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The Open Protein Structure Annotation Network
PDB Keyword
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3cnx

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

    Title Crystal structure of NTF2-like protein of unknown function (NP_825848.1) from Streptomyces avermitilis at 2.10 A resolution. To be published
    Site JCSG
    PDB Id 3cnx Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1706,NP_825848.1, 3.10.450.50, 335786
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 2
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.67 Rfactor 0.199
    Waters
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    Solvent Content 53.93

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    Ligand Information
    Ligands
    Metals

    Jmol

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

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    Protein Summary

    Gene SAV4671 from Streptomyces avermitilis ma-4680 encodes the NP_825848 that belongs to the NTF2-like superfamily. A 87% seq id protein (ZP_05019289) is annotated as predicted 3-dehydroquinate dehydratase. The Conserved Domain Database indicates that NP_825848 belongs to COG4319 (ketosteroid isomerase homolog with  function unknown). Genome context analysis suggest (score 0.87) a functional linkage with folP2, a putative dihydropteorate synthase (SAV4672).

    SCOP classifies 3cnx in the alpha+beta class, NTF2-like superfamily, SAV4671-like family. The top DALI hits (Z=16) are with 3GWR (a putative Ca-calmodulin dependent protein), 3D9R (kesteroid isomerase-like), 1OUN (Nuclear Transport Factor 2, NTF2), 2R4I (Unknown Function), 1HKX (Association domain of Ca2+/Calmodulin Protein Kinase II). The top hit with FFAS is 1HKX.

    3cnx crystal structure reveals that the protomer is a four stranded beta-sheet surrounding a helix with a few  flanking helices. There are 3 molecules per asymmetric unit of the unit cell. Crystal packing analysis suggests that two protomers form a dimer via the beta sheet as shown below. Size-exclusion chromatography supports the assignment of a dimer as the significant oligomerization state in solution.




    Superimposition of 3cnx protein dimer (red, orange) with a dimer of the 1HKX (cyan, which is a tetradecameric assembly forming two rings of seven protomers each) indicates that the structures of these proteins are very similar as is the nature of their dimers.

    The predicted dimeric nature of the 3cnx structure resembles NTF2 which is seen to be dimeric in solution. However, in NTF2, the monomers forming the dimer are at ~60 degrees to each other, whereas the dimeric association of this target is similar to the dimeric association seen in the Ca2+/Cal PK II.

    A putative binding site is seen in 3cnx formed by His61 (yellow), His150 (yellow) and Glu109 (green). A UNL (Unidentified ligand, red spheres) has been modeled in electron density seen at this site. The location of this binding pocket is also conserved in the different isoforms of Ca2+/Cal PK II from different organisms, but the residues are not conserved and the function of this is not known. The pocket location is also conserved in the NTF2 structure as a hydrophobic pocket comprised of phenylalanines, tryptophan and tyrosines and is supposed to bind Ran-GDP during the biochemical function of NTF2 to import cytoplasmic substrate and peptide fragments into the nucleus. A similar pocket is also observed in the structurally related scytalone dehydratase which forms trimers in solution.
    UNL.jpgUNLcartoon.png

     

     

     

    A second "protease-like" catalytic triad is also formed in this region by Cys59, His150 and Glu109, with the NE2 group of His150 at ~4.0A from the Cys59 S atom, and the Glu109 carboxylate O atoms within H-bonding distance of His150 as shown below. See Ref 2.

    Ligand Summary

    Two putative active sites seem possible in the same region: a metal binding site formed by His61, His150 and Glu109 or a protease-like catalytic triad formed by Cys59, His150 and Glu109. An unknown ligand (UNL) has been modeled here.

    References

    Reviews

    References

     

    No references found.

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