Structural and theoretical studies suggest domain movement produces an active conformation of thymidine phosphorylase

Pugmire, Matthew J; Cook, William J.; Jasanoff, Alan; Walter, Mark R.; Ealick, S.E.

doi:10.1006/jmbi.1998.1941

Cited by 70 publications

(75 citation statements)

References 55 publications

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“…In this latter structure, two dimers appeared in the asymmetric unit, and residues 406-415 were visible as an arginine-rich surface loop that extends across the active site cleft and appears to stabilize the closed conformation of the enzyme and the dimer interface through hydrogen bonds. Taking these two crystal structures together, it is clear that the overall fold of human TP is similar to that previously reported for E. coli TP [24,25] and comprises a large a/b domain connected by three loops to a smaller a domain. These three loops act as a hinge that allows the motion of one domain relative to the other so that the enzyme can interconvert from an open, inactive form to a closed conformation that is catalytically active.…”

Section: Introductionsupporting

confidence: 77%

Identification of aspartic acid-203 in human thymidine phosphorylase as an important residue for both catalysis and non-competitive inhibition by the small molecule “crystallization chaperone” 5′-O-tritylinosine (KIN59)

Bronckaers

Aguado

Negri

et al. 2009

Biochemical Pharmacology

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Section: Introductionsupporting

confidence: 77%

Identification of aspartic acid-203 in human thymidine phosphorylase as an important residue for both catalysis and non-competitive inhibition by the small molecule “crystallization chaperone” 5′-O-tritylinosine (KIN59)

Bronckaers

Aguado

Negri

et al. 2009

Biochemical Pharmacology

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“…S3a). The sulfate ion, located in the C-terminal domain, is bound at positions similar to those of the phosphate ions in other members of the NP-II family 8,9 (Fig. S3b).…”

Section: The N-terminal Domain Participates In Domain Closurementioning

confidence: 95%

“…5 AMPpase from T. kodakarensis (Tk-AMPpase, AP006878, 503 residues, 54 kDa) was originally annotated as a homolog of thymidine phosphorylase (TP: EC 2.4.2.4) 5 and recognizes AMP, CMP, and UMP as substrates. 6 However, its primary structure and sequence alignment indicate that AMPpase belongs to the nucleoside phosphorylase (NP) II family, whose members catalyze the phosphorolysis of only pyrimidine nucleosides into pyrimidine base and ribose 1-phosphate [7][8][9][10] (Fig. 2).…”

Section: Introductionmentioning

confidence: 99%

Structure Analysis of Archaeal AMP Phosphorylase Reveals Two Unique Modes of Dimerization

Nishitani

Aono

Nakamura

et al. 2013

Journal of Molecular Biology

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“…The structure of uridine phosphorylase from E. coli (15) represents a second example of the hexameric class. The structures of thymidine phosphorylase from E. coli (16,17) and pyrimidinenucleoside phosphorylase from Bacillus stearothermophilus (18) show that these enzymes belong to a separate structural family.…”

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

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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 ...

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Structural and theoretical studies suggest domain movement produces an active conformation of thymidine phosphorylase

Cited by 70 publications

References 55 publications

Identification of aspartic acid-203 in human thymidine phosphorylase as an important residue for both catalysis and non-competitive inhibition by the small molecule “crystallization chaperone” 5′-O-tritylinosine (KIN59)

Identification of aspartic acid-203 in human thymidine phosphorylase as an important residue for both catalysis and non-competitive inhibition by the small molecule “crystallization chaperone” 5′-O-tritylinosine (KIN59)

Structure Analysis of Archaeal AMP Phosphorylase Reveals Two Unique Modes of Dimerization

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

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