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The Open Protein Structure Annotation Network
PDB Keyword
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3giw

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

    Title Crystal structure of Rossmann-fold protein of unknown function (DUF574) (NP_823353.1) from Streptomyces avermitilis MA-4680 at 1.45 A resolution. To be published
    Site JCSG
    PDB Id 3giw Target Id 381519
    Related PDB Ids 3go4 
    Molecular Characteristics
    Source Streptomyces avermitilis ma-4680
    Alias Ids TPS20132,NP_823353.1, PF04672, 103788 Molecular Weight 30186.37 Da.
    Residues 276 Isoelectric Point 4.72
    Sequence mggaalpdngwpadridtesahsariydyiiggkdyypadkeagdamsrewpalpvhmranrdwmnrav ahlakeagirqfldigtgiptspnlheiaqsvapesrvvyvdndpivltlsqgllastpegrtayvead mldpasildapelrdtldltrpvaltviaivhfvldeddavgivrrlleplpsgsylamsigtaefapq evgrvareyaarnmpmrlrthaeaeeffeglelvepgivqvhkwhpdaatadgirdediamygavarkp
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.45 Rfree 0.176
    Matthews' coefficent 2.36 Rfactor 0.156
    Waters 305 Solvent Content 47.88

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3giw
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     
    2. Ligands in crystal structures that aid in functional characterization
    AE Speers, BF Cravatt - Acta Crystallographica Section F: Structural , 2010 - scripts.iucr.org
     

    Protein Summary

    Pfam update: This protein is in family DUF574 (PF04672). Thanks to the information in TOPSAN I have been able to update the annotation and rename the DUF as Methyltransf_17.

    Gene SAV_2177 from Streptomyces avermitilis ma-4680 encodes the NP_823353 protein belonging to DUF574 (PF04672). Genome context analysis of SAV_2177 shows a 0.9 scored hit with SAV_2175, a putative DNA-binding protein.

    Pre-SCOP puts 3giw in the alpha/beta class, S-adenosyl-L-methionine-dependent methyltransferase superfamily. An FFAS alignment indicates very significant structural similarity to another protein of unknown function from Thermobifida fusca, PDB id PDB:2qed6 also solved by JCSG. Dali top hits are with 2qe6 (Z-scr=36), and the carboxy-methyl transferases PDB:2ob2 (Z-scr=19), and PDB:1rjd (Z-scr=19). PDB:2uyo is next with a Z-scr=18.

    The structure reveals a SAM (S-adenosyl methyltransferase) domain protein with a central beta sheet with 3 alpha-helices on both sides. Crystal packing analysis suggests that a monomer is the solution state oligomeric form. An unidentified ligand (UNL, cyan) was found at the putative active site surrounded by the residues His57, His170, Phe171, Tyr216 and Met223 (pink sticks, below). The UNL is likely to be a phenylalanine (PHE) or phenylalanine-like molecule:

    Fig1.png

    The difference electron density/omit map (Fo-Fc) map at 3.0 sigma contour level shows the fit of the ligand (UNL, could be PHE or PHE-like) in the structure:

    ligden.jpg

    We have also determined the structure of this protein by molecular replacement from another crystal co-crystallized with 1mM SAM in which we can clearly see the SAM at the putative active site (there are no significant changes in the protein structure):

    xtal100019_SAH.jpg

     

    This protein structure superimposes rather well with the 2QE6 structure, with an r.m.s.d of 1.9A over 257 aligned Ca residues and 36% sequence identity, Dali Z-score ~33). The 2QE6 structure has the SAM molecule (blue spheres, below) at the putative active site. On superimposing the 2QE6 (orange, below) on to this protein, we can get an idea of how the SAM and UNL (PHE or PHE-like) ligand may be positioned at the putative active site:

    Fig2.png

    If we superimpose the SAM bound structure of 2qe6 with the Phe-like UNL structure of 3giw:

    xtal100019_SAHfig.png

    A search for other proteins of similar structure using DALI indicates that the 2QE6 protein is the most similar (Z-score ~33) followed by many other SAM domain methyltransferases (Z-score of next one is ~19). The SAM domain is highly conserved in structure in SAM methyltransferases.

     

    No PHE ligand was added during protein purification or crystallization which it suggests that this is an endogenous ligand which may be functionally relevant. If that is the case, then this putative enzyme may be involved in methylation of PHE or PHE-like substrate using the SAM. One possibility is that this may be like the phenylethanolamine N-methyltransferase (PNMT) that methylates phenylethanolamine. In humans, it is in the adrenal medulla and converts norepinephrine (noradrenalin) to epinephrine (adrenalin). These hormones resemble the amino acids tyrosine and phenylalanine. The crystal structure of the human PNMT has been solved under PDB id 1YZ3 (grey below, with SAH in yellow and inhibitor SKA in red, superimposed on the 3giw structure [Z=13]). Alternatively, 3giw could be related to the histamine N-methyltransferase (HNMT, Ref1; PDB_ID: 1jqd [Z=13]) whose ligand would also be a molecule similar in structure to Phe.

    Fig3.png

     References:

    1. The histamine N-methyltransferase T105I polymorphism affects active site structure and dynamics.

    Rutherford K, Parson WW, Daggett V.

    Ligand Summary

     

    A UNL has been modeled at the putative active site which looks like the amino acid PHE (Phenylalanine).

    Reviews

    References

     

    No references found.

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