Crystal structure of calf spleen purine nucleoside phosphorylase in a complex with hypoxanthine at 2.15 Å resolution

Koellner, G.; Luić, Marija; Shugar, David; Bzowska, Agnieszka

doi:10.1006/jmbi.1996.0730

Cited by 78 publications

(106 citation statements)

References 51 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The overall structure of this complex is similar to those with hypoxanthine [21] and a multisubstrate inhibitor [22], as well as several others described by Mao et al [7]. Some residues showed no electron density in the final structure.…”

Section: Structure Descriptionsupporting

confidence: 82%

Crystal structure of calf spleen purine nucleoside phosphorylase complexed to a novel purine analogue

Pereira

Berdini²,

Cleasby³

et al. 2007

FEBS Letters

View full text Add to dashboard Cite

The combined use of a rapid virtual screen of a small fragment library together with a single point enzyme assay has been used for the discovery of novel PNP inhibitors. The availability of readily soakable crystals of bovine PNP has allowed the approach to be experimentally validated by determining the crystal structure of one of the inhibitor-PNP complexes. Comparison of the experimentally determined binding mode with that predicted by the virtual screening shows them to be similar. This represents a starting point for the growth of the ligand into a higher affinity inhibitor.

show abstract

Section: Structure Descriptionsupporting

confidence: 82%

Crystal structure of calf spleen purine nucleoside phosphorylase complexed to a novel purine analogue

Pereira

Berdini²,

Cleasby³

et al. 2007

FEBS Letters

View full text Add to dashboard Cite

show abstract

“…The core can be divided into a large eightstranded ␤-sheet and a smaller five-stranded ␤-sheet that pack together to form a distorted ␤-barrel, an arrangement also found in human PNP (2), bovine PNP (32,33), and human 5Ј-deoxy-5Ј-methylthioadenosine phosphorylase (48), although there is little sequence homology between the E. coli enzyme and the trimeric class mammalian enzymes (10).…”

Section: Resultsmentioning

confidence: 99%

“…We have also performed kinetic studies on the substrates and carried out computer modeling to examine the role of sugar modifications on reactivity. This information, together with knowledge about the structure of mammalian PNPs (32,33), should aid in the design of more effective prodrugs that can be readily cleaved by E. coli PNP. Furthermore, an understanding of substrate analog binding should allow us to rationally change the enzyme to cleave novel prodrugs that are not cleaved by either human or wild type bacterial PNPs.…”

mentioning

confidence: 99%

Structural Basis for Substrate Specificity of Escherichia coli Purine Nucleoside Phosphorylase

Bennett

Allan

et al. 2003

Journal of Biological Chemistry

125

View full text Add to dashboard Cite

Purine nucleoside phosphorylase catalyzes reversible phosphorolysis of purine nucleosides and 2-deoxypurine nucleosides to the free base and ribose (or 2-deoxyribose) 1-phosphate. Whereas the human enzyme is specific for 6-oxopurine ribonucleosides, the Escherichia coli enzyme accepts additional substrates including 6-oxopurine ribonucleosides, 6-aminopurine ribonucleosides, and to a lesser extent purine arabinosides. These differences have been exploited in a potential suicide gene therapy treatment for solid tumors. In an effort to optimize this suicide gene therapy approach, we have determined the three-dimensional structure of the E. coli enzyme in complex with 10 nucleoside analogs and correlated the structures with kinetic measurements and computer modeling. These studies explain the preference of the enzyme for ribose sugars, show increased flexibility for active site residues Asp 204 and Arg 24 , and suggest that interactions involving the 1-and 6-positions of the purine and the 4-and 5-positions of the ribose provide the best opportunities to increase prodrug specificity and enzyme efficiency.

show abstract

“…28) from Sulfolobus solfataricus (SsMTAP) 1 functions in the purine salvage pathway where it catalyzes the phosphorolysis of 5Ј-deoxy-5Ј-methylthioadenosine (MTA) (1), a sulfur-containing nucleoside generated as a by-product of polyamine biosynthesis (2). The products of the MTA cleavage reaction are adenine and 5-methylthio-D-ribose 1-phosphate.…”

mentioning

confidence: 99%

Three-dimensional Structure of a Hyperthermophilic 5′-Deoxy-5′-methylthioadenosine Phosphorylase from Sulfolobus solfataricus

Appleby

Mathews

Porcelli

et al. 2001

Journal of Biological Chemistry

View full text Add to dashboard Cite

The structure of 5-deoxy-5-methylthioadenosine phosphorylase from Sulfolobus solfataricus (SsMTAP) has been determined alone, as ternary complexes with sulfate plus substrates 5-deoxy-5-methylthioadenosine, adenosine, or guanosine, or with the noncleavable substrate analog Formycin B and as binary complexes with phosphate or sulfate alone. The structure of unliganded SsMTAP was refined at 2.5-Å resolution and the structures of the complexes were refined at resolutions ranging from 1.6 to 2.0 Å. SsMTAP is unusual both for its broad substrate specificity and for its extreme thermal stability. The hexameric structure of SsMTAP is similar to that of purine-nucleoside phosphorylase (PNP) from Escherichia coli, however, only SsMTAP accepts 5-deoxy-5-methylthioadenosine as a substrate. The active site of SsMTAP is similar to that of E. coli PNP with 13 of 18 nearest residues being identical. The main differences are at Thr 89 , which corresponds to serine in E. coli PNP, and Glu 163 , which corresponds to proline in E. coli PNP. In addition, a water molecule is found near the purine N-7 position in the guanosine complex of SsMTAP. Thr 89 is near the 5-position of the nucleoside and may account for the ability of SsMTAP to accept either hydrophobic or hydrophilic substituents in that position. Unlike E. coli PNP, the structures of SsMTAP reveal a substrate-induced conformational change involving Glu 163 . This residue is located at the interface between subunits and swings in toward the active site upon nucleoside binding. The high-resolution structures of SsMTAP suggest that the transition state is stabilized in different ways for 6-amino versus 6-oxo substrates. SsMTAP has optimal activity at 120°C and retains full activity after 2 h at 100°C. Examination of the three-dimensional structure of SsMTAP suggests that unlike most thermophilic enzymes, disulfide linkages play a key in role in its thermal stability. 5Ј-Deoxy-5Ј-methylthioadenosine phosphorylase (EC 2.4.2.28)from Sulfolobus solfataricus (SsMTAP) 1 functions in the purine salvage pathway where it catalyzes the phosphorolysis of 5Ј-deoxy-5Ј-methylthioadenosine (MTA) (1), a sulfur-containing nucleoside generated as a by-product of polyamine biosynthesis (2). The products of the MTA cleavage reaction are adenine and 5-methylthio-D-ribose 1-phosphate. S. solfataricus is a thermophilic microorganism belonging to Archaea, the third primary domain (3). The biosynthesis of the symmetrical polyamines, sym-norspermine and sym-norspermine, is highly operative in thermophilic archaebacteria (4), suggesting an important role for MTAP in the catabolism of large quantities of MTA in these organisms (Scheme 1).SsMTAP has been classified as a hyperthermophilic enzyme since its optimum temperature (120°C) is higher than the boiling point of water (1). The enzyme is also characterized by extreme thermostability, demonstrating full activity after 2 h at 100°C and showing an apparent melting temperature of 132°C. In addition, the enzyme remains stable in the presence of protein ...

show abstract

Crystal structure of calf spleen purine nucleoside phosphorylase in a complex with hypoxanthine at 2.15 Å resolution

Cited by 78 publications

References 51 publications

Crystal structure of calf spleen purine nucleoside phosphorylase complexed to a novel purine analogue

Crystal structure of calf spleen purine nucleoside phosphorylase complexed to a novel purine analogue

Structural Basis for Substrate Specificity of Escherichia coli Purine Nucleoside Phosphorylase

Three-dimensional Structure of a Hyperthermophilic 5′-Deoxy-5′-methylthioadenosine Phosphorylase from Sulfolobus solfataricus

Contact Info

Product

Resources

About