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The Open Protein Structure Annotation Network
PDB Keyword
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3no4

    Title Crystal structure of a creatinine amidohydrolase (Npun_F1913) from Nostoc punctiforme PCC 73102 at 2.00 A resolution. To be published
    Site JCSG
    PDB Id 3no4 Target Id 398890
    Molecular Characteristics
    Source Nostoc punctiforme pcc 73102
    Alias Ids TPS30573,NPUN_22DEC03_CONTIG1_REVISED_GENENPF1913, _0038.001354_, 384445 Molecular Weight 26667.71 Da.
    Residues 248 Isoelectric Point 5.54
    Sequence mllhlstwqeveaylqqskgiifpigsteqhgptgligtdaicaeaiaagvgdatgaivgptinvgmal hhtafpgtislrpstliqvvrdyvtclakagfskfyfinghggniatlkaafsetyahledlqianaqq vqcqvanwfmcgsvyklakelygdqegshatpsevaltqyvypeaikqaplspevasghriysaadfrv rypdgrmgsnpglatpehgkqfydlavkelsngylefvnad
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.00 Rfree 0.192
    Matthews' coefficent 2.39 Rfactor 0.151
    Waters 588 Solvent Content 48.59

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3no4

    Protein Summary

    YP_001865509.1 is the creatinase enzyme that belongs to the Creatinine amidohydrolase family PFAM PF02633 Creatininase. It catalyzes the chemical reaction

    creatine + H2O <=> sarcosine + urea

    Momomer structure in rainbow representation is shown below.

    MI15797C.png

     

    The protein most likely assembles as a hexamer in solution, as shown below.

    MI15797C_hex.png

     

     

    Each monomer has a Ni ion bound to the protein which is supported by Anomalous Difference Fourier map. Structural homologs (pdb id 3a6k) of this protein have Zn ion bound to them. However, it seems that Zn has been replaced by Ni during IMAC purification in this protein. The presense of Zn vrs. Ni was confiremed by metal scan and ADF maps from datasets collected above and below the peak energies of both Zn and Ni.

     Density around Ni ion suggest the binding of creatine, but it is too weak to model the creatine.

    MI15797C_Zn.png

     

    There is a cluster of five Histidine residues near Ni ion, as shown below.

    MI15797C_His.png

    Of these, two Histidine residues (70, 71) shown in the lower right corner in the above figure are not conserved. A sequence and structure alignment of this region are shown below. The functions of these His residues are not clear. The protein YP_001865509.1 lacks five residues in this region compared to other homologs resulting in the short helix to draw in closer therfore. The residues corresponding to these Histidines in other structures are Glutamines 75, 76  which point away. In contrast the Histidines point toward the Ni ion.

     

    aln2.png

    all_His_Gln.png

     

     

    There are several homologs of this structure already known.

    DALI Structural Homologs
    N PDB Z-score RMSD LALI NRES %ID Description
    1 3a6k 27.3 2.1 240 256 23 CREATININE AMIDOHYDROLASE
    2 3a6g 27.3 2.0 240 257 24 CREATININE AMIDOHYDROLASE
    3 3a6e 27.3 2.1 240 257 24 CREATININE AMIDOHYDROLASE
    4 1v7z 27.3 2.0 239 257 24 CREATININE AMIDOHYDROLASE
    5 1q3k 27.3 2.1 241 259 23 CREATININASE
    6 1j2u 27.3 2.0 239 257 23 CREATININE AMIDOHYDROLASE
    7 1j2t 27.3 2.0 239 257 24 CREATININE AMIDOHYDROLASE
    8 3a6l 27.2 2.1 240 256 24 CREATININE AMIDOHYDROLASE
    9 3a6j 27.2 2.1 240 257 24 CREATININE AMIDOHYDROLASE
    10 3a6f 27.2 2.1 240 257 23 CREATININE AMIDOHYDROLASE

    Ligand Summary

    Reviews

    References

     

    No references found.

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