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

    Title Crystal structure of RmlC-like cupin with unknown function (YP_294607.1) from RALSTONIA EUTROPHA JMP134 at 2.60 A resolution. To be published
    Site JCSG
    PDB Id 3ebr Target Id 371684
    Molecular Characteristics
    Source Ralstonia eutropha jmp134
    Alias Ids TPS6515,YP_294607.1,, 103446 Molecular Weight 17900.34 Da.
    Residues 158 Isoelectric Point 5.56
    Sequence mlfesintgcldgndtpwmpfapysndvmvkyfkidpvrgetitllkapagmemprhhhtgtvivytvq gswrykehdwvahagsvvyetastrhtpqsayaegpdiitfnivagellylddkdniiavenwktsmdr ylnyckahgirpkdlstfeg
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.60 Rfree 0.262
    Matthews' coefficent 2.77 Rfactor 0.227
    Waters 25 Solvent Content 55.65

    Ligand Information


    Google Scholar output for 3ebr

    Protein Summary

    Gene Reut_A0381 from Ralstonia eutropha JMP134 encodes the YP_294607 protein with 158 residues. Residues 44-113 of this target contain a cupin-2 domain (PF07883) from Pfam (E-value: 0.044).  BLAST hits also suggest that this target is a cupin-2 like domain protein. 

    Structurally, 3ebr belongs to the all beta class, RmlC-like cupins superfamily from SCOP. 3ebr structure is constructed primarily of beta-strands (only one α-helix in the folding core) in a β-barrel shape.

    Figure 1.  The 3ebr structure contains a β-barrel for the main folding-core.   


    There is one subunit in each asymmetric unit of the 3ebr crystal. The interface interaction calculation shows that the likely biomolecule of 3ebr should be a tetramer with the total interacting area of 10810 Å2.  The N-terminal strand (residues 5 to 13) of each subunit interacts with a neighboring subunit and participates in its β-barrel formation. The whole architecture of this target is very typical of a cupin-like protein. A conserved metal-complex site in the 3ebr structure is found, consisting of H57, H59, H95 and E89.


    Figure 2. The biomolecule of 3ebr is a tetramer.


    According to searches in the secondary structural matching (SSM) and DALI servers, 3ebr is structurally similar to the protein YP_298765.1 (PDB:3cjx, TOPSAN page, Zscr=20), which has a cupin-like fold with unknown function. In addition to 3cjX, a search in  FFAS (Fold & Function Assignment System) and DALI, also suggests two homologues based sequence similarity: acetylacetone dioxygenase from Acinetobacter johnsonii (PDB:3bal, Z=17) and the alpha subunit of a putative acetyl/propionyl-CoA carboxylase from Rubrivivax gelatinosus PM1 (PDB:2o1q, TOPSAN page, Z=17). 


    Figure 3.  Protein 3ebr (green) is structurally similar to 2O1Q (magenta), 3BAL (cyan) and 3CJX (Yellow).   



    1.    Dunwell JM; , Biotechnol Genet Eng Rev 1998;15:1-32.: Cupins: a new superfamily of functionally diverse proteins that include germins and plant storage proteins.  











    Ligand Summary




    No references found.

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    Files (3)

    FileSizeDateAttached by 
    The YP_294607.1 molecule contains a β-barrel for the main folding-core.
    145.14 kB00:11, 22 Jul 2008kevinjinActions
    The biomolecule of YP_294607.1 is a tetramer.
    258.87 kB00:11, 22 Jul 2008kevinjinActions
    Protein YP_294607.1 (green) is structural homolog to 2O1Q(magenta), 3BAL(cyan) and 3CJX(Yellow).
    172.81 kB00:11, 22 Jul 2008kevinjinActions
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