The Open Protein Structure Annotation Network
PDB Keyword


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

    Title Crystal structure of NifX-associated protein of unknown function (YP_002425942.1) from Acidithiobacillus ferrooxidans ATCC 23270 at 2.00 A resolution. To be published
    Site JCSG
    PDB Id 3g7p Target Id 381741
    Molecular Characteristics
    Source Acidithiobacillus ferrooxidans atcc 23270
    Alias Ids TPS14557,AFE_1570, PF03270, 86734 Molecular Weight 17700.73 Da.
    Residues 155 Isoelectric Point 5.32
    Sequence mpentamaallpeeslffrelvkqwraqdsygtwekksdmellapyvldkeqrraipiigdpdpeilwr velfynavglaterasgvmvspmmkmshegfgrmvliagrlivvnkqlrdvhrfgfpsmeklaeegdkl vagalemiekfpevarf
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.00 Rfree 0.249
    Matthews' coefficent 2.44 Rfactor 0.204
    Waters 105 Solvent Content 49.61

    Ligand Information


    Google Scholar output for 3g7p
    1. Crystal structure of cce_0566 from Cyanothece 51142, a protein associated with nitrogen fixation in the DUF269 family
    GW Buchko, H Robinson - FEBS letters, 2012 - Elsevier

    Protein Summary

    Gene AFE_1514 from Acidithiobacillus ferrooxidans atcc 23270 encodes the YP_002425942 protein that belongs to the DUF269 group involved in nitrogen fixation (PF0320). Genome context analysis of a homologous protein from Methylococcus capsulatus indicates a functional link with the nitrogenase molybdenum iron protein NifX. 


    Shown below is a ribbon representation of the dimeric structure of 3g7p. The crystal strucure indicates that the dimer is biologicdimer_ribbons.pngally-relevant oligomeric state. The structure was determined at a resolution of 2.0 Angstroms from  a hexagonal crystal form (space group P6122). Primary phasing was accomplished by Se-Met based MAD phasing. The crystallographic asymmetric consists of a monomer, each monomer in the dimer are related by a crystallographic two fold axis of symmetry. In the figure, the ribbons are color coded with the N-termini in blue and the C-termini in red.


    A DALI search provides only very weak hits with the EcoRI endonuclease 1qri (Z=4.7), a prolyl-tRNA synthetase 2j3l (Z=4.3) and the APC35702 protein 1ylx (Z=4).  An EBI fold match search of the PDB shows that the following targets are structurally related to 3g7p

     Hit   Z-score   No. 
     1  3.2 4 2.65  17.0%   1ylxA  Crystal structure of a protein of unknown function from bacillus stearothermophilus
     2  1.7 4 2.75  26.6%   3dexA  Crystal structure of sav_2001 protein from streptomyces avermitilis, northeast structural genomics consortium target svr107.
     3  1.9 5 2.79  20.2%   2okaA  Crystal structure of q9hyq7_pseae from pseudomonas aeruginosa. Northeast structural genomics consortium target par82
     4  1.4 3 3.20  17.0%   1soyA  Solution structure of the bacterial frataxin orthologue, cyay
     5  1.7 4 2.72  19.2%   2p0gA  Crystal structure of selenoprotein w-related protein from vibrio cholerae. Northeast structural genomics target vcr75
     6  1.9 5 2.80  21.5%   2ojlA  Crystal structure of q7waf1_borpa from bordetella parapertussis. Northeast structural genomics target bpr68.
     7  0.8 5 3.53  21.6%   2npbA  Nmr solution structure of mouse selw
     8  1.4 3 3.45  21.6%   2afdA  Solution structure of asl1650, an acyl carrier protein from anabaena sp. Pcc 7120 with a variant phosphopantetheinylation-site sequence
     9  1.8 3 3.89  32.9%   2fq2A  Solution structure of minor conformation of holo-acyl carrier protein from malaria parasite plasmodium falciparum
     10  1.5 5 3.24  19.0%   2obkA  X-ray structure of the putative se binding protein from pseudomonas fluorescens. Northeast structural genomics consortium target plr6.


    This protein contains domain of unknown function (DUF269), that was found only in the nitrogen-fixing species (Okamoto et al. 2007). Among the functionally-annotated targets shown in the above table is PDB ID 1SOY, (DALI Zscr=3.7) an NMR structure of a CyaY protein from E. coli (Nair et al., 2004). CyaY is the bacterial ortholog of frataxin. Cya is a small mitochondrial iron binding protein thought to be involved in iron sulphur cluster formation. Loss of frataxin function leads to the neurodegenerative disorder Friedreich's ataxia. Shown below is an alpha-carbon superpositioning of the structures of 3g7p and 1SOY.







    Shown below is 2fo-fc omit map electron density (pink) contoured at 1.0 standard deviations above background level. Superimposed on this electron density is a molecule of polyethyleneglycol.  The structure shows that a polyethylene glycol molecule from the crystallization solution is bound between dimers related by crystallograhic symmetry. The PEG is positioned near a special position in the crystal structure.


    peg_density (2).png

    The homolog structure (PDB 4NJ2) was recently reported. The superposed structures are shown below:



    Superposition of two DUF269 structures from Cyanothece 51142 (wheat, 3NJ2) and A. ferrooxidans (blue, 3G7P), cce_0566 and B7JA91_ACIF2, respectively. (From [Ref])

    Ligand Summary




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