Sulfate-binding protein dislikes protonated oxyacids

Jacobson, Bruce L.; Quiocho, Florante A.

doi:10.1016/0022-2836(88)90369-5

Cited by 118 publications

(106 citation statements)

References 12 publications

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“…The finding strongly suggests that the effectiveness of dipoles is limited to those closest to the sulfate. Assuming a normal pK of His 42, the mutagenesis result is consistent with previous data showing that dianion binding to SBP from both S. typhimurium (Pardee, 1966;Jacobson & Quiocho, 1988) and E. coli (J.J. He & F.A.…”

Section: Resultssupporting

confidence: 90%

“…Methods for purifying native and mutant proteins and determining equilibrium sulfatebinding constant were as described elsewhere (Pardee, 1966;Jacobson & Quiocho, 1988;Jacobson et al, 1991). All purified proteins migrate as a single band on polyacrylamide gel electrophoresis in the presence and absence of sodium dodecyl sulfate and on isoelectric focusing.…”

Section: Methodsmentioning

confidence: 99%

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Dominant role of local dipoles in stabilizing uncompensated charges on a sulfate sequestered in a periplasmic active transport protein

1993

Protein Science

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Electrostatic interactions are among the key factors determining the structure and function of proteins. Here we report experimental results that illuminate the functional importance of local dipoles to these interactions. The refined 1.7-A X-ray structure of the liganded form of the sulfate-binding protein, a primary sulfate active transport receptor of Salmonella typhirnurium, shows that the sulfate dianion is completely buried and bound by hydrogen bonds (mostly main-chain peptide NH groups) and van der Waals forces. The sulfate is also closely linked, via one of these peptide units, to a His residue. It is also adjacent to the N-termini of three a-helices, of which the two shortest have their C-termini "capped" by Arg residues. Site-directed mutagenesis of the recombinant Escherichia coli sulfate receptor had no effect on sulfate-binding activity when an Asn residue was substituted for the positively charged His and the two Arg (changed singly and together) residues. These results, combined with other observations, further solidify the idea that stabilization of uncompensated charges in a protein is a highly localized process that involves a collection of local dipoles, including those of peptide units confined to the first turns of helices. The contribution of helix macrodipoles appears insignificant.

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Section: Resultssupporting

confidence: 90%

Section: Methodsmentioning

confidence: 99%

Dominant role of local dipoles in stabilizing uncompensated charges on a sulfate sequestered in a periplasmic active transport protein

1993

Protein Science

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“…1B). Consistent with the stringent specificity of SBP for fully ionized tetrahedral oxydianions (15), the sequestered sulfate is the recipient of seven hydrogen bonds solely from uncharged protein donor groups, of which five are backbone peptide NH (3). A similar open model generated from the closed structure of the E. coli SBP shows an even more intense electronegative surface cleft (unpublished data).…”

Section: Resultsmentioning

confidence: 65%

Negative electrostatic surface potential of protein sites specific for anionic ligands.

Ledvina

Yao

Choudhary

1996

Proc. Natl. Acad. Sci. U.S.A.

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Determination of the crystal structure of an "open" unliganded active mutant (T141D) form of the Escherichia coli phosphate receptor for active transport has allowed calculation of the electrostatic surface potential for it and two other comparably modeled receptor structures (wild type and D137N). A discovery of considerable implication is the intensely negative potential of the phosphate-binding cleft. We MATERIALS AND METHODST141D mutant E. coli was prepared as described previously (5) and extensively dialyzed at pH 8.5 to remove any phosphate. Crystals were grown in a hanging drop containing 7 mg/ml protein and a 1:4 dilution of the well solution: 20% (w/v) polyethylene glycol 6000, 50 mM KCl, 100 mM NH4Cl, and 20 mM CH3COOK, pH 4.5. The crystal has the spacegroup of P21 and unit cell dimensions of a = 73.22 A, b = 39.59 A, c = 113.61 A, and ,B = 92.80. The asymmetric unit contains two molecules, which were identified as A and B. Intensity data were collected at 4°C and processed as described previously (2, 5). As the crystal decayed rapidly in the x-ray beam, only data to 2.4 A were collected (14,157 unique reflections with 46% complete in the last 2.51 to 2.40 A shell). As the crystal was not isomorphous with any previous crystals of PBP, we used molecular replacement technique as implemented in XPLOR (6) to determine the structure. We succeeded in obtaining solutions to the rotation and translation searches only by using domain II fragment of the wild-type structure (2) as a search model. The rotation solutions at Euler angles and translation in fractions of the unit cell for one domain II fragment are (01 = 278.23, 02 = 63.76, and 03 = 195.91) and (x = 0.033, y = 0, and z = 0.117), respectively, and for the other domain 11 (01 = 98.29, 02 = 117.87, and 03 = 163.93) and (x = 0.458, y = 0.017, and z = 0.383), respectively. Displaying the two models of the domain II fragment and symmetry related fragments using the program CHAIN (7) revealed no bad intermolecular contacts and a large empty area where domain I of both models could be placed. Guided by this observation, we successfully pieced together the two complete PBP models in the asymmetric unit. Each of the domain II models was overlapped with the identical domain of the complete structure of the ligandbound PBP. Domain I of both models was then rotated with respect to domain II about a hinge between the two domains connecting the a-carbons of residues 86 and 254 to place the domain in the empty space. This required about 250 rotation relative to the bound structure for both models to generate the open unliganded form with no bad contacts between the dimer and symmetry related molecules. These models were suitable for XPLOR rigid body refinement against the data to 3 A, with the two domain II fragments fixed and the two fitted domain I fragments treated as rigid bodies. This refinement brought the crystallographic R-factor down from an initial value of 0.495 to 0.349. A simulated annealing refinement further considerably reduced the R-factor...

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“…Despite similarities between the oxyanions phosphate, sulfate, and molybdate, the respective BPs exhibit exquisite specificity for their substrates (209,225,297,387,511). In each of the BPs, these molecules are accommodated through ion-dipole interactions consisting of hydrogen bonds with backbone NH and side chain OH groups of the protein.…”

Section: Bpd Uptake Systemsmentioning

confidence: 99%

Structure, Function, and Evolution of Bacterial ATP-Binding Cassette Systems

Davidson

Dassa

Orelle

et al. 2008

Microbiol Mol Biol Rev

1,186

1,137

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SUMMARY ATP-binding cassette (ABC) systems are universally distributed among living organisms and function in many different aspects of bacterial physiology. ABC transporters are best known for their role in the import of essential nutrients and the export of toxic molecules, but they can also mediate the transport of many other physiological substrates. In a classical transport reaction, two highly conserved ATP-binding domains or subunits couple the binding/hydrolysis of ATP to the translocation of particular substrates across the membrane, through interactions with membrane-spanning domains of the transporter. Variations on this basic theme involve soluble ABC ATP-binding proteins that couple ATP hydrolysis to nontransport processes, such as DNA repair and gene expression regulation. Insights into the structure, function, and mechanism of action of bacterial ABC proteins are reported, based on phylogenetic comparisons as well as classic biochemical and genetic approaches. The availability of an increasing number of high-resolution structures has provided a valuable framework for interpretation of recent studies, and realistic models have been proposed to explain how these fascinating molecular machines use complex dynamic processes to fulfill their numerous biological functions. These advances are also important for elucidating the mechanism of action of eukaryotic ABC proteins, because functional defects in many of them are responsible for severe human inherited diseases.

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Sulfate-binding protein dislikes protonated oxyacids

Cited by 118 publications

References 12 publications

Dominant role of local dipoles in stabilizing uncompensated charges on a sulfate sequestered in a periplasmic active transport protein

Dominant role of local dipoles in stabilizing uncompensated charges on a sulfate sequestered in a periplasmic active transport protein

Negative electrostatic surface potential of protein sites specific for anionic ligands.

Structure, Function, and Evolution of Bacterial ATP-Binding Cassette Systems

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