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The Open Protein Structure Annotation Network
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3er7

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

    Title Crystal structure of NTF2-like protein of unknown function (YP_001812677.1) from EXIGUOBACTERIUM SP. 255-15 at 1.50 A resolution. To be published
    Site JCSG
    PDB Id 3er7 Target Id 390833
    Molecular Characteristics
    Source Exiguobacterium sibiricum 255-15
    Alias Ids TPS18283,YP_001812677.1, 3.10.450.50, 85537 Molecular Weight 14741.55 Da.
    Residues 130 Isoelectric Point 4.27
    Sequence mmntttldryfdlfdasrtdekafddlislfsdeitfvlngqeqhgidawkqfvrmvftanqdikhmya gwvpsetgdtmetrwavcgksadgsvftqdgtdiarlnadgkivylanvpddtamfnqynd
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.50 Rfree 0.209
    Matthews' coefficent 2.03 Rfactor 0.176
    Waters 309 Solvent Content 39.37

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Pfam update: This sequence matches the Pfam SnoaL family (PF07366).

    Gene Exig_0174 from Exiguobacterium sp. 255-15 encodes the YP_001812677 protein that belongs to the SnoaL-like polyketide cyclase group (PF07366). Two rounds of iterative PSI-BLAST indicates hits only to some similar sequences from B. pumilus with seq id of ~47% and S. mutans with seq id ~30%.

    Pre-SCOP classifies in the alpha+beta class, NTF2-like superfamily. 3er7 in the 3er7 structure contains 2 protomers in the asymmetric unit of the unit cell that form a dimer. Crystal packing analyis using PISA suggest that this dimer should be the stable oligomeric form in solution. Each monomer has a curved, six-stranded beta-sheet structure with three flanking helices.

    Fig1_dimerno.png
     


     

    FFAS shows other proteins with similar structures like PDB ids 2a15 (protein of unknown function) and 2gex (SnoaL2, a hydroxylase involved in polyketide/natural products synthesis in bacteria, Ref1). SnoaL2 catalyzes the hydroxylation of the C1 carbon atom in the polyketide chain. DALI top hits (Z-scr=15) are with putative polyketide cyclases like 1tuh, 2z77, 3f7x, etc.
     

    Comparison of the structures of 3er7 dimer with that of the 2gex dimer indicates that while the protomers are similar in structure, the dimer formation is quite different. It appears that the longer loop formed by residues 73-81 in 3er7 would prevent a dimer association like that observed in 2gex.

    Fig2_comparison.png
     

     The structure-based sequence alignment (CE) below show the amino acids in 2gex that are functionally important (bold, underlined) and the corresponding residues in 3er7.
     

      2GEX:A    8/9     ERCLEMVAAWNRW-----DVSGVVAHWAPDVVHYDDEDKPVSAEEVVRRMNSAVEAFPDL        A    1/6     TTLDRYFDLFDASRTDEKAFDDLISLFSDEITFVLNGQEQHGIDAWKQFVRXVFTANQDI    2GEX:A   63/64    RLDVRSIVGE--GDRVXLRITCSATHQGVFMGIAPTGRKVRWTYLEELRFSEAGKVVEHW
    A 61/66 KHXYAGWVPSETGDTXETRWAVCGKS--------ADGSVFTQDGTDIARLNADGKIVYLA

    2GEX:A 121/122 DVFN
    A 113/118 NVPD

    This protein could thus be a hydroxylase but its substrate is not known.

    Analysis of protein cavities using the CASTp server indicates the most prominent cavity has the residues Tyr10, Phe11 and Phe14 (in gold) which probably interact with the putative substrate:

    Fig3_putactivesite.png
     

    References:

    1) Beinker P, Lohkamp B, Peltonen T, Niemi J, Mäntsälä P, Schneider G. Crystal structures of SnoaL2 and AclR: two putative hydroxylases in the biosynthesis of aromatic polyketide antibiotics. J Mol Biol. 2006 Jun 9;359(3):728-40. Epub 2006 Apr 19.

    Ligand Summary

    Reviews

    References

     

    No references found.

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