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2qcv

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

    Title Crystal structure of a putative 5-dehydro-2-deoxygluconokinase (NP_243185.1) from Bacillus halodurans at 1.90 A resolution. To be published
    Site JCSG
    PDB Id 2qcv Target Id 375195
    Molecular Characteristics
    Source Bacillus halodurans c-125
    Alias Ids TPS1652,NP_243185.1, 3.40.1190.20, 104204 Molecular Weight 36639.35 Da.
    Residues 331 Isoelectric Point 5.04
    Sequence mtyelstdrefdliaigracidlnaveynrpmeetmtfskyvggspanivigssklglkagfigkiadd qhgrfiesymrgvgvdtsnlvvdqeghktglafteikspeecsilmyrqdvadlylspeevneayirrs klllvsgtalskspsreavlkairlakrndvkvvfeldyrpyswetpeetavyyslvaeqsdivigtre efdvlenrtekgdndetirylfkhspelivikhgvegsfaytkageayrgyayktkvlktfgagdsyas aflyalisgkgietalkygsasasivvskhsssdampsveeiealiekdetitia
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.90 Rfree 0.196
    Matthews' coefficent 3.53 Rfactor 0.175
    Waters 221 Solvent Content 65.12

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2qcv
    1. Crystal structure of a fructokinase homolog from Halothermothrix orenii
    TK Chua, J Seetharaman, JM Kasprzak, C Ng - Journal of structural , 2010 - Elsevier
     
    2. The structure of Sulfolobus solfataricus 2-keto-3-deoxygluconate kinase
    JA Potter, M Kerou, HJ Lamble, SD Bull - Section D: Biological , 2008 - scripts.iucr.org
     

    Protein Summary

    The BH2319 (or iolC) gene (PFAM:PF00294cl00192) from Bacillus halodurans encodes for the protein NP_243185, a putative carbohydrate kinase (EC:2.7.1.45). Its functional biomolecule consists of four chains. The structure adopts an alpha/beta ribokinase-like fold. A structurally highly similar protein is pdb:2var [Ref], sharing 30% sequence identity over 290 equivalent residues with a Dali Z-score of 40. Other similar structures (Dali Zscr=~35) determined by the PSI include pdb:2afb [Ref], pdb:2rbc , and pdb:3k9e. Outside PSI, two other structures are notable for their similarity with 2qcv: pdb:2dcn and pdb:2vye (Zscr=40).

    It has been suggested that this protein is a 2-keto-3-deoxyglcuonate kinase (EC:2.7.1.45). In the meanwhile there are several protein structures annotated with this function, 3ktn and 1wye in the PDB and 1v19, 1v1a, 2afb ([Ref], solved by the JCSG), 2v78, and 2var [Ref] (both with a different substrate specificity in the EC number) from a literature scan.

    2qcv,A-1v1a,A.png

    Figure 1. Comparison of 2qcv and 1v1a. This figure shows the superposition (by TopMatch) of chain A from 2qcv (white carbon atoms) and 1v1a (gray carbons) with focus on the binding site of the natural substrate, 2-keto-3-deoxygluconate (KDG, in the center of the figure). There is a considerable amount of identical residues forming the binding site, such as asparagines and arginines. On the other hand, several residues are not conserved such as Tyr-89 which may play a role in packing the ligand by hydrophobic contacts. This tyrosine has been replaced by an alanine in 2qcv and participated in a four residue hydrophopic patch (GLAF, residues 99 to 102) supporting the role as a hydrophopic packing environment. Unfortunately, residues His-306 to Asp-310 (corresponding to residues Arg-285 to -Asp-289 in 1v1a) were not modeled due to poor electron density in 2qcv but they are forming an important part of the binding pocket. Since in both cases five residues are affected we assume the structure alignment be gapless: 

    2qcv,A H-306 S S S D-310
    1v1a,A R-285 G D H E-289

    A crucial binding residue in 1v1a is Asp-287 making a hydrogen bond to an hydroxyl group from the ligand. This residue is replaced by a serine in 2qcv such that the potential to form a hydrogen bond is still fulfilled. Residue Asp-22 from 2qcv may also play a crucial role in establishing the hydrogen bond network involving the stretch of the three serine residues since it is placed closely to the alanine-replaced Tyr-89.

    It has been shown experimentally that 2-keto-3-deoxygluconate kinase also phosphorylates the substrate 2-keto-3-deoxygalactonate ([Ref], PDB accession code 2v78).

    Ligand Summary


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    Files (1)

    FileSizeDateAttached by 
    2qcv,A-1v1a,A.png
    JCSG structure 2qcv superimposed with 1v1a (natural substrate)
    166.54 kB18:40, 26 May 2010chrisxActions
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