1J8D image
Deposition Date 2001-05-21
Release Date 2002-02-27
Last Version Date 2024-11-13
Entry Detail
PDB ID:
1J8D
Keywords:
Title:
Structure Of the metal-free form of the deoxy-D-mannose-octulosonate 8-phosphate phosphatase (YrbI) From Haemophilus Influenzae (HI1679)
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.30 Å
R-Value Free:
0.25
R-Value Work:
0.17
Space Group:
I 2 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:deoxy-D-mannose-octulosonate 8-phosphate phosphatase
Gene (Uniprot):HI_1679
Chain IDs:A, B, C, D
Chain Length:180
Number of Molecules:4
Biological Source:Haemophilus influenzae Rd
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
MSE A MET SELENOMETHIONINE
Ligand Molecules
Primary Citation
From structure to function: YrbI from Haemophilus influenzae (HI1679) is a phosphatase.
Proteins 46 393 404 (2002)
PMID: 11835514 DOI: 10.1002/prot.10057

Abstact

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.

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Primary Citation of related structures