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The Open Protein Structure Annotation Network
PDB Keyword
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3c3p

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

    Title Crystal structure of a methyltransferase (NP_951602.1) from Geobacter sulfurreducens at 1.90 A resolution. To be published
    Site JCSG
    PDB Id 3c3p Target Id 372382
    Molecular Characteristics
    Source Geobacter sulfurreducens pca
    Alias Ids TPS1607,NP_951602.1 Molecular Weight 23241.47 Da.
    Residues 209 Isoelectric Point 5.73
    Sequence mipivdsrigayldgllpeadpvvaameqiarernipivdrqtgrllyllarikqpqlvvvpgdglgca swwfaraisissrvvmidpdrdnveharrmlhdnglidrvelqvgdplgiaagqrdidilfmdcdvfng advlermnrclaknalliavnalrrgsvaeshedpetaalrefnhhlsrrrdffttivpvgngvllgyrls
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 3
    Resolution (Å) 1.90 Rfree 0.232
    Matthews' coefficent 3.16 Rfactor 0.199
    Waters 195 Solvent Content 61.06

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    This protein belongs to Pfam PF01596 (O-methyltransferases) in the methyltransferase superfamily clan. Bacterial members of this family may play a role in antibiotic production.
    JCSG Structure Refinement Summary

    PSI-BLAST (1 round) returns hits mainly to O-methytransferases, hypothetical proteins and catechol-O-methyltransferases from many organisms with sequence identities ranging from 52% (exp=3e-55) to 27% (exp=5e-24). There are several protein structures in this range: 2HNK.pdb (27%, 7e-10, Crystal Structure Of Sam-Dependent O-Methyltransferase From Pathogenic Bacterium Leptospira Interrogans, Ref. 2), 2GPY.pdb (25%, 4e-9, Crystal Structure Of Putative O-Methyltransferase From Bacillus Halodurans)

    According to FFAS, the proteins most similar in structure have PDB ids 2AVD (catechol-O-methyltransferase), 2HNK (SAM-dependent O-methyltransferase) and 2GPY (O-methyltransferase). The top hits in DALI are 2GPY, 1VID and 1I9G. The function of this protein and several of the similar proteins remains unknown.

    The figure depicts the structure of this protein (red) superimposed on that of 2AVD (cyan, with bound SAM ligand, green, Ref. 1) showing the similarity between the two structures.



    Although the amino acids of 2AVD that are essential for interaction with the SAM ligand have not been reported yet, a struture-based sequence alignment (2AVD sequence in pink) of the two proteins reveals that some of the amino acids in 2AVD that are in the vicinity of the ligand (bold, underlined) are conserved in this protein.

    JCSG Structure Refinement SummaryJCSG Structure Refinement Summary

    IGAYLDGLLPEADPVVAAXEQIARERNI--PIVDRQTGRLLYLLARIKQPQLVVVPGDGL

    LWQYLLSRSMREHPALRSLRLLTLEQPQGDSMMTCEQAQLLANLARLIQAKKALDLGTFT


    GCASWWFARAISISSRVVXIDPDRDNVEHARRXLHDNGLIDRVELQVGDPLGIAAGQR--

    GYSALALALALPADGRVVTCEVDAQPPELGRPLWRQAEAEHKIDLRLKPALETLDELLAA


    ----DIDILFXDCDVFNGADVLERXNRCLAKNALLIAVNAL

    GEAGTFDVAVVDADKENCSAYYERCLQLLRPGGILAVLRVL


    The secondary structure elements in 2AVD in the region of the bound SAM are also conserved in this protein.

    The crystal structure of this protein contains 3 molecules in the asymmetric unit. Crystal packing analysis supported by size-exclusion chromatography suggests the dimer formed by chains A & B as the significant oligomeric form.

    Ligand Summary

    None

    References

    Reviews

    References

     

    No references found.

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