006 - scripts.iucr.org
     
    16. A structural pattern_based method for protein fold recognition
    WR Taylor, I Jonassen - PROTEINS: Structure, Function, and , 2004 - Wiley Online Library
     
    17. Shotgun crystallization strategy for structural genomics II: crystallization conditions that produce high resolution structures for T. maritima proteins
    R Page, AM Deacon, SA Lesley - Journal of structural and , 2005 - Springer
     
    18. Intermediate states of ribonuclease III in complex with double-stranded RNA
    J Gan, JE Tropea, BP Austin, DS Waugh, X Ji - Structure, 2005 - Elsevier
     
    19. A fold-recognition approach to loop modeling
    C Levefelt, D Lundh - Journal of molecular modeling, 2006 - Springer
     
    20. Comparing protein contact maps via Universal Similarity Metric: an improvement in the noise-tolerance
    S Rahmati, JI Glasgow - journal of computational biology and drug , 2009 - Inderscience
     
    21. Thermotoga maritima ribonuclease III. Characterization of thermostable biochemical behavior, and analysis of conserved base-pairs that function as reactivity epitopes
    L Nathania, AW Nicholson - Biochemistry, 2010 - ACS Publications
     
    22. Protein Structure Prediction Using an Augmented Homology Modeling Method: Key Importance of Iterative-Procedures for Obtaining Consistent Quality Models
    S McDonald, S Mylvaganam - Current , 2005 - ingentaconnect.com
     
    23. Ribonuclease III and the Role of Double-Stranded RNA Processing in Bacterial Systems
    AW Nicholson - Ribonucleases, 2011 - Springer
     
    24. Of sequence and structure: Strategies of protein thermostability in evolutionary perspective
    IN Berezovsky, EI Shakhnovich - Arxiv preprint q-bio/0408007, 2004 - arxiv.org
     
    25. Aminoglycoside induced nephrotoxicity: molecular modeling studies of calreticulin-gentamicin complex
    G Hariprasad, M Kumar, K Rani, P Kaur - Journal of Molecular , 2011 - Springer
     
    26. Structures of the Klebsiella oxytoca phage phi KO2 and Vibrio harveyi myovirus-like protelomerase far C-terminal domains
    DK Smith - 2011 - gradworks.umi.com
     
    27. RNA recognition by double-stranded RNA binding domains: a matter of shape and sequence
    G Masliah, P Barraud, FHT Allain - Cellular and Molecular Life Sciences, 2012 - Springer
     
    28. The Universal Similarity Metric, applied to contact maps comparison in a two-dimensional space
    S Rahmati - 2008 - catspaw.its.queensu.ca
     

    Protein Summary

    The gene TM1102 from Thermotoga maritima encodes ribonuclease III enzyme EC:3.1.26.3.  The enzyme has two domains belonging to distinct superfamilies.  The N-terminal domain encodes ribonuclease III domain PF00636, while the C-terminal domain contains the double-stranded RNA binding motif (DsRBD) PF00035. The ribonuclease III catalyzes the digestion of double-stranded RNA. It is involved in the processing of ribosomal RNA precursors and of some mRNAs [Ref].  The DsRBD domain is found in a variety of RNA-binding proteins with different structures and exhibiting a diversity of functions [Ref]. It is involved in localisation of at least five different mRNAs in the early Drosophila embryo and by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.

    Ligand Summary



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