1K1E

Structure Of the cobalt-bound form of the deoxy-D-mannose-octulosonate 8-phosphate phosphatase (YrbI) From Haemophilus Influenzae (HI1679)

Summary for 1K1E

• Entry DOI: 10.2210/pdb1k1e/pdb
• Related: 1j8d
• Descriptor: deoxy-D-mannose-octulosonate 8-phosphate phosphatase, COBALT (II) ION, MERCURY (II) ION, ... (7 entities in total)
• Functional Keywords: hi1679, structural genomics, kdo 8-p phosphatase, structure 2 function project, s2f, hydrolase
• Biological source: Haemophilus influenzae Rd
• Total number of polymer chains: 12
• Total formula weight: 239445.08

Authors

Lim, K.,Herzberg, O.,Structure 2 Function Project (S2F) (deposition date: 2001-09-25, release date: 2002-02-27, Last modification date: 2023-08-16)

Primary citation

Parsons, J.F.,Lim, K.,Tempczyk, A.,Krajewski, W.,Eisenstein, E.,Herzberg, O.
From structure to function: YrbI from Haemophilus influenzae (HI1679) is a phosphatase.
Proteins, 46:393-404, 2002

PubMed Abstract: The crystal structure of the YrbI protein from Haemophilus influenzae (HI1679) was determined at a 1.67-A resolution. The function of the protein had not been assigned previously, and it is annotated as hypothetical in sequence databases. The protein exhibits the alpha/beta-hydrolase fold (also termed the Rossmann fold) and resembles most closely the fold of the L-2-haloacid dehalogenase (HAD) superfamily. Following this observation, a detailed sequence analysis revealed remote homology to two members of the HAD superfamily, the P-domain of Ca(2+) ATPase and phosphoserine phosphatase. The 19-kDa chains of HI1679 form a tetramer both in solution and in the crystalline form. The four monomers are arranged in a ring such that four beta-hairpin loops, each inserted after the first beta-strand of the core alpha/beta-fold, form an eight-stranded barrel at the center of the assembly. Four active sites are located at the subunit interfaces. Each active site is occupied by a cobalt ion, a metal used for crystallization. The cobalt is octahedrally coordinated to two aspartate side-chains, a backbone oxygen, and three solvent molecules, indicating that the physiological metal may be magnesium. HI1679 hydrolyzes a number of phosphates, including 6-phosphogluconate and phosphotyrosine, suggesting that it functions as a phosphatase in vivo. The physiological substrate is yet to be identified; however the location of the gene on the yrb operon suggests involvement in sugar metabolism.

PubMed: 11835514
DOI: 10.1002/prot.10057

Experimental method

X-RAY DIFFRACTION (1.67 Å)