1YMQ

HAD Superfamily Phosphotransferase Substrate Diversification: Structure and Function Analysis of the HAD Subclass IIB Sugar Phosphatase BT4131

Summary for 1YMQ

• Entry DOI: 10.2210/pdb1ymq/pdb
• Descriptor: sugar-phosphate phosphatase BT4131, MAGNESIUM ION, SULFATE ION, ... (4 entities in total)
• Functional Keywords: had superfamily phosphotransferase, transferase
• Biological source: Bacteroides thetaiotaomicron
• Total number of polymer chains: 1
• Total formula weight: 29033.80

Authors

Lu, Z.,Dunaway-Mariano, D.,Allen, K.N. (deposition date: 2005-01-21, release date: 2005-06-28, Last modification date: 2023-08-23)

Primary citation

Lu, Z.,Dunaway-Mariano, D.,Allen, K.N.
HAD Superfamily Phosphotransferase Substrate Diversification: Structure and Function Analysis of HAD Subclass IIB Sugar Phosphatase BT4131.
Biochemistry, 44:8684-8696, 2005

PubMed Abstract: The BT4131 gene from the bacterium Bacteroides thetaiotaomicron VPI-5482 has been cloned and overexpressed in Escherichia coli. The protein, a member of the haloalkanoate dehalogenase superfamily (subfamily IIB), was purified to homogeneity, and its X-ray crystal structure was determined to1.9 A resolution using the molecular replacement phasing method. BT4131 was shown by an extensive substrate screen to be a broad-range sugar phosphate phosphatase. On the basis of substrate specificity and gene context, the physiological function of BT4131 in chitin metabolism has been tentatively assigned. Comparison of the BT4131 structure alpha/beta cap domain structure with those of other type IIB enzymes (phosphoglycolate phosphatase, trehalose-6-phosphate phosphatase, and proteins of unknown function known as PDB entries , , and ) identified two conserved loops (BT4131 residues 172-182 and 118-130) in the alphabetabeta(alphabetaalphabeta)alphabetabeta type caps and one conserved loop in the alphabetabetaalphabetabeta type caps, which contribute residues for contact with the substrate leaving group. In BT4131, the two loops contribute one polar and two nonpolar residues to encase the displaced sugar. This finding is consistent with the lax specificity BT4131 has for the ring size and stereochemistry of the sugar phosphate. In contrast, substrate docking showed that the high-specificity phosphoglycolate phosphatase (PDB entry ) uses a single substrate specificity loop to position three polar residues for interaction with the glycolate leaving group. We show how active site "solvent cages" derived from analysis of the structures of the type IIB HAD phosphatases could be used in conjunction with the identity of the residues stationed along the cap domain substrate specificity loops, as a means of substrate identification.

PubMed: 15952775
DOI: 10.1021/bi050009j

Experimental method

X-RAY DIFFRACTION (1.9 Å)