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The Open Protein Structure Annotation Network
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2htd

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

    Title Crystal structure of Predicted flavin-nucleotide-binding protein from COG3576 family structurally related to pyridoxine 5'-phosphate oxidase (ZP_00387536.1) from Lactobacillus delbrueckii bulgaricus ATCC BAA-365 at 1.60 A resolution. To be published
    Site JCSG
    PDB Id 2htd Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1503,YP_812335.1, BIG_750, 2.30.110.10, 90911
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 2
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 1.89 Rfactor 0.158
    Waters
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    Solvent Content 34.39

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 2htd
    1. The structure of a Xanthomonas general stress protein involved in citrus canker reveals its flavin-binding property
    E Hilario, Y Li, D Niks, L Fan - Acta Crystallographica Section D: , 2012 - scripts.iucr.org
     

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    Protein Summary

    The Ldb0262 (YP_812335 (formerly ZP_00387536)) gene from L. delbrueckii bulgaricus ATCC BAA-365 encodes a protein with similarity to pyridoxamine 5'-phosphate (PMP) oxidases (Pfam01243). Two polypeptide chains are present in he asymmetric unit arranged in a predicted dimer according to the PQS server {Henrick, 1998 #73}. The dimer arrangement is closely similar to that of PMP oxidases (for example 1nrg), but Ldb0262 lacks helices 4 and 5 and has a shorter beta-sheet, resulting ia more compact, rather than elongated, subunit structure.

     

    No cofactor (riboflavin 5'-phosphate, FMN) or substrate is present in the putative binding cleft, located at two symmetric sites at the dimerization interface. Only two sulfate ions, one at the position occupied by the  FMN phosphate, are seen in each copy of the binding site. Since part of the cleft is provided by the missing extended beta-sheet (see above) and the only relatively well conserved residue from putative pyridoxamine 5'-phosphate binding cleft is Leu24, the data suggest that YP_812335 despite similarity to Pfam01243 is not a pyridoxamine 5'-phosphate oxidase.

     

    The highly conserved residues in sequence alignment between YP_812335 and members of Pfam01243 indicates that a functionally important site is located close to Asp30, and that a putative pyridoxamine 5'-phosphate binding cleft (occupied in this structure by SO4) is far away from a cluster of conserved residues located near this Asp30. A pair of residues Asn/Asp-Pro (located close to Asp30) that is conserved in Pfam01243 is replaced by Gly66-Ser67 in YP_812335.

    YP_812335 has structural similarity to proteins such as FMN-binding protein (PDB structure 1axj; PubMed:9406543; DALI Z-score 12.4; RMSD 2.5; 15% sequence identity within 108 superimposed residues; a member of SCOP family: PNP-oxidase like [50476]). The FMN-binding site from PDB structure 1axj overlaps with the putative pyridoxamine 5'-phosphate binding cleft (described above).

    Ligand Summary



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