The 1.6 Å crystal structure of the AraC sugar-binding and dimerization domain complexed with d-fucose

Soisson, S.M.; MacDougall-Shackleton, Beth; Schleif, Robert; Wolberger, Cynthia

doi:10.1006/jmbi.1997.1314

Cited by 66 publications

(74 citation statements)

References 44 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, an examination of several dimeric structures in the Protein Data Base shows that the APx dimer interface is not so unusual. For example, the E. coli regulatory protein, AraC, forms a homodimer (1 ARC) (Soisson et al, 1997) and has a water molecule near the center of the dimer interface with related Gln and Asn residues from each subunit hydrogen bonded with the central water. This is very similar to the interactions involving Glu106 in APx (Figs.…”

Section: Discussionmentioning

confidence: 99%

The role of quaternary interactions on the stability and activity of ascorbate peroxidase

Mandelman

Schwarz

et al. 1998

Protein Science

View full text Add to dashboard Cite

Point mutations at the dimer interface of the homodimeric enzyme ascorbate peroxidase (APx) were constructed to assess the role of quaternary interactions in the stability and activity of APx. Analysis of the APx crystal structure shows that Glu 1 12 forms a salt bridge with Lys20 and Arg24 of the opposing subunit near the axis of dyad symmetry between the subunits. Two point mutants, El 12A and El 12K, were made to determine the effects of a neutral (alanine) and repulsive (lysine) mutation on dimerization, stability, and activity. Gel filtration analysis indicated that the ratio of the monomer to dimer increased as the dimer interface interactions went from attractive to repulsive. Differential scanning calorimetry (DSC) data exhibited a decrease in both the transition temperature (T,) and enthalpy of unfolding (AH,) with T, = 58.3 * 0.5 "C, 56.0 f 0.8 "C, and 53.0 * 0.9 "C and AH, = 245 f 29 kcal/mol, 199 * 38 kcal/mol, and 170 f 25 kcal/mol for wild-type APx, El 12A, and El 12K, respectively. Similar changes were observed based on thermal melting curves obtained by absorption spectroscopy. No change in enzyme activity was found for the E l 12A mutant, and only a 25% drop in activity was observed for the El 12K mutant which demonstrates that the non-Michaelis Menten kinetics of APx is not due to the APx oligomeric structure. The cryogenic crystal structures of the wild-type and mutant proteins show that mutation induced changes are limited to the dimer interface including an alteration in solvent structure.

show abstract

Section: Discussionmentioning

confidence: 99%

The role of quaternary interactions on the stability and activity of ascorbate peroxidase

Mandelman

Schwarz

et al. 1998

Protein Science

View full text Add to dashboard Cite

show abstract

“…The close proximity of the amide nitrogen of the glycolipid ceramide could exacerbate the effect, possibly accounting for the simultaneous large magnitude quenching and blue-shifting of the Trp emission signal, which reflects the environmental polarity change brought to Trp-96 by the juxtapositioning of glycolipid. Indeed, stacking interactions between free sugar ligands and Trps of sugar binding and transport proteins reportedly alter Trp fluorescence responses, albeit those responses are vastly reduced in magnitude (42)(43)(44)(45)(46)(47)(48).…”

Section: -40-fold Higher K D Valuesmentioning

confidence: 99%

Glycolipid Acquisition by Human Glycolipid Transfer Protein Dramatically Alters Intrinsic Tryptophan Fluorescence

Zhai

Malakhova

Pike

et al. 2009

Journal of Biological Chemistry

View full text Add to dashboard Cite

Glycolipid transfer proteins (GLTPs) are small, soluble proteins that selectively accelerate the intermembrane transfer of glycolipids. The GLTP fold is conformationally unique among lipid binding/transfer proteins and serves as the prototype and founding member of the new GLTP superfamily. In the present study, changes in human GLTP tryptophan fluorescence, induced by membrane vesicles containing glycolipid, are shown to reflect glycolipid binding when vesicle concentrations are low. Characterization of the glycolipid-induced "signature response," i.e. ϳ40% decrease in Trp intensity and ϳ12-nm blue shift in emission wavelength maximum, involved various modes of glycolipid presentation, i.e. microinjection/dilution of lipidethanol solutions or phosphatidylcholine vesicles, prepared by sonication or extrusion and containing embedded glycolipids. High resolution x-ray structures of apo-and holo-GLTP indicate that major conformational alterations are not responsible for the glycolipid-induced GLTP signature response. Instead, glycolipid binding alters the local environment of Trp-96, which accounts for ϳ70% of total emission intensity of three Trp residues in GLTP and provides a stacking platform that aids formation of a hydrogen bond network with the ceramide-linked sugar of the glycolipid headgroup. The changes in Trp signal were used to quantitatively assess human GLTP binding affinity for various lipids including glycolipids containing different sugar headgroups and homogenous acyl chains. The presence of the glycolipid acyl chain and at least one sugar were essential for achieving a low-tosubmicromolar dissociation constant that was only slightly altered by increased sugar headgroup complexity. Glycolipid transfer protein (GLTP)4 is a soluble (ϳ24-kDa) protein that selectively transfers glycosphingolipids (GSLs) between membranes. GSLs play key roles in cell recognition, adhesion, differentiation, proliferation, and programmed death in normal and disease states (1-8). Phylogenetic/evolutionary analyses show GLTP to be highly conserved among vertebrates (9 -11). The conformational uniqueness of the GLTP fold when compared with other lipid binding/transfer proteins (12-14) has resulted in GLTP being designated the prototype and founding member of the GLTP superfamily (15, 16). GLTP employs a novel two-layer "sandwich motif," dominated by ␣-helices and achieved without intramolecular disulfide bridges, to accommodate glycolipid within a single lipid binding site and to form a membrane-interaction domain that differs from other known membrane targeting/translocation domains, i.e. C1, C2, PH, PX, and FYVE (9, 13, 17-21). The glycolipid binding site of GLTP consists of a sugar headgroup recognition center that anchors the ceramide-linked sugar to the protein surface via multiple hydrogen bonds and a hydrophobic tunnel that accommodates the hydrocarbon chains of ceramide. The crystal structures of glycolipid-free GLTP and of GLTP complexed with a half-dozen glycolipids differing in sugar headgroup and/or lipid acyl c...

show abstract

“…There is much more information available on the DNA binding component, although the specific details of the N-terminal section (particularly of the AraC protein) are more relevant to the present review. This regulator has been subject to detailed structural (269,270) and molecular (250,255) analysis over several years. In summary, the N-terminal section comprises an arabinose-binding, eight-stranded ␤-barrel, which is joined to the DNA-binding domain via a linker region; the barrelshaped section is also responsible for the dimerization of the molecule, a factor which determines its 3D shape and therefore its ability to bend the associated DNA strand.…”

Section: Arac-type Transcription Factorsmentioning

confidence: 99%

“…It is now considered likely that such a His cluster, together with an adjacent conserved Glu, may be the binding site for an Mn 2ϩ ion recently found to be the metal present in OXO, at least in those isolated from cereals (39,238,239). A similar combination of modelling and experimental approaches could be made using the structural data from the sugar-binding domain of the bacterial AraC transcription factor (270) and the sequence data from SBP (bicupins) from higher plants (40,219) in order to identify ligands specifically involved in the binding of either mono-or disaccharides in these subgroups.…”

Section: Structural Aspects Of Cupinsmentioning

confidence: 99%

“…proteins gi2984227 from Aquifex aeolicus and gi2128971 from Methanococcus jannaschii, with optimum growth temperatures of 90 and 95°C, respectively), was probably metal containing, and had a relatively nonspecific ability to bind a range of molecules which included sugar residues. This progenitor protein then assumed other functions, for example as a PMI able to bind mannose-6-phosphate, and it was also involved in a fusion event whereby a sugar-binding form of the cupin domain combined with a DNA-binding domain to generate the multidomain AraC type of transcription factor, in which the sugar-binding element is located within the N-terminal effector-binding domain (270). (In this context it is relevant to note the close association of wheat OXO with the arabinose-rich hemicelluloses [135].)…”

Section: Original Function Of the Ancestral "Protocupin"mentioning

confidence: 99%

See 1 more Smart Citation

Microbial Relatives of the Seed Storage Proteins of Higher Plants: Conservation of Structure and Diversification of Function during Evolution of the Cupin Superfamily

Dunwell

Khuri

Gane

2000

Microbiol Mol Biol Rev

313

297

View full text Add to dashboard Cite

SUMMARY This review summarizes the recent discovery of the cupin superfamily (from the Latin term “cupa,” a small barrel) of functionally diverse proteins that initially were limited to several higher plant proteins such as seed storage proteins, germin (an oxalate oxidase), germin-like proteins, and auxin-binding protein. Knowledge of the three-dimensional structure of two vicilins, seed proteins with a characteristic β-barrel core, led to the identification of a small number of conserved residues and thence to the discovery of several microbial proteins which share these key amino acids. In particular, there is a highly conserved pattern of two histidine-containing motifs with a varied intermotif spacing. This cupin signature is found as a central component of many microbial proteins including certain types of phosphomannose isomerase, polyketide synthase, epimerase, and dioxygenase. In addition, the signature has been identified within the N-terminal effector domain in a subgroup of bacterial AraC transcription factors. As well as these single-domain cupins, this survey has identified other classes of two-domain bicupins including bacterial gentisate 1,2-dioxygenases and 1-hydroxy-2-naphthoate dioxygenases, fungal oxalate decarboxylases, and legume sucrose-binding proteins. Cupin evolution is discussed from the perspective of the structure-function relationships, using data from the genomes of several prokaryotes, especially Bacillus subtilis. Many of these functions involve aspects of sugar metabolism and cell wall synthesis and are concerned with responses to abiotic stress such as heat, desiccation, or starvation. Particular emphasis is also given to the oxalate-degrading enzymes from microbes, their biological significance, and their value in a range of medical and other applications.

show abstract

The 1.6 Å crystal structure of the AraC sugar-binding and dimerization domain complexed with d-fucose

Cited by 66 publications

References 44 publications

The role of quaternary interactions on the stability and activity of ascorbate peroxidase

The role of quaternary interactions on the stability and activity of ascorbate peroxidase

Glycolipid Acquisition by Human Glycolipid Transfer Protein Dramatically Alters Intrinsic Tryptophan Fluorescence

Microbial Relatives of the Seed Storage Proteins of Higher Plants: Conservation of Structure and Diversification of Function during Evolution of the Cupin Superfamily

Contact Info

Product

Resources

About