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3jr1

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

    Title Crystal structure of Putative fructosamine-3-kinase (YP_719053.1) from HAEMOPHILUS SOMNUS 129PT at 2.32 A resolution. To be published
    Site JCSG
    PDB Id 3jr1 Target Id 386978
    Molecular Characteristics
    Source Haemophilus somnus 129pt
    Alias Ids TPS7469,HSOM_08NOV04_CONTIG98_REVISED_GENE622, 87776 Molecular Weight 34487.74 Da.
    Residues 293 Isoelectric Point 7.00
    Sequence mwksisqvlaeqfgayyfikhkeklysgemneiwlindevqtvfvkinersyrsmfraeadqlallakt nsinvplvygignsqghsflllealnksknkqssftifaekiaqlhqiqgpdkygldfdtwlgpiyqpn dwqtswakffsenrigwqlqickekglifgnidlivqivadtlskhnpkpsilhgnlwienciqvddki fvcnpacywgdrecdiafsslfepfptnfyqryneiypleegylerkliyqlyyllnfsyryynkkqsy vsltqklinqilhkidk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.32 Rfree 0.244
    Matthews' coefficent 2.88 Rfactor 0.199
    Waters 162 Solvent Content 57.26

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Pfam Class: This sequence matches Fructosamin_kin (PF03881).

     

    A fructosamine kinase, and member of the PKL fold of kinases, which includes eukaryotic protein kinases, and the CAK (choline and aminoglycoside kinases) class of kinases. Fructosamine kinases are found in all eukaryotes and many bacteria. They phosphorylate sugar residues that become attached to aged proteins, facilitating their removal and correction of the protein. The catalytic aspartate in this protein is replaced by an asparagine, casting some doubts on its catalytic activity.

    The structure to be described here is among the first to be reported for the Fructosamine kinase Pfam group (PF03881); however, a sequence searchversus existing entries shows a 31% sequence id between target ID 386978 and PDB ID 3f7w , a JCSG target that is also believed to function as a fructosamine-3 kinase.  The structure was determined by three wavelength Se-MAD from a monoclinc crystal form (C2) at a resolution of 2.3 Angstroms. Crystal packing suggests that the monomer is a significant oligomerization state in solution. Shown below is a color-coded ribbon representation of the structure of target ID 386978 with the N-terminal region in blue and the C-terminal region in red.

     

     

    monomer_ribbons.png

     

     

     A secondary structure matching search shows the following PDB entries to display topological similarity with target ID  386978

     

    PDB ID RMSD (Angstroms) Seq ID Z-score Name
    3f7w 2.41 23.6 8.4 putative fructosamine-3-kinase (yp_290396.1) from thermobifida fusca yx-er1 at 1.85 Ang
    3dxp 3.12 20.3 3.9 putative acyl-coa dehydrogenase (yp_295230.1) from ralstonia eutropha jmp134 at 2.32 Ang
    3g15 3.17 21.3 5.5 human choline kinase alpha in complex with hemicholinium-3 and adp
    1nd4 3.18 21.2 4.5 aminoglycoside-3'-phosphotransferase- iia  
    2ig7 3.60 22.0 5.4
    human choline kinase b
    1zyl 3.08 22.0 3.1 hypothetical protein yihe from escherichia coli
    2ppq 3.50 22.0 2.8
    homoserine kinase from agrobacterium tumefaciens
    3feg 3.13 22.0 5.7 human choline kinase beta in complex with phosphorylated hemicholinium-3 and adenosine nucleotide
    3csv 2.96 13.5 4.8
    aminoglycoside phosphotransferase (yp_614837.1) from silicibacter sp. Tm1040 at 2.15 Ang resolution
    3c5i 3.31 20.6 4.6 plasmodium knowlesi choline kinase, pkh_134520

     

     Shown below is a superpositioning of the structures of target ID 386978 (green) and PDB ID 3f7w (yellow). The putative active sites on the two proteins are located near the spheres. The sphere represent unknown ligands (UNL) modeled into the putative active sites of the two structures.

    overlap_ribbons.png

     

    Shown below is a comparison of the structures surrounding the putative ATP binding sites on target id 386978 (green) and PDB id 37fw. The unknown ligand atoms are represented by green spheres (target id 386978) and yellow spheres (PDB ID 37fw).

     

    putative_ATP_binding_pocket.bmp

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (3)

    FileSizeDateAttached by 
     monomer_ribbons.png
    ribbon representation, monomer
    205.56 kB21:24, 10 Jun 2009haxelrodActions
     overlap_ribbons.png
    overlap ribbons target id 386978 vs. PDB id 3f7w
    360.93 kB01:14, 11 Aug 2009haxelrodActions
     putative_ATP_binding_pocket.bmp
    No description
    1748.49 kB02:20, 11 Aug 2009haxelrodActions
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