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The Open Protein Structure Annotation Network
PDB Keyword
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387987

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

    Site JCSG
    Status Crystal Structure
    Target Id 387987
    Molecular Characteristics
    Source Bifidobacterium adolescentis atcc 15703
    Alias Ids TPS7498, Molecular Weight 32528.45 Da.
    Residues 300 Isoelectric Point 5.19
    Sequence mshvsyaeppaqgwdihchtvfsdgtetprtlveqarklglhgvaiadhdttagwdeateaseeiglplllgteit avdedvsvhmlafqydpsnehissmfantraarlrrtkrmverlsqdfpitwddvlaqvkegerttigrphiada lvaagvyetrsdafadavsakskyyiptpspstheviaavkgaggvvvaahagdpqrnrrllsdeqldamiadgl dglevwhrgnppeqrerlltiaarhdllvtggsdwhgkgkpnglgenltdddtvreilcrgvdligrvgsshaa
      BLAST   FFAS
    Ligand Information
    Ligands
    Metals
    Google Scholar output for

    Protein Summary

    YP_910028 from Bifidobacterium adolescentis (strain ATCC 15703 / DSM 20083) encodes a protein containing PHP (Polymerase and Histidinol Phosphatase) domain (PF02811) (E-value: 1.4e-21). The active site, at the deep cleft in between PHP domain and extra domain (residue 105-179), occupied by Zn, Fe and PO4 ions. His and Asp residues (His17, His19, Glu74, Asp260, His85, His202, Asp24, His49 and His262) are involving in the metal coordination.

    Fig 1: Two domains - PHP domain (green) and an extra domain (residues 105-179, cyan) and the active site is shown. Zn 1-2 (blue dot), Fe 3 (orange dot) and PO4 (red stick) and residues are involved in the metal coordination are shown.


    Dali hits with DNA polymerase III (PDB id: 2hpi) with 2.8A rmsd (Z=15.8, 18% seq id), histidinol Phosphate Phosphatase (PDB id: 2yz5) with 3.8A rmsd (Z=9.9, 21% seq id) and isoaspartyl dipeptidase (PDB id: 1pok) with 3.1A rmsd (Z=9.3, 15% seq id). When we compare YP_910028 with 2yz5, two metal binding sites are very similar as shown in Fig. 2.


    Fig. 2: Superposition of YP_910028 (green) with 2yz5 (Histidinol Phosphatase, light blue).


    Two Zn ions (Zn1 and Zn2-green) and one Fe ion (Fe3-orange) and PO4 4-5 (green sticks) are from YP_910028. Two Fe ions (Fe502 and Fe503 – light orange) and one Zn ion (Zn501 - ligh blue) are from 2yz5. Please notice that Zn501 of 2yz5 is positioned at the exactly same site of PO4-4.


    We propose that YP_9100028 is a metal-dependent phosphoesterase.


    Ligand Summary

    Zn, Fe and PO4 ions are found in the active site.

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