387987

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