Disodium <i>D</i>-3-phosphoglycerate, a substrate to phosphoglycerate kinase

Fewster, Paul F.; Fenn, R. H.

doi:10.1107/s0567740882002635

Cited by 6 publications

(2 citation statements)

References 6 publications

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“…In compound (III) [HO-PO2--O-CH2-CH(OH)C02-C] the carboxy and phosphate groups carry delocalized negative charges to balance the positive charge of the Ba2+ ion. A comparison of the geometries around As and P atoms in the three crystal structures and in the highly accurately determined structure of the disodium salt of D-3-phosphoglycerate (IV) (Fewster & Fenn, 1982), summarized in Table 8, is consistent with the expected lengthening of the As-X bonds relative to the P-X bonds due to an increase of 0.0lOnm in the covalent radius of the As atom Fig. 4.…”

Section: Discussionsupporting

confidence: 59%

“…4. Projection ofthe crystal structure ofbarium D-3-phosphoglycerate dihydrate (III) on the a-b plane, illustrating the packing ofthe molecules in the unit cell, the hydrogen-bonding and Ba2+ co-ordination (1), DL-2-amino-4-arsonobutanoic acid monohydrate; compound (II), DL-2-amino-4-phosphonobutanoic acid; compound (III), barium D-3-phosphoglycerate; compound (IV), disodium D-3-phosphoglycerate (Fewster & Fenn, 1982 109.0(4) P-l-C-4-C-3 111.5(5) P-1-0-4-C-1 123.2(10) P-1-0-4-C-3 123.2(4) (Pauling, 1948). The arsonate and phosphonate groups have approximate tetrahedral geometries, wvith the largest O-X-O angle contained by the two -O atoms carrying the delocalized negative charge.…”

Section: Discussionmentioning

confidence: 99%

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The arsonomethyl group as an analogue of phosphate. An X-ray investigation

Kamiya¹,

Cruse²,

Kennard³

1983

Biochemical Journal

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The X-ray structure analysis of three compounds of interest as enzyme substrates is reported. They are the hydrated forms of (I) DL-2-amino-4-arsonobutanoic acid [HO-AsO2--CH2-CH2-CH(NH3+)-CO2H], (II) DL-2-amino-4-phosphonobutanoic acid [HO-PO2--CH2-CH2-CH(NH3+)-CO2H] and the hydrated barium salt of (III) D-3-phosphoglycerate [HO-PO2--O-CH2-CH(OH)-CO2-]. The structures were fully refined to R factors of 0.033, 0.053 and 0.046. For the compounds (I) and (II) the charge distribution was directly determined by locating all H atoms. The co-ordination around As and P is approximately tetrahedral, with the valency angle between the two charged O atoms enlarged to 112 degrees in compound (I), 166 degrees in compound (II) and 122 degrees in compound (III). The As-X bond distances are increased relative to P-X to accommodate the increased atomic radius. The analysis establishes that the compounds are structural analogues. Tables of co-ordinates for H atoms, anisotropic thermal parameters, bond lengths and bond angles for the three compounds have been deposited as Supplementary Publication SUP 50122 (5 pages) with the British Library Lending Division, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained directly [see Biochem J. (1983) 209, 5].

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Section: Discussionsupporting

confidence: 59%

Section: Discussionmentioning

confidence: 99%

The arsonomethyl group as an analogue of phosphate. An X-ray investigation

Kamiya¹,

Cruse²,

Kennard³

1983

Biochemical Journal

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Three-dimensional crystal orbital calculations on mononucleotide crystallohydrates. I. Sodium mononucleotide crystallohydrates

Starikov

1996

Int. J. Quantum Chem.

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rnCrystal-orbital calculations on the three-dimensional disodium deoxyguanosine-5'-monophosphate tetrahydrate, disodium uridine-3'-monophosphate tetrahydrate, monosodium monoprotonated deoxyadenosine-5' monophosphate hexahydrate, and disodium deoxycytidine-5'-monophosphate heptahydrate crystallohydrates were carried out in a Hartree-Fock all-valence-electron approximation using the CRYSTAL92 routine package. The first, the second, and the last compounds were found to be insulators, whereas the third one should be considered a two-dimensional semiconductor. The structural basis for these findings is discussed, with special reference to the semiconductivity and intermolecular interactions in solid-state samples of polymeric nucleic acids.

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The adaptability of the active site of trypanosomal triosephosphate isomerase as observed in the crystal structures of three different complexes

et al. 1991

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Crystals of triosephosphate isomerase from Trypanosoma brucei brucei have been used in binding studies with three competitive inhibitors of the enzyme's activity. Highly refined structures have been deduced for the complexes between trypanosomal triosephosphate isomerase and a substrate analogue (glycerol-3-phosphate to 2.2 A), a transition state analogue (3-phosphonopropionic acid to 2.6 A), and a compound structurally related to both (3-phosphoglycerate to 2.2 A). The active site structures of these complexes were compared with each other, and with two previously determined structures of triosephosphate isomerase either free from inhibitor or complexed with sulfate. The comparison reveals three conformations available to the "flexible loop" near the active site of triosephosphate isomerase: open (no ligand), almost closed (sulfate), and fully closed (phosphate/phosphonate complexes). Also seen to be sensitive to the nature of the active site ligand is the catalytic residue Glu-167. The side chain of this residue occupies one of two discrete conformations in each of the structures so far observed. A "swung out" conformation unsuitable for catalysis is observed when sulfate, 3-phosphoglycerate, or no ligand is bound, while a "swung in" conformation ideal for catalysis is observed in the complexes with glycerol-3-phosphate or 3-phosphonopropionate. The water structure of the active site is different in all five structures. The results are discussed with respect to the triosephosphate isomerase structure function relationship, and with respect to an on-going drug design project aimed at the selective inhibition of glycolytic enzymes of T. brucei.

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Disodium D-3-phosphoglycerate, a substrate to phosphoglycerate kinase

Cited by 6 publications

References 6 publications

The arsonomethyl group as an analogue of phosphate. An X-ray investigation

The arsonomethyl group as an analogue of phosphate. An X-ray investigation

Three-dimensional crystal orbital calculations on mononucleotide crystallohydrates. I. Sodium mononucleotide crystallohydrates

The adaptability of the active site of trypanosomal triosephosphate isomerase as observed in the crystal structures of three different complexes

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