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The Open Protein Structure Annotation Network
PDB Keyword
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3ejk

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

    Title Crystal structure of dTDP Sugar Isomerase (YP_390184.1) from DESULFOVIBRIO DESULFURICANS G20 at 1.95 A resolution. To be published
    Site JCSG
    PDB Id 3ejk Target Id 390748
    Molecular Characteristics
    Source Desulfovibrio desulfuricans g20
    Alias Ids TPS14615,DDES_06JUN05_CONTIG143_REVISED_GENEDDE3696, 2.60.120.10, 85549 Molecular Weight 18975.75 Da.
    Residues 173 Isoelectric Point 6.08
    Sequence vdimlntadisaaaillpvegaqlselrqipaeggpvlhmlrldspqfsqfgeiyfsevlprrvkawkr hslmtqlfavpvgcihvvlydgreksptsgrlaqvtlgrpdnyrllrippqvwygfaatgdtpalvanc tdiphrqgeserapqdapfipfswagadlsgtpvm
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.95 Rfree 0.217
    Matthews' coefficent 2.36 Rfactor 0.169
    Waters 132 Solvent Content 47.88

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3ejk
    1. Crystal structures of the apo and GDP_bound forms of a cupin_like protein BbDUF985 from Branchiostoma belcheri tsingtauense
    Y Du, YX He, S Gaowa, X Zhang - Proteins: Structure, , 2010 - Wiley Online Library
     

    Protein Summary

    A BLAST search identifies this protein as YP_390184.1, which contains a polysaccharide biosynthesis domain, and it belongs to the dTDP-sugar-isomerase superfamily (cl09145) from CDD.  This superfamily contains dTDP_sugar_isom (PF00908) , RfbC (COG1898) and  FdtA (PF05523).

    This is an all b-strand structure. The adjoining strands in the sheet come from non-adjoinging regions in the sequence.

    MG8818A.png

       

    Based on crystal packing the protein most likely assembles as a dimer in the solution as shown below.

    MG8818A_dimer.png

       

    The residue CYS 83 shows some additional density beyond the side chain atom SG. The connectivity supports the assignment of this residue as Thio methylated Cysteine (SCH), but the mass spectrometry of the protein prep prior to crystallization gave the expected mass for the unmodified protein, suggesting that protein was not modified at that time. Therefore, an unknown ligand (UNL), covalently connected to SG, has been modeled here . An unbiased electron density (DM) map prior to model buillding supports the modeling of UNL, shown below. SCH as a modified CYS residue has been observed earlier (PDB Id codes: 1AEX 1FXD 1K72 1YAL 1YPV), see reference #2 for 1FXD.
     

    SCH.png
     

    There are a few structural homologs (SSM results) of the protein. A superposition of these structures are shown below. YP_390184.1 (green), dTDP-6-deoxy-d-xylo-4-hexulose 3,5-epimerase from Methanobacterium thermoautotrophicum (cyan, PDB code: 1ep0, TOPSAN page), dTDP-4-dehydrorhamnose 3,5-epimerase homologue from Sulfolobus tokodaii (magenta, PDB code: 1wlt), dTDP-4-dehydrorhamnose 3,5-epimerase from Sulfolobus tokodaii (yellow, PDB code: 2b9u), and dTDP-4-keto-6-deoxy-D-glucose-3,4-ketoisomerase from Aneurinibacillus thermoaerophilus (pink, PDB code: 2pa7).

    all.png

       

    The most notable SSM hit is 2PA7, again a dTDP-4-keto-6-deoxy-d-glucose-3,4-ketoisomerase. A closer look indicates that the bound ligand TYD (yellow) in 2PA7 (magenta) occupies the same region as Citrate/Glycerol (white) molecules occupy in this target (green) (see below). This suggests that Citrate/Glycerol molecules occupy the ligand site in this protein. In addition, Ala-66 --Trp-67 is a cis-peptide in the active site which may be important in ligand binding.

    TYD_CIT_CIS.png

       

    Analysis with the STRING server, shows that Dde_3695: CDP-glucose-4,6-dehydratase, putative (368 aa), Dde_3694: glucose-1-phosphate cytidylyl-transferase (263 aa), Dde_3697: aminotransferase, DegT/DnrJ/EryC1/StrS family (384 aa), Dde_3698: glycosyl transferase, group 2 family protein (327 aa), Dde_3693: pyridoxal phosphate-dependent enzyme apparently (1156 aa), and Dde_3685: HPCH/HPAI aldolase family protein (258 aa) are in the same genomic neighborhood as this protein.

     

    References

    •  Davis, M.L.,  Thoden, J.B.,  Holden, H.M.   (2007) The X-ray Structure of dTDP-4-Keto-6-deoxy-D-glucose-3,4-ketoisomerase.  J.Biol.Chem.   282: 19227-19236
    • Kissinger, C.R.,  Sieker, L.C.,  Adman, E.T.,  Jensen, L.H.   (1991) Refined crystal structure of ferredoxin II from Desulfovibrio gigas at 1.7 A.  J.Mol.Biol.   219: 693-715

     

    Ligand Summary

    Citrate and glycerol occupy the substrate site.

    Residue CYS83 + UNL could be CS0.

    Reviews

    References

     

    No references found.

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