PDBsum entry 2yz5

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Hydrolase PDB id
Protein chains
263 a.a. *
PO4 ×2
_ZN ×2
_FE ×4
Waters ×306
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Histidinol phosphate phosphatase complexed with phosphate
Structure: Histidinol phosphatase. Chain: a, b. Synonym: histidinol phosphate phosphatase. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 274. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
2.10Å     R-factor:   0.195     R-free:   0.232
Authors: R.Omi
Key ref: R.Omi et al. (2007). Crystal structure of monofunctional histidinol phosphate phosphatase from Thermus thermophilus HB8. Biochemistry, 46, 12618-12627. PubMed id: 17929834 DOI: 10.1021/bi701204r
03-May-07     Release date:   27-Nov-07    
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Protein chains
Pfam   ArchSchema ?
Q5SLG2  (Q5SLG2_THET8) -  Histidinol phosphatase
267 a.a.
263 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     dephosphorylation   4 terms 
  Biochemical function     catalytic activity     5 terms  


DOI no: 10.1021/bi701204r Biochemistry 46:12618-12627 (2007)
PubMed id: 17929834  
Crystal structure of monofunctional histidinol phosphate phosphatase from Thermus thermophilus HB8.
R.Omi, M.Goto, I.Miyahara, M.Manzoku, A.Ebihara, K.Hirotsu.
Monofunctional histidinol phosphate phosphatase from Thermus thermophilus HB8, which catalyzes the dephosphorylation of l-histidinol phosphate, belongs to the PHP family, together with the PHP domain of bacterial DNA polymerase III and family X DNA polymerase. We have determined the structures of the complex with a sulfate ion, the complex with a phosphate ion, and the unliganded form at 1.6, 2.1, and 1.8 A resolution, respectively. The enzyme exists as a tetramer, and the subunit consists of a distorted (betaalpha)7 barrel with one linker and one C-terminal tail. Three metal sites located on the C-terminal side of the barrel are occupied by Fe1, Fe2, and Zn ions, respectively, forming a trinuclear metal center liganded by seven histidines, one aspartate, one glutamate, and one hydroxide with two Fe ions bridged by the hydroxide. In the complexes, the sulfate or phosphate ion is coordinated to three metal ions, resulting in octahedral, trigonal bipyramidal, and tetrahedral geometries around the Fe1, Fe2, and Zn ions, respectively. The ligand residues are derived from the four motifs that characterize the PHP family and from two motifs conserved in histidinol phosphate phosphatases. The (betaalpha)7 barrel and the metal cluster are closely related in nature and architecture to the (betaalpha)8 barrel and the mononuclear or dinuclear metal center in the amidohydrolase superfamily, respectively. The coordination behavior of the phosphate ion toward the metal center supports the mechanism in which the bridging hydroxide makes a direct attack on the substrate phosphate tridentately bound to the two Fe ions and Zn ion to hydrolyze the phosphoester bond.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19211662 S.Nakane, N.Nakagawa, S.Kuramitsu, and R.Masui (2009).
Characterization of DNA polymerase X from Thermus thermophilus HB8 reveals the POLXc and PHP domains are both required for 3'-5' exonuclease activity.
  Nucleic Acids Res, 37, 2037-2052.  
18223080 H.S.Lee, Y.Cho, J.H.Lee, and S.G.Kang (2008).
Novel monofunctional histidinol-phosphate phosphatase of the DDDD superfamily of phosphohydrolases.
  J Bacteriol, 190, 2629-2632.  
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