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The Open Protein Structure Annotation Network
PDB Keyword
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2okc

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

    Title Crystal structure of Type I restriction enzyme StySJI M protein (NP_813429.1) from Bacteroides thetaiotaomicron VPI-5482 at 2.20 A resolution. To be Published
    Site JCSG
    PDB Id 2okc Target Id 363548
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS1471,NP_813429.1 Molecular Weight 49981.39 Da.
    Residues 444 Isoelectric Point 5.10
    Sequence matnssteqsltkkvwnlattlagqgigftdyitqltyllflkmdaenvemfgeesaiptgyqwadlia fdgldlvkqyeetlkllseldnligtiytkaqnkidkpvylkkvitmideeqwlimdgdvkgaiyesil ekngqdkksgagqyftprpliqamvdcinpqmgetvcdpacgtggflltaydymkgqsaskekrdflrd kalhgvdntplvvtlasmnlylhgigtdrspivcedslekepstlvdvilanppfgtrpagsvdinrpd fyvetknnqlnflqhmmlmlktggraavvlpdnvlfeagagetirkrllqdfnlhtilrlptgifyaqg vkanvlffskgqptkeiwfydyrtdikhtlatnklerhhlddfvscynnrveiydaennpqgrwrkypv deiiardktslditwikpggevddrslael
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.20 Rfree 0.232
    Matthews' coefficent 2.47 Rfactor 0.182
    Waters 348 Solvent Content 50.28

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2okc
    1. The structure of M. EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein
    CK Kennaway, A Obarska-Kosinska - Nucleic acids , 2009 - Oxford Univ Press
     
    2. Functional analysis of MmeI from methanol utilizer Methylophilus methylotrophus, a subtype IIC restriction-modification enzyme related to type I enzymes
    J Nakonieczna, T Kaczorowski - Applied and , 2009 - Am Soc Microbiol
     
    3. The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016: implications for DNA restriction and translocation activity
    NT Uyen, SY Park, JW Choi, HJ Lee - Nucleic acids , 2009 - Oxford Univ Press
     
    4. Characterization and crystal structure of the type IIG restriction endonuclease RM. BpuSI
    BW Shen, D Xu, SH Chan, Y Zheng, Z Zhu - Nucleic acids , 2011 - Oxford Univ Press
     
    5. Structural and Functional Analysis of the Engineered Type I DNA Methyltransferase EcoR124I NT
    JE Taylor, P Callow, A Swiderska, GG Kneale - Journal of molecular biology, 2010 - Elsevier
     
    6. Crystallization and preliminary X-ray diffraction analysis of the HsdR subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016
    NT Uyen, K Nishi, SY Park, JW Choi - Section F: Structural , 2008 - scripts.iucr.org
     
    7. Expression, crystallization and preliminary X-ray diffraction analysis of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016
    HJ Lee, K Nishi, JM Song, JS Kim - Acta Crystallographica Section F: , 2009 - scripts.iucr.org
     

    Protein Summary

    Bacteroides thetaiotaomicron descr protein NP_813429.1 is closely homologous to E.coli Type I restriction enzyme EcoKI M protein (EC 2.1.1.72)  (2ar0)  with ~30% sequence identity.  However, the  two  domains  forming  these proteins have different mutual orientations, RMSD in flexible (FATCAT) alignment is 1.8 A over 390 aminoacids as compared to 13.9 A over 340 aa in a rigid alignment.

    Ligand Summary



    References

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