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The Open Protein Structure Annotation Network
PDB Keyword
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3ebt

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

    Title Crystal structure of NTF2-like protein of unknown function (YP_110153.1) from BURKHOLDERIA PSEUDOMALLEI K96243 at 1.30 A resolution. To be published
    Site JCSG
    PDB Id 3ebt Target Id 390547
    Molecular Characteristics
    Source Burkholderia pseudomallei k96243
    Alias Ids TPS14582,YP_110153.1, 3.10.450.50, 85680 Molecular Weight 14807.07 Da.
    Residues 131 Isoelectric Point 6.43
    Sequence msnnmqtvresyeafhrrdlpgvlaalapdvrwthpdgmspyglggtkhghdeviafirhvpthiaemr lapdefiesgerivvlgtrrvtavngrsatlkfvhvwrfengravtfedhfdtaemirlita
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.30 Rfree 0.162
    Matthews' coefficent 2.74 Rfactor 0.140
    Waters 214 Solvent Content 55.12

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3ebt
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     
    2. Dimensionality reduction in computational demarcation of protein tertiary structures
    RR Joshi, PR Panigrahi, RN Patil - Journal of Molecular Modeling, 2011 - Springer
     

    Protein Summary

    Gene BPSS0132 from Burkholderia pseudomallei k96243 encodes the protein YP_110153 that belongs to PF07858 (Limonene-1,2-epoxide hydrolase catalytic domain family). Genome context analysis reveals (score 0.78) the presence of a putative dehydratase (BPSS0131) in the neighborhood of this target.

    SCOP classifies 3ebt in the alpha+beta class, cystatin-like fold, NTF2-like superfamily. DALI top hits (Zscr=18) are with PDB:3ec9, PDB:3grd, PDB:3g8z. Polyketide cyclases PDB:3i0y and PDB:3f7x appear next with Z=17, followed by the limonene-1,2-epoxide hydrolase PDB:1nu3 (Z=15).

    mol_dimer.png

    Fig 1. Structure of 3ebt. The protein associates as a dimer in the crystal environment and may represent its functional oligomeric state.

    mol_1z1s.png

    Fig 2. 3ebt monomer structure is a sort of barrel composed of both strands and helices. Superposition of a structurally similar protein, PDB:1z1s (Z=14), highlights the secondary structure and the fold of the protein. 3ebt is shown in rainbow colors while 1z1s is in grey. The N-terminal section folds as a helix in most homologs.

    all.png

    Fig 3. 3ebt structurally similar proteins: PDB:1nu3 (cyan), PDB:1nww (magenta), PDB:1s5a (yellow), PDB:1tuh (pink), PDB:1z1s (grey), PDB:2inx (blue), PDB:2pzv (orange), PDB:3bb9 (lime), PDB:3ebt (green).

    all_as.png

    Fig 4. Most similar structures have some ligand bound in the core of the protein which may represent it active site.

    MG14545A_UNL.png

    Fig 5. 3ebt (green) has some unidentified electron density in the putative active site of the protein. This density has been modeled as an unknown ligand (UNL). The structure 1nu3 (cyan) has a ligand VPR (Valpromide) (shown in stick) bound to it at the corresponding position.

         

    References:
     

    • Sultana A, Kallio P, Jansson A, Wang JS, Niemi J, Mantsala P, Schneider G; , EMBO J 2004;23:1911-1921.: Structure of the polyketide cyclase SnoaL reveals a novel mechanism for enzymatic aldol condensation. PUBMED:15071504
    • Arand M, Hallberg BM, Zou J, Bergfors T, Oesch F, van der Werf MJ, de Bont JA, Jones TA, Mowbray SL; , EMBO J 2003;22:2583-2592.: Structure of Rhodococcus erythropolis limonene-1,2-epoxide hydrolase reveals a novel active site. PUBMED:12773375
    • 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.



     

    Ligand Summary

    an unknown ligand (UNL)

    Reviews

    References

     

    No references found.

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