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3fm2

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

    Title Crystal structure of uncharacterized protein, distantly related to a heme binding/degrading HemS (PF05171) family (YP_324846.1) from Anabaena variabilis ATCC 29413 at 1.80 A resolution. To be published
    Site JCSG
    PDB Id 3fm2 Target Id 392439
    Molecular Characteristics
    Source Anabaena variabilis atcc 29413
    Alias Ids TPS24349,YP_324846.1, 323900 Molecular Weight 15345.78 Da.
    Residues 134 Isoelectric Point 5.61
    Sequence mshslkdfleacetlgtlrlivtssaavleargkieklfyaelakgkyanmhtegfefhlnmekitqvk fetgeakrgnfttyairfldekqesalslflqwgkpgeyepgqveawhtlkekygevweplpvql
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.80 Rfree 0.219
    Matthews' coefficent 2.15 Rfactor 0.196
    Waters 174 Solvent Content 42.71

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3fm2
    1. Assessment of template based protein structure predictions in CASP9
    V Mariani, F Kiefer, T Schmidt, J Haas - Proteins: Structure, , 2011 - Wiley Online Library
     
    2. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     
    3. Blind prediction of quaternary structures of homo-oligomeric proteins from amino acid sequences based on templates
    M Morita, M Kakuta, K Shimizu, S Nakamura - 2012 - hoajonline.com
     

    Protein Summary

    Pfam update: This protein is now in family PF06228.6 DUF1008 CL0312.

    The Ava_4353 gene from Anabaena variabilis encodes the YP_324846 protein from DUF1008 (PF06228).

    3fm2 crystal structure is a dimer and packing analysis suggests that this dimer should be the significant oligomeric form in solution.

    The protein has mostly beta sheet secondary structure with two segments of beta-sheet, one with 5 strands and the other with 3 strands. It forms a very interesting dimer with 5 strands from the one sheet in one protomer packed against the 3 strands from the other sheet from the second protomer to form a highly curved 8-stranded beta sheet structure of the dimer. It appears that this dimer could be stabilized by a zinc ion coordinated to Glu30 from one molecule and Glu57 and His59 from the other molecule in this curved sheet region.

    Fig1.1.png

    A search for other proteins of similar structure using the Protein structure comparison service SSM, shows that there are only 3 other proteins  of significant structural similarity: 2ovi (Heme binding protein ChuX, Q-score 0.46, 1.71A rmsd over 114 aligned Ca), 2ph0 (Protein Q6D2T7_ERWCT from Erwinia carotovora, Q-score 0.42, 1.97A rmsd over 115 aligned Ca) and 2hqv (Ref1, Protein AGR_C_4470 from Agrobacterium tumefaciens, Q-score 0.39, 1.95A over 114 aligned Ca). 

    Interestingly, all these structures have been solved by Structural Genomics initiatives.

    The AGR_C_4470 protein (Ref1), was found to have some structural similarity to two proteins involved in heme utilization, the Escherichia coli heme oxygenase ChuS (Ref2) and the Yersinia enterocolitica heme transport protein HemS (Ref3). However, AGR_C_4470 is similar in size to our protein and about half the size of the ChuS (PDB id 1u9t) and HemS.

    The heme binding site of the HemS (PDB id 2j0p and 2j0s for the heme-HemS complex and apo-HemS) is not conserved in AGR_C_4470.

    The structure based sequence alignment (using the CE algorithm) of our protein with the AGR_C_4470 (2hqv) shows that there are several residues conserved (bold) between these two proteins and specifically the Glu30 and His59 which are involved in metal coordination in this proten are also conserved in the AGR_C_4470 (bold underlined):

    USR1:A    4/4     HSLKDFLEACETLGTLRLIVTSSAAVLEARGKIEKLFYAELAKGKYANXHTEGFEFHLNX
    2hqv:H 70/71 DRFDAIWNEXRGWGEILXIVQTGDIVLEVPGHL-PEGTESH--GWFNIHGDSPIGGHIKK


    USR1:A 64/64 EKITQVKFETGEAKRGNFTTYAIRFLDEKQESALSLFLQWGKPGEYEPGQVEAWHTLKEK
    2hqv:H 127/128 DNCAAITFVDRGFH--GRRSCSVWFXNAAGGAXFKIFVRRDENKELLAGQLAKFEELRDG


    USR1:A 124/124 YG
    2hqv:H 185/186 FR

     

    The structure-based sequence alignment of our protein with the HemS (2j0p) also shows that there are some conserved residues, and the Glu30 is identical in both proteins.

    USR1:A    5/5     SLKDFLEACETLGTLRLIVTSSAAVLEARGKIEKLFYAELAKGKYANXHTEGFEFHLNXE
    2jop:J 50/51 DARALLAALEAVGEVKAITRNTYAVHEQMGRYENQHLNG---HAGLILNPRNLDLRLFLN


    USR1:A 65/65 KITQVKFETGEAKRGNFTTYAIRFLDEKQESALSLFLQWGKPGEYEPGQVEAWHTLKEKY
    2jop:J 107/108 QWASAFTLTEETRH--GVRHSIQFFDHQGDALHKVYVTEQ-------TDMPAWEALLAQF


    USR1:A 125/125 G
    2jop:J 158/159 I

    The binding sites of our protein (brown and magenta) superimposed on the 2hqv (pink) and 2j0p (brown-grey, with the heme in cyan) is shown:

    Fig2.png

    It should be noted that the dimer of our protein appears to be similar to the two-domain monomer of the HemS indicating a gene duplication event.

    The AGR_C_4470 (2hqv) belongs to Pfam PF06228 (DUF1008) which now has consists of 92 proteins from 87 species.

    References:

    1. Crystal structure of AGR_C_4470p from Agrobacterium tumefaciens. Protein Sci. 16: 535-538

    2. Suits, M.D., Pal, G.P., Nakatsu, K., Matte, A., Cygler, M., and Jia, Z. 2005. Identification of an Escherichia coliO157:H7 heme oxygenase with tandem functional repeats. Proc. Natl. Acad. Sci. 102: 16955–16960

    3. Schneider, S., Sharp, K.H., and Paoli, M. 2006. An induced fit conformational change underlies the binding mechanism of the heme-transport proteobacteria-protein HemS. J. Biol. Chem. 281: 32606–32610. 

    Ligand Summary

    Zinc

    Reviews

    References

     

    No references found.

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