The Open Protein Structure Annotation Network
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    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title Crystal structure of protein with a cupin-like fold and unknown function (YP_298765.1) from Ralstonia eutropha JMP134 at 2.60 A resolution. To be published
    Site JCSG
    PDB Id 3cjx Target Id 380353
    Molecular Characteristics
    Source Ralstonia eutropha jmp134
    Alias Ids TPS1755,YP_298765.1, Molecular Weight 18142.56 Da.
    Residues 164 Isoelectric Point 5.52
    Sequence atithqeklltvdttahpflkalgghegtdifplfmdpynglmvmrasfapgltlplhfhtgtvhmyti sgcwyyteypgqkqtagcylyepggsihqfntprdnegqtevifmlsgcnvnftqdgtylglsdagvik nwvdraireqdnglryiaaavptyaa
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.60 Rfree 0.237
    Matthews' coefficent 2.54 Rfactor 0.203
    Waters 183 Solvent Content 51.60

    Ligand Information


    Google Scholar output for 3cjx

    Protein Summary

    The Reut_B4571 gene from Ralstonia eutropha jmp134 encodes the YP_298765 protein that could belong (very weak e-val=0.006) to the cupin2 family (PF07883). The genomic neighborhood of the homologous protein from Shewanella sp. shows a potential functional link of this target with an alcohol dehydrogenase (score 0.8).

    Pre-SCOP classifies 3cjx in the all beta class, RmlC-like cupins superfamily, TM1287-like family. The 3cjx structure folds into a 10 anti-parallel beta-strands and an alpha-helix at the C-terminal end of the chain. The beta-strands are arranged to form two five stranded anti-parallel beta-sheets. The two individual beta-sheets, in turn, are twisted to form a jellyroll beta-sandwich with a topology characteristic of a cupin barrel-fold. In solution and in the crystal, a tetramer most likely represents the biologically significant oligomerization state. Pairs of monomers (figure1 blue:green and yellow:red) are tighly packed across the beta-barrel interface. However, additional inter-subunit contacts form in the tetramer with the N-terminal region of one subunit forming a two stranded anti-parallel beta-sheet with the C-terminal beta strand of a second subunit.

    DALI returns as top hit the uncharacterized cupin 3ebr (Z=20), followed by the putative alpha carboxylase 2o1q (Z=17) and the acetylacetone cleaving enzyme 3bal (Z=16). From a search of the EBI Secondary Fold Matching Server (EBI SSM server) using the refined coordinates of 3cjx as query shows as top hit the PDB ID 1LRH (Z=12). 1RLH is an auxin binding protein from the maize plant. Even though the two structures show only a 15% sequence identity, there is only a 1.9 Angstrom RMS between their 129 aligned Ca atoms.

    Figure 1. Ribbon representation of the 3cjx crystal structure. The biologically relevant oligomerization state is believed to be a tetramer. Each monomer within the tetramer is rendered in a unique color.





    Ligand Summary

    Glycerol molecules from the cryoprotectant and chloride molecules from the crystallization buffer were modeled into the 3cjx structure.





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