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The Open Protein Structure Annotation Network
PDB Keyword
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3fh1

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

    Title Crystal structure of NTF2-like protein of unknown function (NP_108339.1) from MESORHIZOBIUM LOTI at 1.60 A resolution. To be published
    Site JCSG
    PDB Id 3fh1 Target Id 390988
    Molecular Characteristics
    Source Mesorhizobium loti maff303099
    Alias Ids TPS20192,NP_108339.1, 3.10.450.50, 85257 Molecular Weight 14397.52 Da.
    Residues 128 Isoelectric Point 5.12
    Sequence mkqdsiitlhpddrseqtaeimrrfndvfqlhdpaalpeliaeecvientvpapdgarhagrqacvqlw saiatqpgtrfdleetfvagdratirwrywmadgnsvrgvnlmrvqdgriveamgyvkg
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.60 Rfree 0.200
    Matthews' coefficent 2.36 Rfactor 0.167
    Waters 114 Solvent Content 47.94

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3fh1
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     
    2. Searching for Amelia Earhart at the Molecular Level: Peptide AMELIAEARHART
    D Wade - 2010 - wade-research.com
     

    Protein Summary

    Gene mll8193 from MESORHIZOBIUM LOTI encodes the NP_108339 protein that belongs to the SnoaL group (PF07366). STRING genome context analysis provides a reliable (score=0.8) hit with gene mll8194, that translates into the osmotically inducible protein OsmC.

    SCOP classifies 3fh1 in the alpha+beta class, NTF2-like superfamily. DALI top hits are with the NTF2-like 3gzr (Zscr=16), 1tuh (Zscr=15), 2k54, the steroid delta isomerase 1oh0 (Zscr=15), and the nogalonic acid methyl ester cyclase 1sjw (Zscr=12). SSM alignment suggests that 3fh1 has structural similarity to 1TUH, 1SJW and 1OH0

    3fh1 structure consists of a single domain, which is formed by alpha and beta motifs. 3fh1 carries a hydrophobic cavity for a predicted substrate binding function. Trp 69 and Trp 96 are highly conserved resiudes delimiting this pocket. There is an unidentified large and elongated electron density at the bottom of this cavity near to these residues.  The biomolecule of 3fh1 is suggested to be a dimer according to the result from interface interaction calculation. 

     

    390822_3.png 

     

     Figure 1. 3fh1 crystal structure presents one molecule in each asymmetric unit.

     

    390822_1.png

     

    Figure 2.  The biomolecule of 3fh1 is likely to be a dimer.

     

    390822_4.png

     

    Figure 3. 3fh1 (light blue) is a structurally similar to 1SJW (yellow), 1TUH (orange) and 1OH0 (magenta)

     

     

    390822_2.png

     

     Figure 4.  3fh1 carries a very hydrophobic cavity with an unknown electron density

     visible around residues Trp 69 and Trp 96.
     

     

     

     

    Literature
     
    1.     Sultana, A.,  Kallio, P.,  Jansson, A.,  Wang, J.S.,  Niemi, J.,  Schneider, G.   (2004) Structure of the polyketide cyclase SnoaL reveals a novel mechanism for enzymatic aldol condensation.  Embo J.   23: 1911-1921  
     
    2.    Cho, H.S.,  Ha, N.C.,  Choi, G.,  Kim, H.J.,  Lee, D.,  Oh, K.S.,  Kim, K.S.,  Lee, W.,  Choi, K.Y.,  Oh, B.H.  (1999) Crystal structure of delta(5)-3-ketosteroid isomerase from Pseudomonas testosteroni in complex with equilenin settles the correct hydrogen bonding scheme for transition state stabilization.  J.Biol.Chem.   274: 32863-32868   
     
    3.    Kim, S.W.,  Cha, S.S.,  Cho, H.S.,  Kim, J.S.,  Ha, N.C.,  Cho, M.J.,  Joo, S.,  Kim, K.K.,  Choi, K.Y.,  Oh, B.H.   (1997) High-resolution crystal structures of delta5-3-ketosteroid isomerase with and without a reaction intermediate analogue.  Biochemistry   36: 14030-14036  

    Ligand Summary

    Cl, EDO, UNL

    Reviews

    References

     

    No references found.

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