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The Open Protein Structure Annotation Network
PDB Keyword
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3dlc

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

    Title Crystal structure of a Putative S-adenosyl-L-methionine-dependent Methyltransferase (NP_988299.1) from Methanococcus maripaludis JJ (DSM 2067) at 1.15 A resolution. To be published
    Site JCSG
    PDB Id 3dlc Target Id 387106
    Molecular Characteristics
    Source Methanococcus maripaludis s2
    Alias Ids TPS9379,NP_988299.1, BIG_646, 86624 Molecular Weight 24584.53 Da.
    Residues 218 Isoelectric Point 5.03
    Sequence msenkkkfdkkgaknmdeisktlfapiypiiaeniinrfgitagncidigsgpgalsialakqsdfsir aldfskhmneialkniadadlndriqivqgdvhnipiednyadlivsrgsvffwedvttafreiyrilk sggktyigggfgnkelrdsisaemirknpdwkefnrknisqenverfqnvldeigvssyeiiledegfw iiisktdqevi
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.15 Rfree 0.138
    Matthews' coefficent 1.92 Rfactor 0.120
    Waters 338 Solvent Content 35.81

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3dlc
    1. Comparison of structure_based and threading_based approaches to protein functional annotation
    M Brylinski, J Skolnick - Proteins: Structure, Function, and , 2010 - Wiley Online Library
     
    2. Technologies of protein interactomics: A review
    AS Ivanov, VG Zgoda, AI Archakov - Russian Journal of Bioorganic , 2011 - Springer
     
    3. Protein Physics by Advanced Computational Techniques: Conformational Sampling and Folded State Discrimination
    PC Tejada - 2011 - sissa.it
     
    4. A New Library of Surface Patches: Design and Applications
    R Gamliel, K Kedem, R Kolodny, C Keasar - 2009 - cs.bgu.ac.il
     
    5. Combining Emperical and Experimental Data in Protein Structure Determination
    Y Zhang - Masters Theses, 2009 - scholarworks.umass.edu
     
    6. __________ ________ _____________
    __ _____, __ _______ - 2011 - rjbc.ru
     

    Protein Summary

    The MMP1179 gene from Methanococcus maripaludis s2 encodes a SAM-dependent methyltransferase type 11 (PF08241, COG0500, EC 2.1.1.-). Although the precise function of MMP1179 is unknown, analysis of the genome context of MMP1179 suggests a role in metal uptake. However, remote homology suggests a stronger link with the ubiE/COQ5 methyltransferase (PF01209, P-value 4.8E-32, residues 5-206) than with PF08241, a hypothesis supported by structural similarity to precorrin methyltransferases (PDB id: PDB:1f38 [Ref]).

    3dlc structure, according to pre-SCOP, belongs to the SAM-dependent methyltransferase superfamily, inside the family UbiE/COQ5-like. A DALI search returns as top hits methyltransferases like PDB:1wzn, and PDB:3dh0 (Z=19); next is the hypothetical proteins PH0226 PDB:1ve3, TTHA0223 2yqz, BH2331 PDB:1vl5, and the YCGJ protein 1xxl (Z=18). 3dlc shows significant structural similarity to other better characterized methyltransferases like PDB:2pxx [Z=16], or PDB:1f38 [Z=13]. 

     

     

    To do: closer comparison of 1F38 and 3DLC.

    Ligand Summary

    Reviews

    References

     

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