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3h3z

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

    Title Crystal structure of PUTATIVE CAMP-BINDING REGULATORY PROTEIN (YP_165150.1) from SILICIBACTER POMEROYI DSS-3 at 2.35 A resolution. To be published
    Site JCSG
    PDB Id 3h3z Target Id 391453
    Molecular Characteristics
    Source Silicibacter pomeroyi dss-3
    Alias Ids TPS20253,YP_165150.1, 2.60.120.10, 336125 Molecular Weight 25819.18 Da.
    Residues 234 Isoelectric Point 5.67
    Sequence maheaqkaiarnsllirslpeqhvdallsqavwrsydrgetlflqeekaqaihvvidgwvklfrmtptg seavvsvftrgesfgeavalrntpypvsaeavtpcevmhipspvfvslmrrdpeicisilattfghlhs lvaqleqlkaqtgaqrvaefllelcdcdtgacevtlpydkmliagrlgmkpeslsrafsrlkaagvtvk rnhaeiediallrdyaesdpadswsks
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.35 Rfree 0.236
    Matthews' coefficent 3.28 Rfactor 0.202
    Waters 98 Solvent Content 62.45

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3h3z

    Protein Summary

     

    Pfam: this target is reassigned to PF00027.   22 cNMP_binding along with other structures

     

    Gene SPOA0323 from Silicibacter pomeroyi dss-3 encodes the YP_165150 protein that has been annotated as cyclic nucleotide-binding protein based on a BLAST sequence alignment. According to Pfam, YP_165150 belongs to the cNMP binding domain family (PF00027).

    Pre-SCOP classifies 3h3z N-terminal domain (11-146) in the all beta class, cAMP binding domain-like superfamily; and the C-terminal domain (153-227) in the all alpha class, winged helix DNA binding domain superfamily, CAP C-terminal domain-like family. DALI top hits are with the DNR protein PDB:3dkw (Z=18), the putative transcriptional regulator PDB:2pqq (Z=17) and PDB:3d0s (Z=16). 3h3z has significant structural similarity to PDB:1cgp (Z=12) and PDB:1g6n (Z=12) with conserved K188, R194, R198 and K200 for possible DNA binding.  3h3z exists as a dimer in the crystal asymmetric unit. Interface interaction calculation also predicts the biomolecule of this target as a dimer.

     

    391453_1.png

    Figure 1. Protein structure 3h3z consists of two domains linked by a long helix.

     

    391453_2.png

    Figure 2. The biomolecule of 3h3z is a dimer.

     

    391453_2a.png

    Figure 3. The side view of the 3h3z dimer.

     

    391453_3.png

    Figure 4. 3h3z (grey) is structurally similar to the CAP protein 1CGP (blue) and 1G6N (magenta) that bind DNA.  

     

     

    391453_4.png

     

    Figure 5. K188, R194, R198 and K200 in 3h3z are conserved for putaitve DNA binding. A simple superimposition between 3h3z and 1CGP suggests how YP_165150 could interact with DNA.

     

     

    Literature
     
    1.    Schultz, S.C.,  Shields, G.C.,  Steitz, T.A.   (1991) Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees.  Science   253: 1001-1007      
     
    2.     Passner, J.M.,  Schultz, S.C.,  Steitz, T.A.   (2000) Modeling the cAMP-induced allosteric transition using the crystal structure of CAP-cAMP at 2.1 A resolution.  J.Mol.Biol.   304: 847-859

    Ligand Summary

    Reviews

    References

     

    No references found.

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