The crystal structure of dihydrodipicolinate reductase from the human-pathogenic bacterium<i>Bartonella henselae</i>strain Houston-1 at 2.3 Å resolution

Cala, Ali R.; Nadeau, Maria T.; Abendroth, Jan; Staker, Bart L.; Reers, Alexandra R.; Dobson, Renwick C. J.; Myler, Peter J.; Hudson, André O.

doi:10.1107/s2053230x16018525

Cited by 3 publications

(3 citation statements)

References 43 publications

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“…henselae ( Bh )DHDPR (PDB: 3IJP; sequence identity: 27%) also contains an NLL region, but its interaction with the adenine phosphate of NADPH differs significantly from that of Pa DHDPR (Fig. 6B ) due to differences in local structure and amino acid sequence 24 . Arg34 of Bh DHDPR, which is the equivalent to His35 in Pa DHDPR, forms a charged interaction with the adenine phosphate of NADPH.…”

Section: Resultsmentioning

confidence: 99%

Crystal structure of dihydrodipicolinate reductase (PaDHDPR) from Paenisporosarcina sp. TG-14: structural basis for NADPH preference as a cofactor

Lee

Park

Lee

et al. 2018

Sci Rep

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Dihydrodipicolinate reductase (DHDPR) is a key enzyme in the diaminopimelate- and lysine-synthesis pathways that reduces DHDP to tetrahydrodipicolinate. Although DHDPR uses both NADPH and NADH as a cofactor, the structural basis for cofactor specificity and preference remains unclear. Here, we report that Paenisporosarcina sp. TG-14 PaDHDPR has a strong preference for NADPH over NADH, as determined by isothermal titration calorimetry and enzymatic activity assays. We determined the crystal structures of PaDHDPR alone, with its competitive inhibitor (dipicolinate), and the ternary complex of the enzyme with dipicolinate and NADPH, with results showing that only the ternary complex had a fully closed conformation and suggesting that binding of both substrate and nucleotide cofactor is required for enzymatic activity. Moreover, NADPH binding induced local conformational changes in the N-terminal long loop (residues 34–59) of PaDHDPR, as the His35 and Lys36 residues in this loop interacted with the 2′-phosphate group of NADPH, possibly accounting for the strong preference of PaDHDPR for NADPH. Mutation of these residues revealed reduced NADPH binding and enzymatic activity, confirming their importance in NADPH binding. These findings provide insight into the mechanism of action and cofactor selectivity of this important bacterial enzyme.

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Section: Resultsmentioning

confidence: 99%

Crystal structure of dihydrodipicolinate reductase (PaDHDPR) from Paenisporosarcina sp. TG-14: structural basis for NADPH preference as a cofactor

Lee

Park

Lee

et al. 2018

Sci Rep

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“…In the Crystal Screen HT (Hampton Research), 0.1 m of NaAc acts as a buffer but at the concentration of 0.2 m , it is considered a salt. Intriguingly, when the concentration of NaAc is increased to 1.0 m , it is considered as a precipitant …”

Section: Overview Of Commercial Screening Kitsmentioning

confidence: 99%

“…However, its advantages still outweigh its disadvantages. In prevailing screening kits, about 60% of the kits are designed by sparse matrix screening, including Index HT (Hampton Research), Crystal Screen HT (Hampton Research), Wizard I–IV (Rigaku and Emerald BioSystems), Structure Screen (Molecular Dimensions), JBScreen Basic HT (Jena Bioscience), Classics and Classics II (Qiagen), and Xtalquest Kit (Xtalquest) …”

Section: Overview Of Commercial Screening Kitsmentioning

confidence: 99%

An Analysis on Commercial Screening Kits and Chemical Components in Biomacromolecular Crystallization Screening

Qin

Xie

Zhang

et al. 2019

Crystal Research and Technology

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Obtaining diffraction-quality crystals is still a bottleneck for biomacromolecular structure determination using X-ray diffraction. In practice, the bottleneck mainly comprises two aspects: difficulties in screening and in optimization, and both of them need screening kits. The paper aims at an investigation of the chemical components employed in 86 common commercial screening kits, and comparison with those in the Biological Macromolecules Crystallization Database (BMCD). First, the 86 screening kits are systematically analyzed in terms of design methods, classification, applicable scope, and manufacturing company. Second, the chemical components applied in these screening kits are investigated in detail in terms of the classification and utilization frequency, which are compared with those in BMCD. Third, four main chemical reagents of screening kits including salts, buffers, precipitants, and additives are analyzed in detail. The top ten utilized chemical components are listed. Last, the paper summarizes new progress and further innovation in crystallization condition screening practice and screening kits design. The analysis result would be a valuable reference for rational selection and design of screening kits, and even for personalized screening of a target biomacromolecule, which would provide new ideas to solve the bottleneck problem of biomacromolecular structure determination.

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Dihydrodipicolinate reductase from Paenisporosarcina sp. TG-14

Lee

Park

Lee

et al. 2019

View full text Add to dashboard Cite

The crystal structure of dihydrodipicolinate reductase from the human-pathogenic bacteriumBartonella henselaestrain Houston-1 at 2.3 Å resolution

Cited by 3 publications

References 43 publications

Crystal structure of dihydrodipicolinate reductase (PaDHDPR) from Paenisporosarcina sp. TG-14: structural basis for NADPH preference as a cofactor

Crystal structure of dihydrodipicolinate reductase (PaDHDPR) from Paenisporosarcina sp. TG-14: structural basis for NADPH preference as a cofactor

An Analysis on Commercial Screening Kits and Chemical Components in Biomacromolecular Crystallization Screening

Dihydrodipicolinate reductase from Paenisporosarcina sp. TG-14

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