1GSO

GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE (GAR-SYN) FROM E. COLI.

Summary for 1GSO

• Entry DOI: 10.2210/pdb1gso/pdb
• Descriptor: PROTEIN (GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE) (2 entities in total)
• Functional Keywords: gar-syn, glycinamide ribonucleotide synthetase, atp-grasp, purine de novo biosynthetic pathway, substrate channeling, ligase
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 46283.53

Authors

Wang, W.,Kappock, T.J.,Stubbe, J.,Ealick, S.E. (deposition date: 1998-09-08, release date: 1998-12-09, Last modification date: 2024-02-07)

Primary citation

Wang, W.,Kappock, T.J.,Stubbe, J.,Ealick, S.E.
X-ray crystal structure of glycinamide ribonucleotide synthetase from Escherichia coli.
Biochemistry, 37:15647-15662, 1998

PubMed Abstract: Glycinamide ribonucleotide synthetase (GAR-syn) catalyzes the second step of the de novo purine biosynthetic pathway; the conversion of phosphoribosylamine, glycine, and ATP to glycinamide ribonucleotide (GAR), ADP, and Pi. GAR-syn containing an N-terminal polyhistidine tag was expressed as the SeMet incorporated protein for crystallographic studies. In addition, the protein as isolated contains a Pro294Leu mutation. This protein was crystallized, and the structure solved using multiple-wavelength anomalous diffraction (MAD) phase determination and refined to 1.6 A resolution. GAR-syn adopts an alpha/beta structure that consists of four domains labeled N, A, B, and C. The N, A, and C domains are clustered to form a large central core structure whereas the smaller B domain is extended outward. Two hinge regions, which might readily facilitate interdomain movement, connect the B domain and the main core. A search of structural databases showed that the structure of GAR-syn is similar to D-alanine:D-alanine ligase, biotin carboxylase, and glutathione synthetase, despite low sequence similarity. These four enzymes all utilize similar ATP-dependent catalytic mechanisms even though they catalyze different chemical reactions. Another ATP-binding enzyme with low sequence similarity but unknown function, synapsin Ia, was also found to share high structural similarity with GAR-syn. Interestingly, the GAR-syn N domain shows similarity to the N-terminal region of glycinamide ribonucleotide transformylase and several dinucleotide-dependent dehydrogenases. Models of ADP and GAR binding were generated based on structure and sequence homology. On the basis of these models, the active site lies in a cleft between the large domain and the extended B domain. Most of the residues that facilitate ATP binding belong to the A or B domains. The N and C domains appear to be largely responsible for substrate specificity. The structure of GAR-syn allows modeling studies of possible channeling complexes with PPRP amidotransferase.

PubMed: 9843369
DOI: 10.1021/bi981405n

Experimental method

X-RAY DIFFRACTION (1.6 Å)