The structure of SAICAR synthase: an enzyme in the de novo pathway of purine nucleotide biosynthesis.
BACKGROUND
The biosynthesis of key metabolic components is of major interest to biologists. Studies of de novo purine synthesis are aimed at obtaining a deeper understanding of this central pathway and the development of effective chemotherapeutic agents. Phosphoribosylaminoimidazolesuccinocarboxamide (SAICAR) synthase catalyses the seventh step out of ten in the biosynthesis of purine nucleotides. To date, only one structure of an enzyme involved in purine biosynthesis has been reported: adenylosuccinate synthetase, which catalyses the first committed step in the synthesis of AMP from IMP.


RESULTS
We report the first three-dimensional structure of a SAICAR synthase, from Saccharomyces cerevisiae. It is a monomer with three domains. The first two domains consist of antiparallel beta sheets and the third is composed of two alpha helices. There is a long deep cleft made up of residues from all three domains. Comparison of SAICAR synthases by alignment of their sequences reveals a number of conserved residues, mostly located in the cleft. The presence of two sulphate ions bound in the cleft, the structure of SAICAR synthase in complex with ATP and a comparison of this structure with that of other ATP-dependent proteins point to the interdomain cleft as the location of the active site.


CONCLUSIONS
The topology of the first domain of SAICAR synthase resembles that of the N-terminal domain of proteins belonging to the cyclic AMP-dependent protein kinase family. The fold of the second domain is similar to that of members of the D-alanine:D-alanine ligase family. Together these enzymes form a new superfamily of mononucleotide-binding domains. There appears to be no other enzyme, however, which is composed of the same combination of three domains, with the individual topologies found in SAICAR synthase.
Levdikov
V M
VM
Institute of Crystallography, Russian Academy of Sciences, Leninsky, Moscow. Vladimir@sunchem.chem.uga.edu
Barynin
V V
VV
Grebenko
A I
AI
Melik-Adamyan
W R
WR
Lamzin
V S
VS
Wilson
K S
KS
D000255:Adenosine Triphosphate / Q000378:metabolism; D000595:Amino Acid Sequence; D000620:Aminoimidazole Carboxamide / Q000031:analogs & derivatives / Q000378:metabolism; D001665:Binding Sites; D017124:Conserved Sequence; D018360:Crystallography, X-Ray; D017868:Cyclic AMP-Dependent Protein Kinases / Q000737:chemistry / Q000378:metabolism; D005981:Glutathione Synthase / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010453:Peptide Synthases / Q000737:chemistry* / Q000378:metabolism*; D011487:Protein Conformation; D017510:Protein Folding; D011687:Purines / Q000096:biosynthesis*; D012265:Ribonucleotides / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000201:enzymology; D013329:Structure-Activity Relationship; D013431:Sulfates / Q000737:chemistry / Q000378:metabolism
D011687:Purines; D012265:Ribonucleotides; D013431:Sulfates; D000620:Aminoimidazole Carboxamide; D000255:Adenosine Triphosphate; D017868:Cyclic AMP-Dependent Protein Kinases; D010453:Peptide Synthases; D005981:Glutathione Synthase; C019638:D-alanylalanine synthetase; C022379:phosphoribosylaminoimidazole-succinocarboxamide synthetase; C031143:AICA ribonucleotide