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The Open Protein Structure Annotation Network
PDB Keyword
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2p4g

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

    Title Crystal structure of hypothetical protein (NP_939744.1) from Corynebacterium diphtheriae at 2.30 A resolution. To be published
    Site JCSG
    PDB Id 2p4g Target Id 366862
    Molecular Characteristics
    Source Corynebacterium diphtheriae nctc 13129
    Alias Ids TPS1482,NP_939744.1, _0078.007649_, 432988 Molecular Weight 29210.82 Da.
    Residues 269 Isoelectric Point 5.96
    Sequence mltdmqrdsassstvtteqivygalplttinepecraiaitsingsatlsgvsgpmgdqtdadlliqlr gwadaivvgaetarkenygpvvlphgiknqrqklgrcglpkltllskslyfdfsselfspdlpselspl vitqqpannseqwdqrlqklidvgvevivaptstnplkiafdalharrlkkisieggpsvyrqalslgi vdrlhltiapniicpvesplfgkisddsfttrlvlemlssspnglifsrykvirdtlgnptq
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.30 Rfree 0.225
    Matthews' coefficent 3.53 Rfactor 0.173
    Waters 113 Solvent Content 65.12

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2p4g
    1. Complex Structure of Bacillus subtilis RibG
    SC Chen, YH Lin, HC Yu, SH Liaw - Journal of Biological Chemistry, 2009 - ASBMB
     
    2. Distributed structure determination at the JCSG
    H van den Bedem, G Wolf, Q Xu - Section D: Biological , 2011 - scripts.iucr.org
     

    Protein Summary

    The DIP1392 gene translates into the NP_939744.1 amino acid sequence which corresponds to a 269 residues single domain protein and member of the Riboflavin Deaminase (RibD) C-terminal domain family PF01872, characterized by its pyrimidine reductase activity. Some members of this family present a two domain architecture with a deaminase inserted at the N-terminus (PF00383).

     

    2p4g belongs to the alpha/beta SCOP class, DiHydro-Folate Reductase-like superfamily, RibD C-terminal domain-like family. Regarding structural similarity, the highest score (FFAS score -70; HHpred P-val=1e-40; SSM 70%; Dali Z-scr=23.5; FATCAT P-val=2.1e-10) belongs to 2azn, a pyrimidine reductase of the riboflavin biosynthetic pathway [Ref]. The PF00383 member structure 2hxv scores as second hit (FFAS score -48; HHpred P-val=1e-41; Dali Z-scr=20.7; FATCAT P-val=3.3e-9) although only when considering its C-terminal reductase domain.

    Based on the crystal structure, the biologically relevant form is a dimer. This is reinforced by the observation of a similar dimeric architecture is some of its structural homologs, such as 2b3z, 2hxv and 2o7p.

    Ligand Summary



    References

    Reviews

    References

     

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