Crystal Structure of the Bifunctional Dihydroneopterin Aldolase/6-hydroxymethyl-7,8-dihydropterin Pyrophosphokinase from Streptococcus pneumoniae

Garçon, Arnaud; Levy, Colin; Derrick, Jeremy P.

doi:10.1016/j.jmb.2006.05.038

Cited by 30 publications

(30 citation statements)

References 44 publications

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“…10 The active site of the enzyme has been identified by the crystal structures of enzymeproduct complexes SaDHNA • HP (PDB entry 2DHN) 6 and MtDHNA • HP (PDB entry 1NBU). 9 An active site lysine residue (K100) has been proposed to function as the general base and a bound water as a proton donor, leading to the first reaction scheme predicted for DHNA.…”

Section: Introductionmentioning

confidence: 99%

Structural Basis for the Aldolase and Epimerase Activities of Staphylococcus aureus Dihydroneopterin Aldolase

Błaszczyk

Gan

et al. 2007

Journal of Molecular Biology

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Dihydroneopterin aldolase (DHNA) catalyzes the conversion of 7,8-dihydroneopterin (DHNP) to 6-hydroxymethyl-7,8-dihydropterin (HP) and the epimerization of DHNP to 7,8-dihydromonopterin (DHMP). Although crystal structures of the enzyme from several microorganisms have been reported, no structural information is available about the critical interactions between DHNA and the trihydroxypropyl moiety of the substrate, which undergoes bond cleavage and formation. Here, we present the structures of Staphylococcus aureus DHNA (SaDHNA) in complex with neopterin (NP, an analog of DHNP) and with monapterin (MP, an analog of DHMP), filling the gap in the structural analysis of the enzyme. In combination with previously reported SaDHNA structures in its ligand-free form (PDB entry 1DHN) and in complex with HP (PDB entry 2DHN), four snapshots for the catalytic center assembly along the reaction pathway can be derived, advancing our knowledge about the molecular mechanism of SaDHNA-catalyzed reactions. An additional step appears to be necessary for the epimerization of DHMP to DHNP. Three active site residues (E22, K100, and Y54) function coordinately during catalysis: together, they organize the catalytic center assembly, and individually, each plays a central role at different stages of the catalytic cycle.

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Section: Introductionmentioning

confidence: 99%

Structural Basis for the Aldolase and Epimerase Activities of Staphylococcus aureus Dihydroneopterin Aldolase

Błaszczyk

Gan

et al. 2007

Journal of Molecular Biology

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“…1). The DHNA structure from three organisms has been solved by X-ray crystallography (S. aureus [78], S. pneumonia [79] and M. tuberculosis [80]). Much information has been derived using the S. aureus enzyme from structures of the holoenzyme [80] and in complex with the product HP [81], and substrate analogs, neopterin (NP) and monopterin (MP) [81], and product [80].…”

Section: Formation Of Hp -Dhnamentioning

confidence: 99%

“…Over twenty HPPK structures have been deposited from five different species to date e.g. E. coli [86], H. influenza [87], S. pneumoniae [79], and S. cerevisiae [88], Y. pestis [89]). Those from S. cerevisiae and S. pneumoniae have been solved as bifunctional enzymes with either DHPS or DHNA respectively.…”

Section: Pyrophosphoryl Transfer -Hppkmentioning

confidence: 99%

Folate Biosynthesis - Reappraisal of Old and Novel Targets in the Search for New Antimicrobials

Swarbrick

Iliades

Simpson

et al. 2008

TOEIJ

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Folate biosynthesis remains a key target for antimicrobial therapy. Folate is an essential vitamin (vitamin B9) that is required for many one-carbon transfer reactions and is a critical precursor for the biosynthesis of purines, pyrimidines, and amino acids. Unlike higher eukaryotes that scavenge preformed folates, prokaryotic and lower eukaryotic microorganisms are dependent on several enzymes for the de novo biosynthesis of folate. One of these enzymes, dihydropteroate synthase (DHPS), is the target of the first chemically-synthesized antimicrobial agents, the sulfadrugs, which date back to the 1940s. Others are essential enzymes that remain to be explored as drug targets. Resistance to the sulfadrugs rapidly emerges due to the ability of the microbe to alter its susceptibility to the drug by various means. Recently a number of new structures of the enzymes in the pathway has become available. We review the recent literature relating to these targets (the enzymes: GTP cyclohydrolase (GTP-CH); 7,8-dihydroneopterin aldolase (DHNA), 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK), dihydropteroate synthase (DHPS), dihydrofolate synthase (DHFS)), their mode of action and how current drugs may modulate this on a structural level. Furthermore, these data advance our understanding of the emergence of drug resistance and may aid efforts and play a major role in the design of new, more effective compounds as antimicrobial agents. To this end we also review the recent literature in the development of inhibitors of these enzymes. Future progress in this key area has the potential to benefit the war against devastating organisms such as drug-resistant Staphylococcus aureus and Plasmodium falciparum.

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“…To date, crystal structures have been reported for DHNAs from Gram-positive bacteria S. aureus [14–16], Mycobacterium tuberculosis (MtDHNA) [17], Streptococcus pneumoniae [18], and the plant Arabidopsis thaliana [19]. The active site of the enzyme has been identified by the protein-product (HP) structures of SaDHNA [PDB:2DHN] [14] and MtDHNA [PDB:1NBU] [17].…”

Section: Introductionmentioning

confidence: 99%

Crystallographic and molecular dynamics simulation analysis of Escherichia coli dihydroneopterin aldolase

Błaszczyk

et al. 2014

Cell Biosci

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BackgroundDihydroneopterin aldolase (DHNA) catalyzes the conversion of 7,8-dihydroneopterin to 6-hydroxymethyl-7,8-dihydropterin and also the epimerization of DHNP to 7,8-dihydromonapterin. Previously, we determined the crystal structure of Staphylococcus aureus DHNA (SaDHNA) in complex with the substrate analogue neopterin (NP). We also showed that Escherichia coli DHNA (EcDHNA) and SaDHNA have significantly different binding and catalytic properties by biochemical analysis. On the basis of these structural and functional data, we proposed a catalytic mechanism involving two proton wires.ResultsTo understand the structural basis for the biochemical differences and further investigate the catalytic mechanism of DHNA, we have determined the structure of EcDHNA complexed with NP at 1.07-Å resolution [PDB:2O90], built an atomic model of EcDHNA complexed with the substrate DHNP, and performed molecular dynamics (MD) simulation analysis of the substrate complex. EcDHNA has the same fold as SaDHNA and also forms an octamer that consists of two tetramers, but the packing of one tetramer with the other is significantly different between the two enzymes. Furthermore, the structures reveal significant differences in the vicinity of the active site, particularly in the loop that connects strands β3 and β4, mainly due to the substitution of nearby residues. The building of an atomic model of the complex of EcDHNA and the substrate DHNP and the MD simulation of the complex show that some of the hydrogen bonds between the substrate and the enzyme are persistent, whereas others are transient. The substrate binding model and MD simulation provide the molecular basis for the biochemical behaviors of the enzyme, including noncooperative substrate binding, indiscrimination of a pair of epimers as the substrates, proton wire switching during catalysis, and formation of epimerization product.ConclusionsThe EcDHNA and SaDHNA structures, each in complex with NP, reveal the basis for the biochemical differences between EcDHNA and SaDHNA. The atomic substrate binding model and MD simulation offer insights into substrate binding and catalysis by DHNA. The EcDHNA structure also affords an opportunity to develop antimicrobials specific for Gram-negative bacteria, as DHNAs from Gram-negative bacteria are highly homologous and E. coli is a representative of this class of bacteria.

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Crystal Structure of the Bifunctional Dihydroneopterin Aldolase/6-hydroxymethyl-7,8-dihydropterin Pyrophosphokinase from Streptococcus pneumoniae

Cited by 30 publications

References 44 publications

Structural Basis for the Aldolase and Epimerase Activities of Staphylococcus aureus Dihydroneopterin Aldolase

Structural Basis for the Aldolase and Epimerase Activities of Staphylococcus aureus Dihydroneopterin Aldolase

Folate Biosynthesis - Reappraisal of Old and Novel Targets in the Search for New Antimicrobials

Crystallographic and molecular dynamics simulation analysis of Escherichia coli dihydroneopterin aldolase

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