7LCE

Structure of D-Glucosaminate-6-phosphate Ammonia-lyase

Summary for 7LCE

• Entry DOI: 10.2210/pdb7lce/pdb
• Related: 7LC0
• Descriptor: D-glucosaminate-6-phosphate ammonia lyase, DIMETHYL SULFOXIDE, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: aminotransferase fold, d-glucosaminate metabolism, lyase
• Biological source: Salmonella typhimurium
• Total number of polymer chains: 4
• Total formula weight: 159485.87

Authors

Phillips, R.S. (deposition date: 2021-01-10, release date: 2021-06-09, Last modification date: 2023-11-15)

Primary citation

Phillips, R.S.,Ting, S.C.,Anderson, K.
Structure and Mechanism of d-Glucosaminate-6-phosphate Ammonia-lyase: A Novel Octameric Assembly for a Pyridoxal 5'-Phosphate-Dependent Enzyme, and Unprecedented Stereochemical Inversion in the Elimination Reaction of a d-Amino Acid.
Biochemistry, 60:1609-1618, 2021

PubMed Abstract: d-Glucosaminate-6-phosphate ammonia-lyase (DGL) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that produces 2-keto-3-deoxygluconate 6-phosphate (KDG-6-P) in the metabolism of d-glucosaminic acid by serovar typhimurium. We have determined the crystal structure of DGL by SAD phasing with selenomethionine to a resolution of 2.58 Å. The sequence has very low identity with most other members of the aminotransferase (AT) superfamily. The structure forms an octameric assembly as a tetramer of dimers that has not been observed previously in the AT superfamily. PLP is covalently bound as a Schiff base to Lys-213 in the catalytic dimer at the interface of two monomers. The structure lacks the conserved arginine that binds the α-carboxylate of the substrate in most members of the AT superfamily. However, there is a cluster of arginines in the small domain that likely serves as a binding site for the phosphate of the substrate. The deamination reaction performed in DO gives a KDG-6-P product stereospecifically deuterated at C3; thus, the mechanism must involve an enamine intermediate that is protonated by the enzyme before product release. Nuclear magnetic resonance (NMR) analysis demonstrates that the deuterium is located in the - position in the product, showing that the elimination of water takes place with inversion of configuration at C3, which is unprecedented for a PLP-dependent dehydratase/deaminase. On the basis of the crystal structure and the NMR data, a reaction mechanism for DGL is proposed.

PubMed: 33949189
DOI: 10.1021/acs.biochem.1c00106

Experimental method

X-RAY DIFFRACTION (2.58 Å)