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The Open Protein Structure Annotation Network
PDB Keyword
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2itb

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

    Title Crystal structure of putative tRNA-(ms(2)io(6)a)-hydroxylase (NP_744337.1) from Pseudomonas Putida KT2440 at 2.05 A resolution. To be published
    Site JCSG
    PDB Id 2itb Target Id 360824
    Molecular Characteristics
    Source Pseudomonas putida kt2440
    Alias Ids TPS1454,NP_744337.1, PF06175, 90616 Molecular Weight 23029.27 Da.
    Residues 205 Isoelectric Point 6.20
    Sequence mslipeidaflgcptpdawieaaladqetllidhkncefkaastalsliakynthldlinmmsrlaree lvhheqvlrlmkrrgvplrpvsagryasglrrlvrahepvklvdtlvvgafiearscerfaalvphlde elgrfyhgllksearhyqgylklahnygdeadiarcvelvraaemeliqspdqelrfhsgipqalaa
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.05 Rfree 0.229
    Matthews' coefficent 1.94 Rfactor 0.171
    Waters 222 Solvent Content 36.60

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2itb
    1. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
     
    2. Structural analysis of metal sites in proteins: non-heme iron sites as a case study
    C Andreini, I Bertini, G Cavallaro - Journal of molecular , 2009 - Elsevier
     
    3. Studies on the inference of protein binding regions across fold space based on structural similarities
    J Teyra, J Hawkins, H Zhu - : Structure, Function, and , 2011 - Wiley Online Library
     

    Protein Summary

    The PP_2188 gene from P. putida KT2440 encodes the NP_744337 protein, a bacterial hydroxylase for synthesis of the modified base 2-methylthio-cis-ribozeatin in specific tRNAs (MiaE) (PF06175).

    2itb is classified by SCOP in the all alpha class, ferritin-like superfamily, MiaE-like family. 2itb is a mainly alpha-helical protein. The total beta-sheet, alpha-helical, and 310-helical content is 2.0%, 71.4%, 1.0%, respectively. DALI structural similarity search returns 24 hits with Z-score higher than 10, where the top hit is with PDB structure 2fzf (Z-score 13.4; RMSD 2.9; 19% sequence similarity for 143 superimposed residues).


    Two Fe cations in 2itb chain A interact with conserved residues Glu38, Glu69, Glu122, and a peroxide ion. Each oxygen of the peroxide ion interacts with different Fe cations (located within 2.69Å and 2.66 Å respectively). Analysis of the crystallographic packing of 2itb using the PQS server {Henrick, 1998 #73} indicates that a dimer is the likely biological relevant form.

    Ligand Summary



    References

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