Crystal structure of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, a potential target for the development of novel antimicrobial agents

Xiao, Bing; Shi, Guizhi; Chen, Xin; Yan, Honggao; Ji, Xinhua

doi:10.1016/s0969-2126(99)80065-3

Cited by 62 publications

(88 citation statements)

References 26 publications

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“…2) are as described earlier for the apoenzyme [12]. However, residues showing conformational variability in the apoenzyme structure now appear well-de¢ned in this ternary complex, one such residue, Leu-45, being involved in interaction with the HP substrate analogue.…”

Section: The Pppk Foldsupporting

confidence: 55%

“…The adenine interacts via hydrogen bonds with the carbonyl oxygens of Leu-98 and Thr-112, the ribose is hydrogen-bonded to Arg-110, the K-and L-phosphates interact with Arg-82, -84 and -92 and the Q-phosphate is hydrogen-bonded to Trp-89, Tyr-116 and Arg-121. The side chain of the highly conserved His-115 residue is positioned about 3.7 A î from a Q-phosphoryl oxygen and does not appear to interact with an K-phosphoryl oxygen, as earlier proposed from model-building [12]. Density peaks lying between the L-and Q-phosphates on the one hand and Asp-95 and Asp-97 on the other are identi¢ed as magnesiums.…”

Section: Interaction Of Ligands With Active Site Residuesmentioning

confidence: 65%

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2.0 Å X‐ray structure of the ternary complex of 7,8‐dihydro‐6‐hydroxymethylpterinpyrophosphokinase from Escherichia coli with ATP and a substrate analogue

Stammers¹,

Achari²,

Somers³

et al. 1999

FEBS Letters

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The X-ray crystal structure of 7,8-dihydro-6-hydroxymethylpterinpyrophosphokinase (PPPK) in a ternary complex with ATP and a pterin analogue has been solved to 2.0 A î resolution, giving, for the first time, detailed information of the PPPK/ATP intermolecular interactions and the accompanying conformational change. The first 100 residues of the 158 residue peptide contain a L LK KL LL LK KL L motif present in several other proteins including nucleoside diphosphate kinase. Comparative sequence examination of a wide range of prokaryotic and lower eukaryotic species confirms the conservation of the PPPK active site, indicating the value of this de novo folate biosynthesis pathway enzyme as a potential target for the development of novel broad-spectrum anti-infective agents.z 1999 Federation of European Biochemical Societies.

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Section: The Pppk Foldsupporting

confidence: 55%

Section: Interaction Of Ligands With Active Site Residuesmentioning

confidence: 65%

2.0 Å X‐ray structure of the ternary complex of 7,8‐dihydro‐6‐hydroxymethylpterinpyrophosphokinase from Escherichia coli with ATP and a substrate analogue

Stammers¹,

Achari²,

Somers³

et al. 1999

FEBS Letters

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“…The structure of E. coli hydroxymethyldihydropterin diphosphokinase with a variety of ligands has been determined: these include the ternary complex with a substrate analog and a substrate, enzyme-Mg 2ϩ -␣,␤-methylene ATP-hydroxydihydropterin complex (PDB code 1q0n) (164). Additional reports on crystal or solution structures of hydroxymethyldihydropterin diphosphokinase of E. coli and Haemophilus influenzae have been published (165)(166)(167). Structural and mechanistic properties of this enzyme have been previously reviewed (168).…”

Section: Substitution Reactions At ␣- ␤- or ␥-Phosphatesmentioning

confidence: 99%

Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance

Hove‐Jensen

Andersen

Kilstrup

et al. 2017

Microbiol Mol Biol Rev

157

187

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SUMMARY Phosphoribosyl diphosphate (PRPP) is an important intermediate in cellular metabolism. PRPP is synthesized by PRPP synthase, as follows: ribose 5-phosphate + ATP → PRPP + AMP. PRPP is ubiquitously found in living organisms and is used in substitution reactions with the formation of glycosidic bonds. PRPP is utilized in the biosynthesis of purine and pyrimidine nucleotides, the amino acids histidine and tryptophan, the cofactors NAD and tetrahydromethanopterin, arabinosyl monophosphodecaprenol, and certain aminoglycoside antibiotics. The participation of PRPP in each of these metabolic pathways is reviewed. Central to the metabolism of PRPP is PRPP synthase, which has been studied from all kingdoms of life by classical mechanistic procedures. The results of these analyses are unified with recent progress in molecular enzymology and the elucidation of the three-dimensional structures of PRPP synthases from eubacteria, archaea, and humans. The structures and mechanisms of catalysis of the five diphosphoryltransferases are compared, as are those of selected enzymes of diphosphoryl transfer, phosphoryl transfer, and nucleotidyl transfer reactions. PRPP is used as a substrate by a large number phosphoribosyltransferases. The protein structures and reaction mechanisms of these phosphoribosyltransferases vary and demonstrate the versatility of PRPP as an intermediate in cellular physiology. PRPP synthases appear to have originated from a phosphoribosyltransferase during evolution, as demonstrated by phylogenetic analysis. PRPP, furthermore, is an effector molecule of purine and pyrimidine nucleotide biosynthesis, either by binding to PurR or PyrR regulatory proteins or as an allosteric activator of carbamoylphosphate synthetase. Genetic analyses have disclosed a number of mutants altered in the PRPP synthase-specifying genes in humans as well as bacterial species.

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“…6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) 1 catalyzes the transfer of pyrophosphate from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP, Scheme I), leading to the biosynthesis of folate cofactors (see Fig. 1 …”

mentioning

confidence: 99%

Unusual Conformational Changes in 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase as Revealed by X-ray Crystallography and NMR

Xiao

Shi²,

Gao³

et al. 2001

Journal of Biological Chemistry

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Because the folate pathway is essential for microorganisms but absent from mammals, HPPK, like other enzymes in the pathway, is an important target for developing antimicrobial agents.HPPK belongs to a class of enzymes that catalyze the pyrophosphoryl transfer reaction (2). Although the mechanisms of many kinases that catalyze monophosphoryl transfer have been extensively characterized, little is known about the mechanisms of pyrophosphokinases. As a small (158 residues, ϳ18 kDa), stable, monomeric protein, Escherichia coli HPPK is an excellent model system for studying the mechanisms of enzymatic pyrophosphoryl transfer.We have recently determined the crystal structures of ligand-free (apo-) E. coli HPPK (1) and its complex with HP, ␣,␤-methyleneadenosine 5Ј-triphosphate (AMPCPP), and two Mg 2ϩ ions (3) at 1.5 and 1.25 Å resolution, respectively. Hennig and co-workers (4) have determined the crystal structure of Haemophilus influenzae HPPK in complex with an HP analog at 2.05-Å resolution. Stammers and co-workers (5) have determined the crystal structure of E. coli HPPK in complex with an HP analog, ATP, and two Mg 2ϩ ions at 2.00-Å resolution. Comparative analysis of the crystal structures of the apo-HPPK and its ternary complex has revealed the interactions of the enzyme with the substrates at the atomic resolution and the dramatic substrate-induced conformational changes involving three catalytic loops (3). It appears that the complete active center of HPPK is assembled only after both substrates bind to the enzyme. However, how the catalytic center is assembled is not known. It appears that some catalytic residues cannot move into their catalytic positions because of steric constraints.In this paper, we present the crystal structure of HPPK⅐MgADP at 1.5-Å resolution and the NMR solution structure of HPPK⅐MgAMPPCP. The two structures reveal a dramatic, unusual movement of loop 3 and other significant changes in the conformation and dynamical property of HPPK. The dramatic substrate-induced movement of loop 3 is unusual because it moves away from the active center. Comparative structural analysis suggests that the structures reported here may represent an intermediate conformation required for both substrate binding and product release in the catalytic cycle. EXPERIMENTAL PROCEDURESCrystal Structure Determination of HPPK⅐MgADP-E. coli HPPK was purified as previously described (6). Crystals of HPPK⅐MgADP were grown in hanging drops at 19 Ϯ 1°C. The protein solution contained 4 mg/ml HPPK, 5 mM MgATP in 10 mM Tris buffer (pH 8.0), and the reservoir contained 30% polyethylene glycol 4000, 0.2 M NaAc in 0.2 M Tris buffer (pH 8.5). The 4-l hanging drops contained equal volumes (2 l) of protein solution and reservoir solution. Two rounds of seeding produced diffraction-quality crystals. * This work was supported in part by National Institutes of Health Grant GM51901 (to H. Y.). This study made use of a Varian INOVA-600 NMR spectrometer at Michigan State University funded in part by National Science Foundation Grant...

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Crystal structure of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, a potential target for the development of novel antimicrobial agents

Abstract: The HPPK structure provides a framework to elucidate structure/function relationships of the enzyme and to analyze mechanisms of pyrophosphoryl transfer. Furthermore, this work may prove useful in the structure-based design of new antimicrobial agents.

Cited by 62 publications

References 26 publications

2.0 Å X‐ray structure of the ternary complex of 7,8‐dihydro‐6‐hydroxymethylpterinpyrophosphokinase from Escherichia coli with ATP and a substrate analogue

2.0 Å X‐ray structure of the ternary complex of 7,8‐dihydro‐6‐hydroxymethylpterinpyrophosphokinase from Escherichia coli with ATP and a substrate analogue

Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance

Unusual Conformational Changes in 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase as Revealed by X-ray Crystallography and NMR

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