Structural Studies of Medicago truncatula Histidinol Phosphate Phosphatase from Inositol Monophosphatase Superfamily Reveal Details of Penultimate Step of Histidine Biosynthesis in Plants

Ruszkowski, M.; Dauter, Zbigniew

doi:10.1074/jbc.m115.708727

Cited by 23 publications

(42 citation statements)

References 84 publications

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“…The proteins selected for testing the SeU as a phasing vehicle were: HEW lysozyme16, thaumatin17, bovine trypsin18, cyan fluorescent protein (CFP)19 and histidinol phosphate phosphatase (HPP)20. In addition, a B-DNA Dickerson-Drew dodecamer (DDD)21 was used.…”

Section: Methodsmentioning

confidence: 99%

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Selenourea: a convenient phasing vehicle for macromolecular X-ray crystal structures

Luo

2016

Sci Rep

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Majority of novel X-ray crystal structures of proteins are currently solved using the anomalous diffraction signal provided by selenium after incorporation of selenomethionine instead of natural methionine by genetic engineering methods. However, selenium can be inserted into protein crystals in the form of selenourea (SeC(NH2)2), by adding the crystalline powder of selenourea into mother liquor or cryo-solution with native crystals, in analogy to the classic procedure of heavy-atom derivatization. Selenourea is able to bind to reactive groups at the surface of macromolecules primarily through hydrogen bonds, where the selenium atom may serve as acceptor and amide groups as donors. Selenourea has different chemical properties than heavy-atom reagents and halide ions and provides a convenient way of phasing crystal structures of macromolecules.

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Section: Methodsmentioning

confidence: 99%

“…The HPP protein expression, purification, and crystallization were described elsewhere20. In short, the crystals of HPP were grown in 15% (w/v) PEG 3350, 0.2 M diammonium hydrogen phosphate buffer pH 8.0 at room temperature.…”

Section: Methodsmentioning

confidence: 99%

Selenourea: a convenient phasing vehicle for macromolecular X-ray crystal structures

Luo

2016

Sci Rep

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“…The σ A ‐weighted F ‐map using refined atomic parameters and experimental data reported for 5EQA shows that either a methylene‐bridge (a reduction hypothesis) or an O‐bridge (an oxidation hypothesis) fits the ED feature reasonably well when the map is contoured at 3σ or 5σ (Fig. ).…”

Section: Resultsmentioning

confidence: 88%

“…The σ A ‐weighted F ‐map using the data published for 5EQA at 1.32‐Å resolution (Ref. ) for the bridge “X” in question contoured at +3.0σ (orange) and + 5.0σ (cyan). (A) Between Lys158/Subunit A and Cys245/Subunit B.…”

Section: Resultsmentioning

confidence: 99%

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Crystallographic identification of spontaneous oxidation intermediates and products of protein sulfhydryl groups

Wang

2019

Protein Science

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In the absence of protective reducing agents, Cys residues in purified proteins can be oxidized spontaneously by oxygen in the air, as frequently observed in protein crystal structures. However, the formation of an O‐bridge via dehydration mechanism between a peroxidized Cys side chain and a primary amine of Lys side chain in proteins has not yet been reported. When an electron density feature was observed for an extra group or an extra atom between side chains of Cys‐245 and Lys‐158 in the crystal structure of histidinol phosphate phosphatase, mass spectrometric analysis was carried out for its chemical identification. That analysis led to a conclusion that this extra density corresponded to a methylene group. It was then proposed that these two residues were able to absorb CO2 and reduced it to CH2 spontaneously. Further examination of other protein structures in the PDB showed that the formation of this cross‐linking species was a widespread phenomenon. This claim is examined in this study using methods recently developed for quantification of electrons around nucleus as the means for direct chemical identification. It is found that an O‐bridge is actually formed between Cys and Lys side chains, instead of a CH2‐bridge.

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Structural studies of Medicago truncatula proteins participating in cytokinin signal transduction and nodulation

Ruszkowski

2019

The Model Legume Medicago Truncatula

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Structural Studies of Medicago truncatula Histidinol Phosphate Phosphatase from Inositol Monophosphatase Superfamily Reveal Details of Penultimate Step of Histidine Biosynthesis in Plants

Cited by 23 publications

References 84 publications

Selenourea: a convenient phasing vehicle for macromolecular X-ray crystal structures

Selenourea: a convenient phasing vehicle for macromolecular X-ray crystal structures

Crystallographic identification of spontaneous oxidation intermediates and products of protein sulfhydryl groups

Structural studies of Medicago truncatula proteins participating in cytokinin signal transduction and nodulation

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