2YXO

Histidinol Phosphate Phosphatase complexed with Sulfate

Summary for 2YXO

• Entry DOI: 10.2210/pdb2yxo/pdb
• Descriptor: Histidinol phosphatase, SULFATE ION, ZINC ION, ... (6 entities in total)
• Functional Keywords: metal-dependent, hydrolase
• Biological source: Thermus thermophilus
• Total number of polymer chains: 2
• Total formula weight: 60764.75

Authors

Omi, R. (deposition date: 2007-04-26, release date: 2007-11-27, Last modification date: 2024-03-13)

Primary citation

Omi, R.,Goto, M.,Miyahara, I.,Manzoku, M.,Ebihara, A.,Hirotsu, K.
Crystal Structure of Monofunctional Histidinol Phosphate Phosphatase from Thermus thermophilus HB8.
Biochemistry, 46:12618-12627, 2007

PubMed Abstract: 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.

PubMed: 17929834
DOI: 10.1021/bi701204r

Experimental method

X-RAY DIFFRACTION (1.6 Å)