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The Open Protein Structure Annotation Network
PDB Keyword
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3ccg

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

    Title Crystal structure of predicted HD superfamily hydrolase involved in NAD metabolism (NP_347894.1) from Clostridium acetobutylicum at 1.50 A resolution. To be published
    Site JCSG
    PDB Id 3ccg Target Id 367850
    Molecular Characteristics
    Source Clostridium acetobutylicum atcc 824
    Alias Ids TPS1528,NP_347894.1, BIG_3, 86278 Molecular Weight 21434.34 Da.
    Residues 189 Isoelectric Point 5.55
    Sequence mwsydkitdylmnnlgekrykhslgvmdtavrlagiynedtekariaglvhdcakklpgekiieictne gyelgdedirnsyllhglagrilakkvigiddedvlnaiefhttgrpnmsllekiiyiadyiepgrefk gvdelrkaadedlnkallmsfdntikfvidkggflhhntiearnylisrkg
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.50 Rfree 0.217
    Matthews' coefficent 2.23 Rfactor 0.180
    Waters 198 Solvent Content 44.95

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3ccg
    1. Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers
    H Van Den Bedem, A Dhanik, JC Latombe - Section D: Biological , 2009 - scripts.iucr.org
     
    2. Structural and Biochemical Analysis of Nuclease Domain of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated Protein 3 (Cas3)
    S Mulepati, S Bailey - Journal of Biological Chemistry, 2011 - ASBMB
     

    Protein Summary

    NP_347894 has been annotated as HD superfamily hydrolase. NP_347894 is a member of COG1713: predicted HD superfamily hydrolase involved in NAD metabolism. Its homologs are often seen in genomic neighborhood, or in fusion with probable nicotinate-nucleotide adenylyltransferase (EC 2.7.7.18). NP_347894 is also similar to PF01966, which is metal-dependent HD superfamily phosphohydrolase.  Sequence alignment also agrees with this function annotation. NP_347894 mainly consists of helix bundles.  The directly superposing comparison between NP_347894 and Dali search results suggests the structurally similar preteins with PDB codes: 2QRT and 2O08. An active site with 2 metal-ion has been characterized. The metal ions are assigned as FE.  The following conserved residues against 2QRT are found: His 22, 51 and 85, Asp 52 and 129, which complexes with the Fe ions in the active site. There is also a formic ion from crystallization condition is also observed near to the active site. Arg 19 and Lsy 55 provide H-Bonding force to phosphate. There is one subunit in each asymmetric unit as a dimer. The surface interacting calculation suggests the biomolecule of NP_347894 should be a dimer.




































    Ligand Summary

    Metals: Fe
    Ligands: phosphate ion.

    References

    Reviews

    References

     

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