The Open Protein Structure Annotation Network
PDB Keyword


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

    Title Crystal structure of Putative SAM Dependent Methyltransferase in Complex with SAH (NP_744700.1) from PSEUDOMONAS PUTIDA KT2440 at 2.10 A resolution. To be published
    Site JCSG
    PDB Id 3e8s Target Id 381657
    Molecular Characteristics
    Source Pseudomonas putida kt2440
    Alias Ids TPS7325,NP_744700.1, BIG_666, 86804 Molecular Weight 24873.92 Da.
    Residues 226 Isoelectric Point 4.82
    Sequence mepimrnpedalldswhqnaqawidavrhgaiesrrqvtdqaillailgrqpervldlgcgegwllral adrgieavgvdgdrtlvdaaraagagevhlasyaqlaeakvpvgkdydlicanfallhqdiiellsamr tllvpggalviqtlhpwsvadgdyqdgwreesfagfagdwqpmpwyfrtlaswlnaldmaglrlvslqe pqhpqsavpqsllmvaerh
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.10 Rfree 0.176
    Matthews' coefficent 5.30 Rfactor 0.158
    Waters 226 Solvent Content 76.77

    Ligand Information


    Google Scholar output for 3e8s

    Protein Summary

    This is a protein of unknown function.  It has sequence similarity to the Methyltransf_12(PF08242, E-value: 9.3e-13) family from pfam which is a type of SAM dependent methyltransferase.

    SAM dependent methyltransferases use SAM (S-adenosyl-L-methione) as a cofactor to methylate protein side chains in various cellular pathways. The demethylation of SAM leads to SAH (S-adenosyl-L-homocysteine, AdoHcy). SAH is an intermediate in the synthesis of the amino acid cysteine and also acts as an inhibitor of methyltransferases following demethylation of SAM and is believed to be involved in the regulation of methylation.

    1mM SAM was added during protein crystallization. Interestingly, the crystal structure has SAH bound at the putative active site and not SAM. So, this structure could be that of of a post-methylation/demethylation event or it could be endogenously bound SAH that co-purified with the protein and crystallized in preference to the SAM added during crystallization. Interestingly, there is some unidentified and unmodeled electron density in the vicinity of the SAH and near the protein residues Phe123, Trp23 and Arg35, that could have been involved in the in-situ demethylation of the SAM.

    The modeling of SAH bound to the protein is supported by the electron density map obtained after density modification of the experimental MAD phases used for the structure determination, by the final 2Fo-Fc and Fo-Fc maps after refinement, and the B-factors of the SAH molecule (modeling SAM in the same location results in B-factors of the methyl C-atom to be almost twice as much as the neighboring atoms of the SAH molecule and also results in negative electron density in the difference map).

    There is a single protomer (Figure 1) in the asymmetric unit of the lattice, but crystal packing analysis suggests that the stable oligomeric form in solution should be a dimer (Figure 2)

    Figure 1


    Figure 2:



    Figure 3 shows the location of the SAH binding site in the protein:



    Figure 4 shows a close up of the bound SAH:


    According to FFAS, this proteins shares sequnece similarity with other proteins that have solved structures including: 3bkw (FFAS score: -49.700, sequence identity: 19%) and 3ccf (FFAS score: -50.800, sequence identity: 20%).

    Structurally, this protein is similar to a ubiquinone/menaquinone biosynthesis methyltransferase-related protein (tm1389) from Thermotoga maritima (PDB code: 2avn, TOPSAN page, RMSD of 2.5 A, 196 aligned residues, 18.9% sequence identity), human PNMT complexed with SAH (PDB code: 1hnn, RMSD of 2.9 A, 193 aligned residues, 13.5% sequence identity), and S-adenosylmethionine dependent methyltransferase (NP_104914.1) from Mesorhizobium loti (PDB code: 3bkw, TOPSAN page, RMSD of 2.2 A, 172 aligned residues, 28.4% sequence identity)(Figure 5).

    Figure 5: This protein (magneta) superposed with 2avnB (blue), 1hnnB (brown), and 3bkwA (green).


    Ligand Summary

    Endogenous S-adenosyl-L-homocysteine (SAH, AdoHcy) is bound to the protein.




    No references found.

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