Molecular structure of Escherichia coli PurT-encoded glycinamide ribonucleotide transformylase.
In Escherichia coli, the PurT-encoded glycinamide ribonucleotide transformylase, or PurT transformylase, catalyzes an alternative formylation of glycinamide ribonucleotide (GAR) in the de novo pathway for purine biosynthesis. On the basis of amino acid sequence analyses, it is known that the PurT transformylase belongs to the ATP-grasp superfamily of proteins. The common theme among members of this superfamily is a catalytic reaction mechanism that requires ATP and proceeds through an acyl phosphate intermediate. All of the enzymes belonging to the ATP-grasp superfamily are composed of three structural motifs, termed the A-, B-, and C-domains, and in each case, the ATP is wedged between the B- and C-domains. Here we describe two high-resolution X-ray crystallographic structures of PurT transformylase from E. coli: one form complexed with the nonhydrolyzable ATP analogue AMPPNP and the second with bound AMPPNP and GAR. The latter structure is of special significance because it represents the first ternary complex to be determined for a member of the ATP-grasp superfamily involved in purine biosynthesis and as such provides new information about the active site region involved in ribonucleotide binding. Specifically in PurT transformylase, the GAR substrate is anchored to the protein via Glu 82, Asp 286, Lys 355, Arg 362, and Arg 363. Key amino acid side chains involved in binding the AMPPNP to the enzyme include Arg 114, Lys 155, Glu 195, Glu 203, and Glu 267. Strikingly, the amino group of GAR that is formylated during the reaction lies at 2.8 A from one of the gamma-phosphoryl oxygens of the AMPPNP.
Thoden
J B
JB
Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53705, USA.
Firestine
S
S
Nixon
A
A
Benkovic
S J
SJ
Holden
H M
HM
D000266:Adenylyl Imidodiphosphate / Q000737:chemistry / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D002262:Carboxy-Lyases; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000201:enzymology*; D029968:Escherichia coli Proteins; D005561:Formates / Q000378:metabolism; D005998:Glycine / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism; D019877:Hydroxymethyl and Formyl Transferases / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D051026:Phosphoribosylglycinamide Formyltransferase; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D012265:Ribonucleotides / Q000737:chemistry / Q000378:metabolism; D013329:Structure-Activity Relationship
D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; D005561:Formates; D012265:Ribonucleotides; C402896:glycinamide ribonucleotide; D000266:Adenylyl Imidodiphosphate; D019877:Hydroxymethyl and Formyl Transferases; C494825:purT protein, E coli; D051026:Phosphoribosylglycinamide Formyltransferase; D002262:Carboxy-Lyases; C075015:purK protein, E coli; D005998:Glycine