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PDBsum entry 2gqr

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protein ligands metals Protein-protein interface(s) links
Ligase PDB id
2gqr
Jmol
Contents
Protein chains
237 a.a. *
Ligands
ADP ×2
Metals
_MG ×2
Waters ×363
* Residue conservation analysis
PDB id:
2gqr
Name: Ligase
Title: Saicar synthetase complexed with adp-mg2+
Structure: Phosphoribosylaminoimidazole-succinocarboxamide synthase. Chain: a, b. Synonym: saicar synthetase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: purc. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.204     R-free:   0.239
Authors: N.D.Ginder,R.B.Honzatko
Key ref:
N.D.Ginder et al. (2006). Nucleotide complexes of Escherichia coli phosphoribosylaminoimidazole succinocarboxamide synthetase. J Biol Chem, 281, 20680-20688. PubMed id: 16687397 DOI: 10.1074/jbc.M602109200
Date:
21-Apr-06     Release date:   16-May-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A7D7  (PUR7_ECOLI) -  Phosphoribosylaminoimidazole-succinocarboxamide synthase
Seq:
Struc:
237 a.a.
237 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.3.2.6  - Phosphoribosylaminoimidazolesuccinocarboxamide synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
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
ATP
+ 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate
+ L-aspartate
=
ADP
Bound ligand (Het Group name = ADP)
corresponds exactly
+ 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!
  Cellular component     membrane   2 terms 
  Biological process     purine nucleotide biosynthetic process   2 terms 
  Biochemical function     nucleotide binding     4 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M602109200 J Biol Chem 281:20680-20688 (2006)
PubMed id: 16687397  
 
 
Nucleotide complexes of Escherichia coli phosphoribosylaminoimidazole succinocarboxamide synthetase.
N.D.Ginder, D.J.Binkowski, H.J.Fromm, R.B.Honzatko.
 
  ABSTRACT  
 
Phosphoribosylaminoimidazole-succinocarboxamide synthetase (SAICAR synthetase) converts 4-carboxy-5-aminoimidazole ribonucleotide (CAIR) to 4-(N-succinylcarboxamide)-5-aminoimidazole ribonucleotide (SAICAR). The enzyme is a target of natural products that impair cell growth. Reported here are the crystal structures of the ADP and the ADP.CAIR complexes of SAICAR synthetase from Escherichia coli, the latter being the first instance of a CAIR-ligated SAICAR synthetase. ADP and CAIR bind to the active site in association with three Mg(2+), two of which coordinate the same oxygen atom of the 4-carboxyl group of CAIR; whereas, the third coordinates the alpha- and beta-phosphoryl groups of ADP. The ADP.CAIR complex is the basis for a transition state model of a phosphoryl transfer reaction involving CAIR and ATP, but also supports an alternative chemical pathway in which the nucleophilic attack of l-aspartate precedes the phosphoryl transfer reaction. The polypeptide fold for residues 204-221 of the E. coli structure differs significantly from those of the ligand-free SAICAR synthetase from Thermatoga maritima and the adenine nucleotide complexes of the synthetase from Saccharomyces cerevisiae. Conformational differences between the E. coli, T. maritima, and yeast synthetases suggest the possibility of selective inhibition of de novo purine nucleotide biosynthesis in microbial organisms.
 
  Selected figure(s)  
 
Figure 3.
FIGURE 3. Variation in the folds of eSS and tSS. The superposition of subunits A and B of tSS onto eSS using the -sheet of domain 2 reveals significant variations between subunit A (white) and subunit B (gray) of tSS, as well as an even larger conformational difference between each of the tSS subunits and subunit A of eSS (black). Subunit B of eSS (not shown) is virtually identical in conformation to subunit A. Parts of this figure were drawn with MOLSCRIPT (42).
Figure 8.
FIGURE 8. Alternative pathways for the chemical transformation catalyzed by SAICAR synthetase. RibP represents the 5'-phosphoribosyl group. See text for details.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 20680-20688) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19182782 S.Schmelz, N.Kadi, S.A.McMahon, L.Song, D.Oves-Costales, M.Oke, H.Liu, K.A.Johnson, L.G.Carter, C.H.Botting, M.F.White, G.L.Challis, and J.H.Naismith (2009).
AcsD catalyzes enantioselective citrate desymmetrization in siderophore biosynthesis.
  Nat Chem Biol, 5, 174-182.
PDB codes: 2w02 2w03 2w04
18712276 Y.Zhang, M.Morar, and S.E.Ealick (2008).
Structural biology of the purine biosynthetic pathway.
  Cell Mol Life Sci, 65, 3699-3724.  
18069798 Y.Zhang, R.H.White, and S.E.Ealick (2008).
Crystal structure and function of 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase from Methanocaldococcus jannaschii.
  Biochemistry, 47, 205-217.
PDB codes: 2r7k 2r7l 2r7m 2r7n 2r84 2r85 2r86 2r87
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