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3mcp

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

    Title Crystal structure of Glucokinase (BDI_1628) from Parabacteroides distasonis ATCC 8503 at 3.00 A resolution. To be published
    Site JCSG
    PDB Id 3mcp Target Id 400675
    Molecular Characteristics
    Source Parabacteroides distasonis atcc 8503
    Alias Ids TPS28030,YP_001303002.1, _0120.002476_, 326786 Molecular Weight 38824.28 Da.
    Residues 365 Isoelectric Point 5.02
    Sequence mmytndnrivmtldaggtnfvfsaiqggkeiadpvvlpacadcldkclgnlvegfkaiqadlpeapvai sfafpgpadyqagiigdlpnfpsfrggvalgpfledifgipvfinndgslfaygealtgvlpeinrrlr eagstkryknllgvtlgtgfgagvvidgellrgdnaaggyvwclrnkkypeyiveesvsiravmrvyae rsgdagartpkeifeiaegirpgnreaaiaafeelgemagdalasaitlidgliviggglsgaskyilp vllkemnaqtgmmdgarfgrlqkevydlddeksfagfargeavevlvpgtnrkvgydpckrigvtfskq ganrsiamgayvfalnhlsk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 3.00 Rfree 0.249
    Matthews' coefficent 2.96 Rfactor 0.206
    Waters 13 Solvent Content 58.39

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3mcp
    1. Distributed structure determination at the JCSG
    H van den Bedem, G Wolf, Q Xu - Section D: Biological , 2011 - scripts.iucr.org
     

    Protein Summary

    Gene BDI_1628 from Parabacteroides distasonis atcc 8503 translates into the YP_001303002 proteins that belongs to the family ROK (Repressor, ORF, Kinase) (PF0048). 24 structures have been determined from this Pfam group, and this family includes several bacterial xylose operon repressors, N-acetylglucosamine repressors, glucokinase, fructokinase, and several hypothetical proteins. Shown below is a ribbon representation of the structure of 3mcp color-coded with the N-terminal end in blue and the C-terminal end in red.

    MH1224A_monomer.png

    3mcp structure consists of two domains. Both the N-terminal (residues 1-131) and C-terminal domains (residues 145-349) belong to the Ribonuclease H-like SCOP fold and the Actin-like ATPase domain SCOP superfamily. This superfamily contains duplication of two domains of this fold. 

     

    Crystal packing analysis suggests that the dimer is a significant oligomerization state. Shown below is a ribbons representation of a dimer with the individual subunits colored in blue and yellow.

    MH1224A_dimer.png

     

     

    A DALI search shows that 3mcp shares significant structural similarity with the following targets:

    PDB ID
    DALI Z-Score
    rmsd(Ang)
    aligned residues
    number residues in target
    % Sequence ID
    Description
    2qm1 28.4 3.1 292 324 23 Glucokinase from Enterococcus faecalis
    2aa4 27.1 2.4 273 289 21 Putative N-acetylmannosamine kinase from E. coli
    1z05 26.9 2.5 291 396 21 ROK family transcriptional regulator homolog of E. coli MLC protein
    1z6r 26.8 2.6 292 382 20  Mlc protein, a global regulator of sugar metabolism in E. coli.
    2gup 25.5 2.9 279 289 22 ROK family protein from Streptococcus pneumoniae in complex with sucrose
    2ap1 24.9 3.1 286 305 22 putative regulatory protein
    1xc3 24.8 2.7 266 295 21 putative fructokinase from Bacillus subtilis
    3epq 24,7 2.7 265 294 22 fructokinase from B. subtilis in complex with ADP
    3bp8 24.9 3.3 291 381 19 putative nagc-like transcriptional regulator

     

     

     

    Ligand Summary

    Reviews

    References

     

    No references found.

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