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Title: Preliminary X-ray Diffraction Analysis of the Cytoplasmic N-terminal Domain of the Na/HCO3 Cotransporter NBCe1-A

Abstract

The N-terminal cytoplasmic domain of the Na{sup +}-coupled HCO{sub 3}{sup -} cotransporter NBCe1-A (NtNBCe1) has been linked with proximal renal tubular acidosis. In a previous purification study of recombinant NtNBCe1, crystal growth at a suboptimal protein concentration (<1 mg ml{sup -1}) yielded small single diamond-shaped crystals that diffracted poorly. In the present study, by increasing the protein concentration 50-fold, the crystal size was doubled and robustness was also improved. Crystal annealing made the crystals suitable for X-ray diffraction. The crystals either belong to space group P3121 or P31 with pseudo P3121 symmetry, with unit-cell parameters a = 51.7, b = 51.7, c = 200.6 Angstroms, {alpha} = {beta} = 90, {gamma} = 120 deg, and diffract X-rays to 3.0 Angstroms resolution. The calculated Matthews number is 1.9 Angstroms{sup 3} Da{sup -1}, with two monomers of molecular weight {approx}83 kDa in the asymmetric unit. The molecular- replacement packing solution shows that the molecules form dimers by a domain-swapping mechanism.

Authors:
;
Publication Date:
Research Org.:
Brookhaven National Laboratory (BNL) National Synchrotron Light Source
Sponsoring Org.:
Doe - Office Of Science
OSTI Identifier:
914352
Report Number(s):
BNL-78920-2007-JA
TRN: US200809%%194
DOE Contract Number:
DE-AC02-98CH10886
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta Cryst. F; Journal Volume: 62
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; ANNEALING; CRYSTAL GROWTH; DIMERS; MOLECULAR WEIGHT; MONOMERS; PROTEINS; PURIFICATION; RESOLUTION; SPACE GROUPS; SYMMETRY; X-RAY DIFFRACTION; national synchrotron light source

Citation Formats

Gill,H., and Boron, W.. Preliminary X-ray Diffraction Analysis of the Cytoplasmic N-terminal Domain of the Na/HCO3 Cotransporter NBCe1-A. United States: N. p., 2006. Web. doi:10.1107/S1744309106015181.
Gill,H., & Boron, W.. Preliminary X-ray Diffraction Analysis of the Cytoplasmic N-terminal Domain of the Na/HCO3 Cotransporter NBCe1-A. United States. doi:10.1107/S1744309106015181.
Gill,H., and Boron, W.. Sun . "Preliminary X-ray Diffraction Analysis of the Cytoplasmic N-terminal Domain of the Na/HCO3 Cotransporter NBCe1-A". United States. doi:10.1107/S1744309106015181.
@article{osti_914352,
title = {Preliminary X-ray Diffraction Analysis of the Cytoplasmic N-terminal Domain of the Na/HCO3 Cotransporter NBCe1-A},
author = {Gill,H. and Boron, W.},
abstractNote = {The N-terminal cytoplasmic domain of the Na{sup +}-coupled HCO{sub 3}{sup -} cotransporter NBCe1-A (NtNBCe1) has been linked with proximal renal tubular acidosis. In a previous purification study of recombinant NtNBCe1, crystal growth at a suboptimal protein concentration (<1 mg ml{sup -1}) yielded small single diamond-shaped crystals that diffracted poorly. In the present study, by increasing the protein concentration 50-fold, the crystal size was doubled and robustness was also improved. Crystal annealing made the crystals suitable for X-ray diffraction. The crystals either belong to space group P3121 or P31 with pseudo P3121 symmetry, with unit-cell parameters a = 51.7, b = 51.7, c = 200.6 Angstroms, {alpha} = {beta} = 90, {gamma} = 120 deg, and diffract X-rays to 3.0 Angstroms resolution. The calculated Matthews number is 1.9 Angstroms{sup 3} Da{sup -1}, with two monomers of molecular weight {approx}83 kDa in the asymmetric unit. The molecular- replacement packing solution shows that the molecules form dimers by a domain-swapping mechanism.},
doi = {10.1107/S1744309106015181},
journal = {Acta Cryst. F},
number = ,
volume = 62,
place = {United States},
year = {Sun Jan 01 00:00:00 EST 2006},
month = {Sun Jan 01 00:00:00 EST 2006}
}
  • The N-terminal, cytoplasmic domain of the Na{sup +}-coupled HCO{sub 3} cotransporter NBCe1-A crystallizes in the trigonal space group P3{sub 1}21 or P3{sub 1} with pseudo P3{sub 1}21 symmetry and diffracts X-rays to 3.0 Å resolution. The crystal packing demonstrates a domain-swap mechanism for dimerization. The N-terminal cytoplasmic domain of the Na{sup +}-coupled HCO cotransporter NBCe1-A (NtNBCe1) has been linked with proximal renal tubular acidosis. In a previous purification study of recombinant NtNBCe1, crystal growth at a suboptimal protein concentration (<1 mg ml{sup −1}) yielded small single diamond-shaped crystals that diffracted poorly. In the present study, by increasing the protein concentrationmore » 50-fold, the crystal size was doubled and robustness was also improved. Crystal annealing made the crystals suitable for X-ray diffraction. The crystals either belong to space group P3{sub 1}21 or P3{sub 1} with pseudo P3{sub 1}21 symmetry, with unit-cell parameters a = 51.7, b = 51.7, c = 200.6 Å, α = β = 90, γ = 120°, and diffract X-rays to 3.0 Å resolution. The calculated Matthews number is 1.9 Å{sup 3} Da{sup −1}, with two monomers of molecular weight ∼83 kDa in the asymmetric unit. The molecular- replacement packing solution shows that the molecules form dimers by a domain-swapping mechanism.« less
  • The cytoplasmic, N-terminal domain (Nt) of the electrogenic sodium/bicarbonate cotransporter -- NBCe1 -- over-expresses in Escherichia coli and yields a large amount of soluble protein. A novel purification strategy, which involves a streptomycin precipitation, overcomes obstacles of instability and copurifying proteins, and leads to the first seen Nt-NBCe1 crystals. The purification procedure generally lends itself to the purification of Nts from other classes of the SLC4 family. Size-exclusion chromatography suggests that the Nt of NBCe1 as well as the Nt of other SLC4 members form dimers. A comparison of Nt-NBCe1 to SLC4 member Nt-AE1, based on purification properties and predictedmore » secondary-structure sequence alignments, suggests a similar mechanism for dimer stabilization.« less
  • The crystallization and data collection of topoisomerase IV from S. aureus is described. Phasing by molecular replacement proved difficult owing to the presence of translational NCS and strategies used to overcome this are discussed. DNA topoisomerase IV removes undesirable topological features from DNA molecules in order to help maintain chromosome stability. Two constructs of 56 and 59 kDa spanning the DNA-cleavage domain of the A subunit of topoisomerase IV from Staphylococcus aureus (termed GrlA56 and GrlA59) have been crystallized. Crystals were grown at 291 K using the sitting-drop vapour-diffusion technique with PEG 3350 as a precipitant. Preliminary X-ray analysis revealedmore » that GrlA56 crystals belong to space group P2{sub 1}, diffract to a resolution of 2.9 Å and possess unit-cell parameters a = 83.6, b = 171.5, c = 87.8 Å, β = 90.1°, while crystals of GrlA59 belong to space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 41.5, b = 171.89, c = 87.9 Å. These crystals diffract to a resolution of 2.8 Å. This is the first report of the crystallization and preliminary X-ray analysis of the DNA-cleavage domain of a topoisomerase IV from a Gram-positive organism.« less
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