PDBsum entry 1a48

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protein ligands links
Atp binding protein PDB id
Protein chain
299 a.a. *
SO4 ×2
Waters ×319
* Residue conservation analysis
PDB id:
Name: Atp binding protein
Title: Saicar synthase
Structure: Phosphoribosylaminoimidazole-succinocarboxamide synthase. Chain: a. Synonym: saicar synthetase. Ec:
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: grf18
1.90Å     R-factor:   0.153    
Authors: V.M.Levdikov,W.R.Melik-Adamyan,V.S.Lamzin,K.S.Wilson
Key ref:
V.M.Levdikov et al. (1998). The structure of SAICAR synthase: an enzyme in the de novo pathway of purine nucleotide biosynthesis. Structure, 6, 363-376. PubMed id: 9551557 DOI: 10.1016/S0969-2126(98)00038-0
12-Feb-98     Release date:   30-Mar-99    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P27616  (PUR7_YEAST) -  Phosphoribosylaminoimidazole-succinocarboxamide synthase
306 a.a.
298 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Phosphoribosylaminoimidazolesuccinocarboxamide synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Purine Biosynthesis (late stages)
      Reaction: ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate = ADP + phosphate + (S)-2-(5-amino-1-(5-phospho-D- ribosyl)imidazole-4-carboxamido)succinate
+ 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate
+ L-aspartate
+ phosphate
+ (S)-2-(5-amino-1-(5-phospho-D- ribosyl)imidazole-4-carboxamido)succinate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     purine nucleotide biosynthetic process   2 terms 
  Biochemical function     nucleotide binding     5 terms  


DOI no: 10.1016/S0969-2126(98)00038-0 Structure 6:363-376 (1998)
PubMed id: 9551557  
The structure of SAICAR synthase: an enzyme in the de novo pathway of purine nucleotide biosynthesis.
V.M.Levdikov, V.V.Barynin, A.I.Grebenko, W.R.Melik-Adamyan, V.S.Lamzin, K.S.Wilson.
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.
  Selected figure(s)  
Figure 1.
Figure 1. Schematic representation of the biosynthesis of purine nucleotides in S. cerevisiae. For each step, the name of the enzyme and the structural gene (in parentheses) are given. The reaction catalysed by SAICAR synthase is shown in red. Abbreviations: AICAR, phosphoribosylaminoimidazolecarboxamide; AIR, phosphoribosylaminoimidazole; CAIR, phosphoribosylcarboxyaminoimidazole; FAICAR, phosphoribosylformylaminoimidazolecarboxamide; FGAM, phosphoribosylformylglycinamidine; FGAR, phosphoribosylformylglycinamide; GAR, phosphoribosylglycinamide; PR, 5-phosphoribosyl; PRA, phosphoribosylamine; PRPP, 5-phosphoribosyl 1-pyrophosphate.
  The above figure is reprinted by permission from Cell Press: Structure (1998, 6, 363-376) copyright 1998.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18712276 Y.Zhang, M.Morar, and S.E.Ealick (2008).
Structural biology of the purine biosynthetic pathway.
  Cell Mol Life Sci, 65, 3699-3724.  
17154526 M.Morar, R.Anand, A.A.Hoskins, J.Stubbe, and S.E.Ealick (2006).
Complexed structures of formylglycinamide ribonucleotide amidotransferase from Thermotoga maritima describe a novel ATP binding protein superfamily.
  Biochemistry, 45, 14880-14895.
PDB codes: 2hru 2hry 2hs0 2hs3 2hs4
16687397 N.D.Ginder, D.J.Binkowski, H.J.Fromm, and R.B.Honzatko (2006).
Nucleotide complexes of Escherichia coli phosphoribosylaminoimidazole succinocarboxamide synthetase.
  J Biol Chem, 281, 20680-20688.
PDB codes: 2gqr 2gqs
15572776 P.H.Zwart, G.G.Langer, and V.S.Lamzin (2004).
Modelling bound ligands in protein crystal structures.
  Acta Crystallogr D Biol Crystallogr, 60, 2230-2239.  
14500881 K.Matsuda, T.Nishioka, K.Kinoshita, T.Kawabata, and N.Go (2003).
Finding evolutionary relations beyond superfamilies: fold-based superfamilies.
  Protein Sci, 12, 2239-2251.  
11389851 H.Yamaguchi, M.Matsushita, A.C.Nairn, and J.Kuriyan (2001).
Crystal structure of the atypical protein kinase domain of a TRP channel with phosphotransferase activity.
  Mol Cell, 7, 1047-1057.
PDB codes: 1ia9 1iah 1iaj
11006546 T.J.Kappock, S.E.Ealick, and J.Stubbe (2000).
Modular evolution of the purine biosynthetic pathway.
  Curr Opin Chem Biol, 4, 567-572.  
11188689 T.Zhou, M.Daugherty, N.V.Grishin, A.L.Osterman, and H.Zhang (2000).
Structure and mechanism of homoserine kinase: prototype for the GHMP kinase superfamily.
  Structure, 8, 1247-1257.
PDB codes: 1fwk 1fwl
10508786 C.Li, T.J.Kappock, J.Stubbe, T.M.Weaver, and S.E.Ealick (1999).
X-ray crystal structure of aminoimidazole ribonucleotide synthetase (PurM), from the Escherichia coli purine biosynthetic pathway at 2.5 A resolution.
  Structure, 7, 1155-1166.
PDB code: 1cli
10584075 S.Roy (1999).
Multifunctional enzymes and evolution of biosynthetic pathways: retro-evolution by jumps.
  Proteins, 37, 303-309.  
9843369 W.Wang, T.J.Kappock, J.Stubbe, and S.E.Ealick (1998).
X-ray crystal structure of glycinamide ribonucleotide synthetase from Escherichia coli.
  Biochemistry, 37, 15647-15662.
PDB code: 1gso
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.