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    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,, 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


    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.



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



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



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



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





    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.



    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




    No references found.

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