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3myx

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

    Title Crystal structure of a PSPTO_0244 (Protein with unknown function which belongs to Pfam DUF861 family) from Pseudomonas syringae pv. tomato str. DC3000 at 1.30 A resolution. To be published
    Site JCSG
    PDB Id 3myx Target Id 403325
    Molecular Characteristics
    Source Pseudomonas syringae pv. tomato str. dc3000
    Alias Ids TPS30654,NP_790095.1, 2.60.120.10, 325402 Molecular Weight 25360.17 Da.
    Residues 237 Isoelectric Point 4.95
    Sequence mpqptvlllaradlspvgtefttgpidahdpfdsgrrtafvdeqgiaagivefgtalsveaypytemlv mhrgsvtltsgtdsvtlstgesavigrgtqvridaqpeslwafcastqasgpdksgitaldrlalltps sppdpsimisplpqcrsnnlfedtastlrigvwdstpyerisrphkihelmnliegrvvlslengsslt vntgdtvfvaqgapckwtstgyvrkfyavt
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.30 Rfree 0.146
    Matthews' coefficent 2.07 Rfactor 0.117
    Waters 830 Solvent Content 40.69

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    This protein is annotated as a member of the Pfam Cupin_3 family/DUF861, PF05899.

    Pfam update: This protein is now in family Cuoin_3, at least in its C-terminal half. The family is in the Cupin clan. The actual function of the family is not known.

    Fig1.png

    There appears to be a gene duplication in the protein with the N-terminal half (approximately residues 3-130) superimposable on the C-terminal half (~residues 131-237) with a DALI Z-score of 9.5 and 2.0A rmsd over 88 Ca residues and a 15% sequence identity:

    Fig2_superimposed.png

    Thus, there are 2 cupin folds in the protein molecule.

     

    Of the 661 unique proteins that have been classified in this Pfam, only 9 have a similar architecture that includes

    two Cupin_3 domains.

    Other related proteins can be found from the FFAS link above, the top hit being PDB id 1sfn.

    A search of other proteins of similar structure using the SSM server at EBI results in only 3 significant hits (Q-scores ~0.2-0.3 and rmsds ~3.0-3.5A, ~16-19% seq id), to PDB ids 1sfn (NYSGXRC structure), 2qdr (JCSG structure) and 2d40 (BSGI structure, Ref1), which are all solved from structural genomics centers.

    A superimposition of this structure (blue-green) with that of the 2d40 (yellow) reveals their structural similarities and also their differences, most notably, the prominent helices in the 2d40 are missing in this protein:

    Fig3_target_2d40.png

     

    The protein with PDB id 2d40 is an eGDO (E. coli gentisate 1,2-dioxygenase) which converts gentisic acid (2,5-dihydroxybenzoic acid, DHB) to maleylpyruvate in aromatic compound metabolism (Ref1). It is similar in structure to the human homogentisate 1,2-dioxygenase (PDB id 1ey2). Neither the 2d40 or the 1ey2 structures have substrate bound but there are some results from molecular docking experiments.

    eGDO, with 2 cupin_3 domains like this protein, was found to be a tetramer in the crystal structure as well as solution conditions. this protein is predicted to be a monomer from the crystal packing analysis. However, size-exclusion chromatography coupled with static light scattering suggest that this protein is likely to be a dimer in solution conditions.

    The active site in eGDO is believed to be be H104, H106, H145, Q93 and D159 (red sticks below) which interacts with the gentisate via an iron atom (brown sphere). However, these residues are not conserved in this proteins 403325, and are instead different residues in the corresponding positions (green sticks). So, this protein has some different function:

    Fig4_activesites.png

     

     

    One of the residues in the second cupin domain of this protein that corresponds to the residues in green above is Lys232 (black stick, below). It could be that there is another active site in this second domain. A 1,2-ethandiol (EDO) molecule from the cryoprotectant solution (magenta spheres) was modeled in the electron density near this residue:

    Fig5_lys232edo.png

     

    References:

    1) Structural and biochemical characterization of gentisate 1,2-dioxygenase from Escherichia coli O157:H7.

    Adams MA, Singh VK, Keller BO, Jia Z., Mol Microbiol., 2006, 61: 1469-1484

    Ligand Summary

    Reviews

    References

     

    No references found.

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