The Open Protein Structure Annotation Network
PDB Keyword


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

    Title Crystal structure of transcriptional regulator of Crp/Fnr family (YP_604437.1) from DEINOCOCCUS GEOTHERMALIS DSM 11300 at 1.86 A resolution. To be published
    Site JCSG
    PDB Id 3e97 Target Id 390750
    Molecular Characteristics
    Source Deinococcus geothermalis dsm 11300
    Alias Ids TPS14617,DGEO_15APR04_CONTIG105_REVISED_GENE503,, 85722 Molecular Weight 25620.92 Da.
    Residues 230 Isoelectric Point 5.86
    Sequence vgrlddlkrsplfqnvpedamrealkvvternfqpdelvveqdaegealhlvttgvvrvsrvslggrer vlgdiyapgvvgetavlahqersasvraltpvrtlmlhrehfelilrrhprvlwnlaemlarrvtflnd eliafgqnteaalthvfanlyrqrlaagvpqpevlplgtqdimartsssretvsrvlkrleahnilevs prsvtlldlaalealsfegaetd
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.86 Rfree 0.246
    Matthews' coefficent 2.49 Rfactor 0.208
    Waters 188 Solvent Content 50.54

    Ligand Information



    Protein Summary

    This protein is annotated as belonging to Pfams PF00027 (cAMP/cGMP binding domain protein) and PF00325(Crp family of bacterial transcriptional regulators). Crp family proteins are very diverse but may be allocated into subfamilies based on sequence and it includes Crp, Clp, CysR, FixK, Flp, Fnr, FnrN, HlyX and NtcA. They are supposed to bind DNA via their C-terminus HTH domain.

     There is one protomer in the asymmetric unit of the crystal structure but crystal packing analysis suggests the following dimer should be stable solution state oligomeric form:



    From a search for similar structures using FFAS, the top hits (with scores ~-70) are to Crp/Fnr family proteins, catabolite gene activator protein (CAP), virulence factor regulator, chlorophenol reduction gene K, etc. These include the crystal structures with PDB ids 2gau, 1g6n, 3dv8, 2oz6, 2h6c, etc. but the sequence identity is < 20%.

    The figure below shows this protein superimposed on the  CAP-cAMP complex (1g6n, magenta with cAMP in white):


    The amino acids from the CAP protein that interact with cAMP (Ref1) are Tyr63, Glu72, Arg 82, Ser83, Arg123, Thr127 and Ser 128. The corresponding positions in this protein based on the superimposition of the structures above are Asp73, Glu82, Arg91 (direction is different), Ser92 (different direction), Arg132, Leu136 and Asn137.


    Weber IT, Steitz TA. Structure of a complex of catabolite gene activator protein and cyclic AMP refined at 2.5 A resolution. J Mol Biol. 1987 Nov 20;198(2):311-26.


    Ligand Summary




    No references found.

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