Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. II. Environment of bound NADPH and implications for catalysis.

Filman, David J.; Bolin, J.T.; Matthews, David A.; Kraut, Joseph

doi:10.1016/s0021-9258(18)33498-7

Cited by 237 publications

(96 citation statements)

References 42 publications

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“…The crystal structures of the other two enzymes of the thymidylate synthase cycle, dihydrofolate reductase [9,10] and thymidylate synthase [11,12], have already been determined. Both enzymes have proven to be clinically successful targets for anticancer chemotherapy [13,14].…”

Section: Introductionmentioning

confidence: 99%

The crystal structure of human cytosolic serine hydroxymethyltransferase: a target for cancer chemotherapy

1998

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The crystal structure shows the evolutionary relationship between SHMT and other alpha class PLP-dependent enzymes, as the fold is highly conserved. Many of the results of site-directed mutagenesis studies can easily be rationalised or re-interpreted in light of the structure presented here. For example, His 151 is not the catalytic base, contrary to the findings of others. A mechanism for the cleavage of serine to glycine and formaldehyde is proposed.

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Section: Introductionmentioning

confidence: 99%

The crystal structure of human cytosolic serine hydroxymethyltransferase: a target for cancer chemotherapy

1998

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“…We report here the crystal structure of (hv-DHFR), the first protein structure to be determined from Haloferax volcanii. DHFR is an excellent subject for comparative structural studies, because the three-dimensional structures of this enzyme have been obtained at high resolution from Escherichia coli [11][12], Lactobacillus casei [11][12][13],…”

Section: Introductionmentioning

confidence: 99%

Structural features of halophilicity derived from the crystal structure of dihydrofolate reductase from the Dead Sea halophilic archaeon, Haloferax volcanii

et al. 1998

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The moderately halophilic behavior of hv-DHFR is consistent with the lack of striking structural features expected to occur in extremely halophilic proteins. The most notable feature of halophilicity is the presence of clusters of non-interacting negatively charged residues. Such clusters are associated with unfavorable electrostatic energy at low salt concentrations, and may account for the instability of hv-DHFR at salt concentrations lower than 0.5 M. With respect to catalysis, the open conformation seen here is indicative of a conformational transition not reported previously. The impact of this conformation on function and/or halophilicity is unknown.

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“…Several inhibitors of DHFR are clinically useful drugs; examples are methotrexate (MTX), trimethoprim, and pyrimethamine. With the aim of understanding the molecular mechanism of DHFR catalysis, our laboratory has carried out numerous studies on the crystal structures of variously liganded complexes of DHFR from Escherichia coli (Bolin et al, 1982;Bystroff et al, 1990;Bystroff & Kraut, 1991;Reyes et al, 1995), Lactobacillus casei (Filman et al, 1982), bacterial R67 plasmid (Matthews et al, 1986), human (Davies et al, 1990), and chicken liver (McTigue et al, 1992). We now report the crystal structure of ecDHFR complexed with folinic acid.…”

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confidence: 99%

Crystal Structures of Escherichia coli Dihydrofolate Reductase Complexed with 5-Formyltetrahydrofolate (Folinic Acid) in Two Space Groups: Evidence for Enolization of Pteridine O4^,

1996

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The crystal structure of Escherichia coli dihydrofolate reductase (ecDHFR, EC 1.5.1.3) as a binary complex with folinic acid (5-formyl-5,6,7,8-tetrahydrofolate; also called leucovorin or citrovorum factor) has been solved in two space groups, P6(1) and P6(5), with, respectively, two molecules and one molecule per asymmetric unit. The crystal structures have been refined to an R-factor of 14.2% at resolutions of 2.0 and 1.9 A. The P6(1) structure is isomorphous with several previously reported ecDHFR binary complexes [Bolin, J.T., Filman, D.J., Matthews, D.A., Hamlin, R.C., & Kraut, J. (1982) J. Biol. Chem. 257, 13650-13662; Reyes, V.M., Sawaya, M.R., Brown, K.A., & Kraut, J. (1995) Biochemistry 34, 2710-2723]; enzyme and ligand conformations are very similar to the P6(1) 5,10-dideazatetrahydrofolate complex. While the two enzyme subdomains of the P6(1) structure are nearly in the closed conformation, exemplified by the methotrexate P6(1) binary complex, in the P6(5) structure they are in an intermediate conformation, halfway between the closed and the fully open conformation of the apoenzyme [Bystroff, C., Oatley, S.J., & Kraut, J. (1990) Biochemistry 29, 3263-3277]. Thus crystal packing strongly influences this aspect of the enzyme structure. In contrast to the P6(1) structure, in which the Met-20 loop (residues 9-23) is turned away from the substrate binding pocket, in the P6(5) structure the Met-20 loop blocks the pocket and protrudes into the cofactor binding site. In this respect, the P6(5) structure is unique. Additionally, positioning of a Ca2+ ion (a component of the crystallization medium) is different in the two crystal packings: in the P6(1) structure it lies at the boundary between the two molecules of the asymmetric unit, while in P6(5) it coordinates two water molecules, the hydroxyl group of an ethanol molecule, and the backbone carbonyl oxygens of Glu-17, Asn-18, and Met-20. The Ca2+ ion thus stabilizes a single turn of 3(10) helix (residues 16-18 in the Met-20 loop), a second unique feature of the P6(5) crystal structure. The disposition of the N5-formyl group in these structures indicates formation, at least half of the time, of an intramolecular hydrogen bond between the formyl oxygen and O4 of the tetrahydropterin ring. This observation is consistent with the existence of an enol-keto equilibrium in which the enolic tautomer is favored when a hydrogen-bond acceptor is present between O4 and N5. Such would be the case whenever a water molecule occupies that site as part of a hypothetical proton-relay mechanism. Two arginine side chains, Arg-52 in the P6(5) structure and Arg-44 in molecule A of the P6(1) structure, are turned away drastically from the ligand (p-aminobenzoyl)glutamic acid moiety as compared with previously reported DHFR binary complex structures. As in the ecDHFR dideazatetrahydrofolate complex, in both the P6(1) and P6(5) structures a water molecule bridges pteridine O4 and Trp-22(N epsilon 1) with ideal geometry for hydrogen bonding, perhaps contributing to the slow release of ...

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Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. II. Environment of bound NADPH and implications for catalysis.

Cited by 237 publications

References 42 publications

The crystal structure of human cytosolic serine hydroxymethyltransferase: a target for cancer chemotherapy

The crystal structure of human cytosolic serine hydroxymethyltransferase: a target for cancer chemotherapy

Structural features of halophilicity derived from the crystal structure of dihydrofolate reductase from the Dead Sea halophilic archaeon, Haloferax volcanii

Crystal Structures of Escherichia coli Dihydrofolate Reductase Complexed with 5-Formyltetrahydrofolate (Folinic Acid) in Two Space Groups: Evidence for Enolization of Pteridine O4^,

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Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. II. Environment of bound NADPH and implications for catalysis.

Cited by 237 publications

References 42 publications

The crystal structure of human cytosolic serine hydroxymethyltransferase: a target for cancer chemotherapy

The crystal structure of human cytosolic serine hydroxymethyltransferase: a target for cancer chemotherapy

Structural features of halophilicity derived from the crystal structure of dihydrofolate reductase from the Dead Sea halophilic archaeon, Haloferax volcanii

Crystal Structures of Escherichia coli Dihydrofolate Reductase Complexed with 5-Formyltetrahydrofolate (Folinic Acid) in Two Space Groups: Evidence for Enolization of Pteridine O4,

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Crystal Structures of Escherichia coli Dihydrofolate Reductase Complexed with 5-Formyltetrahydrofolate (Folinic Acid) in Two Space Groups: Evidence for Enolization of Pteridine O4^,