The Open Protein Structure Annotation Network
PDB Keyword


    Title Crystal structure of Putative exonuclease (RER070207002219) from Eubacterium rectale at 2.19 A resolution. To be published
    Site JCSG
    PDB Id 3l0a Target Id 392282
    Molecular Characteristics
    Source Eubacterium rectale atcc 33656
    Alias Ids TPS27737,YP_002938006.1, 325551 Molecular Weight 30680.71 Da.
    Residues 265 Isoelectric Point 5.33
    Sequence mqltsenyysqeankeymsvsgykdfagtygkmpcefygmeklngrwedekstallvgsyvdsyfegsl dqfkkdnpeiftqkgelkanfkqaeeiiarierdeyfmkymsgqkqvimtgelfgakwkikmdsyipgv aivdlkvmasitdlkwvkdigyldfvrywgydiqgavyqeivrqntgeklpffiagatkqtepdiriih vtdnylqealhmvemnmprilrvkngevepdrcelcdccrhnrvlkkpisimdltagi
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.19 Rfree 0.250
    Matthews' coefficent 2.48 Rfactor 0.208
    Waters 93 Solvent Content 50.48

    Ligand Information


    Google Scholar output for 3l0a

    Protein Summary

    The E. rectale EUBREC_2131 gene encodes the YP_002938006.1 amino acid sequence, which is annotated as a hypothetical protein without Pfam entry yet. However, its structure (3l0a) suggests it possesses an exonuclease-like fold. The highest structural similarity (FFAS scr=-71; Dali Z-scr=18; SSM 53%) is scored with 3h4r, an E. coli exodeoxyribonuclease [Ref]. IsoCleft finder suggest an ATP binding site with a top Z-scr=2.8. Analysis of EUBREC_2131 gene vicinity with ProFunc reveals the presence of a RecT-like DNA binding protein, and an ATP-binding protein with nucleoside-triphosphatase activity.


    This protein was not found in Pfam so I've added it as DUF3799 (PF12684). This protein appears to be related to the Cas_Cas4 family with which it shares the C-terminal 3 cys cluster. That is interesting because there is no structure for that family and as its a Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) related protein then it's quite publishable. Both these families are in the PDDEXK superfamily so they are probably nucleases. It's probably worth checking the genomic location of this protein and see if it's associated with CRISPRS or Cas proteins. -- Alex Bateman @ PFAM, 11/26/2009


    The monomer structure is shown below with a bound Zn ion.



    A closeup of the Zn ion shows four cysteine (35, 240, 243, 246) residues interacting with it.




    The protein most likely assembles as a trimer according to the crystal packing analysis.



    Proteins with significant structural similarity to 3l0a are listed below.

    DALI Structural Similarity
    1 3h4r 17.9 3.2 198 219 15 EXODEOXYRIBONUCLEASE 8
    2 1avq 9.9 3.4 167 228 9 LAMBDA EXONUCLEASE
    3 2w4b 8.0 3.8 173 455 9 ALKALINE EXONUCLEASE
    4 2w45 7.9 3.8 171 449 9 ALKALINE EXONUCLEASE
    5 1w36 7.5 3.6 150 1158 13 DNA HAIRPIN
    6 3fqd 6.3 3.7 154 332 7 5'-3' EXORIBONUCLEASE 2
    7 3fqg 5.6 4.1 150 313 8 PROTEIN DIN1
    8 3fqj 5.3 4.2 154 353 6 PROTEIN DOM3Z

    Some of these are shown below.


    3l0a (green), 1avq (cyan), 3fqj (slate), 3h4r (orange)

    Ligand Summary




    1. (No Results)


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