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The Open Protein Structure Annotation Network
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3di4

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

    Title Crystal structure of protein of unknown function (DUF1989) (YP_165628.1) from SILICIBACTER POMEROYI DSS-3 at 1.60 A resolution. To be published
    Site JCSG
    PDB Id 3di4 Target Id 383110
    Molecular Characteristics
    Source Silicibacter pomeroyi dss-3
    Alias Ids TPS7392,YP_165628.1, BIG_837, BIG_202, 88531 Molecular Weight 31218.36 Da.
    Residues 285 Isoelectric Point 5.70
    Sequence mtdapadapldadarravkpvicypndslprpdlalyraarasarktgevlvppregrcfevkagqffr issvegpqvgdlnlhnlhdlterffsgktralhgthvttgerlwsnlpylrpmatiiedtlgwygidqy ggsvhdvigtrcdpytgnllagghyhhcchsnltraladhtglplheaemlvhdvlnvfmctgftrdtg qyfmkaspvrpgdyleffaeidllgnlsacpggdcssehssdtaschpllveifapaegmlgdwpspsv ngydrshgr
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.60 Rfree 0.175
    Matthews' coefficent 2.16 Rfactor 0.141
    Waters 740 Solvent Content 43.14

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3di4
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     

    Protein Summary

    Gene SPO0365 from Silicibacter pomeroyi dss-3 encodes the uncharacterized protein YP_165628.1, a member of the DUF1989 group (PF09347). Analysis of its genome context identifies the presence of a purine nucleoside phosphorylase, an Arg-decarboxylase (YP_165627) and an ethylmalonyl-CoA mutase.

    3di4 contains a core which is similar to lectins/glucanases (1/3 of the overall length). However, it contains large number of auxillary insertions. When compared to galectin (Dali Z-scr=3; PDB ID 1ww4),  one of the insertions (149-190) is very interesting since it is near the active site (metal site).  It also has longer N-terminus and C-terminus which are involved in dimerization.

    3di4 has a well defined active pocket formed by one monomer and the N-terminus of the 2nd monomer (see below). The residues that are likely functionally important include: D80/C150/C167/C237 (Zn metal coordination), chainA residues C242/M211/C23 & chainB residues Y24/Y209/N195/D144 (pocket). The chemical properties of the binding pocket and its structure similarity to lectins suggest that 3di4 is likely an enzyme which may bind a sugar moiety as well.

    monomerdimer
    active site cavity

    Ligand Summary

    Reviews

    References

     

    No references found.

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