.
The Open Protein Structure Annotation Network
PDB Keyword
.

3gzr

    Title Crystal structure of Domain of unknown function with a NTF2-like fold (NP_421374.1) from CAULOBACTER CRESCENTUS at 1.40 A resolution. To be published
    Site JCSG
    PDB Id 3gzr Target Id 396244
    Molecular Characteristics
    Source Caulobacter crescentus cb15
    Alias Ids TPS25400,NP_421374.1, 3.10.450.50, 326180 Molecular Weight 16264.69 Da.
    Residues 145 Isoelectric Point 6.21
    Sequence gegtdaiqaliqayftawntnaperfaeifwpdgswvnvvgmhwrgrdqivfahtaflktifkdckqel vtieartiapgsalavvtliqdayvtpdgrqmprahdrltllaveregvwrfihghntivnpdaanndp vlrmkpa
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.40 Rfree 0.153
    Matthews' coefficent 2.74 Rfactor 0.138
    Waters 477 Solvent Content 55.14

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3gzr
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     

    Protein Summary

    Gene CC_2572 from Caulobacter crescentus encodes the protein NP_421374.1, that belongs to the PF08332 group, whose representative is the C-terminus domain of the Calcium/calmodulin dependent protein kinases II (CaMKII).

    Structurally similar proteins to 3gzr are mostly Nuclear Transport Factor 2 proteins.

     ----------------------------------------------------------------------------------------------

    Note from PFAM: This protein is also now in family SnoaL_2 PF12680

    ----------------------------------------------------------------------------------------------

     

    DALI Structural Homologs
    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 1ask 18.0 1.9 119 120 12 NUCLEAR TRANSPORT FACTOR 2
    2 1ar0 17.8 1.9 120 121 12 NUCLEAR TRANSPORT FACTOR 2
    3 3cu3 17.7 5.9 137 162 19 DOMAIN OF UNKNOWN FUNCTION WITH A CYSTATIN-LIKE
    4 1oun 17.7 2.0 120 121 12 NUCLEAR TRANSPORT FACTOR 2
    5 1jb5 17.7 2.2 119 123 11 NUCLEAR TRANSPORT FACTOR 2
    6 1gy6 17.6 2.1 121 123 12 NUCLEAR TRANSPORT FACTOR 2
    7 1u5o 17.5 2.0 120 121 12 NUCLEAR TRANSPORT FACTOR 2
    8 1jb4 17.5 2.0 120 123 11 NUCLEAR TRANSPORT FACTOR 2
    9 1gy5 17.5 1.9 120 123 12 NUCLEAR TRANSPORT FACTOR 2
    10 1qma 17.4 2.3 122 124 11 NUCLEAR TRANSPORT FACTOR 2
    SSM Structural Homologs
    N PDB Q-score RMSD TITLE
    1 1ar0 0.6082 1.645 NUCLEAR TRANSPORT FACTOR 2 (NTF2) E42K MUTANT
    2 1oun 0.6062 1.596 NUCLEAR TRANSPORT FACTOR 2 (NTF2)
    3 1ask 0.6061 1.563 NUCLEAR TRANSPORT FACTOR 2 (NTF2) H66A MUTANT
    4 1gy5 0.6017 1.625 D92N,D94N DOUBLE POINT MUTANT OF HUMAN NUCLEAR TRANSPORT FACTOR 2 (NTF2)
    5 1jb4 0.5913 1.626 NTF2 M102E MUTANT
    6 1jb2 0.586 1.719 NTF2 M84E MUTANT
    7 1a2k 0.5849 1.636 GDPRAN-NTF2 COMPLEX
    8 1u5o 0.5829 1.734 STRUCTURE OF THE D23A MUTANT OF THE NUCLEAR TRANSPORT CARRIER NTF2
    9 1jb5 0.5766 1.654 NTF2 M118E MUTANT
    10 1qma 0.5723 1.657 NUCLEAR TRANSPORT FACTOR 2 (NTF2) W7A MUTANT

     

    3gzr superposes well on these proteins as shown below.

    PX15624A_all.png

    3gzr (green), 1a2k (cyan), 1ar0 (lightmagenta), 1ask (yellow), 1gy5 (salmon), 1gy6 (lightgrey), 1jb2 (slate), 1jb4 (orange), 1jb5 (lime), 1oun (deepteal), 1qma (hotpink), 1u5o (yelloworange), 3cu3 (violetpurple).

     

    The protein is most likely a dimer according to the crystal packing analysis.

    PX15624A_dimer.png

    Each monomer in the dimer uses its beta sheet to engage with each other primarily. Additionally, the C-terminal helix reaches accross to the other monomer to add to the dimerization interaction. This interaction is further strengthened by binding of an unknown ligand (UNL) which interacts with both the chains.

    PX15624A_UNL.png

    The unknown ligand (UNL), resembling benzoic acid, interacts with residue ASN 165 of chain B, several hydrophobic residues in chain A, and a sulfate ion. An unbiased electron density (DM) is shown countoured around the UNL  in the above figure.

     

     

    References:

    1. Gangopadhyay SS, Barber AL, Gallant C, Grabarek Z, Smith JL, Morgan KG; , Biochem J 2003;372:347-357.: Differential functional properties of calmodulin-dependent protein kinase IIgamma variants isolated from smooth muscle. PUBMED:12603201

    2. Griffith LC, Lu CS, Sun XX; , Mol Interv 2003;3:386-403.: CaMKII, an enzyme on the move: regulation of temporospatial localization. PUBMED:14993460


     

     

    Ligand Summary

    An unknown ligand (UNL) resembling benzoic acid

    Reviews

    References

     

    No references found.

    Tag page
    • No tags
    You must login to post a comment.
    All content on this site is licensed under a Creative Commons Attribution 3.0 License
    Powered by MindTouch