Fold Protein Family Research Articles

Crystal structure of human SH3BGRL protein: The first structure of the human SH3BGR family representing a novel class of thioredoxin fold proteins

Introduction. The humanSH3BGRL (h-SH3BGRL) gene is a member of the human SH3BGR family. The human SH3BGR (SH3 binding glutamic acid-rich) gene was cloned and characterized in 1997 in an effort to identify new genes located to chromosome 21. After the characterization of SH3BGR, three novel human genes, h-SH3BGRL, h-SH3BGRL2, and h-SH3BGRL3, were identified, showing a high homology to the N-terminal region of the h-SH3BGR protein. They are therefore believed to be a new family of human gene, the h-SH3BGR gene family. The h-SH3BGRL gene located to chromosome Xq13.3 encodes for a small protein of 114 amino acids, which is apparently widely expressed in many tissues including liver and blood. The h-SH3BGRLprotein features a prolinerich sequence (PLPPQIF), which contains both the SH3 binding (PXXP) and the Homer EVH1 binding (PPXXF) motif. This proline-rich region is highly conserved in h-SH3BGR family and was expected to be functionally important. Although it is known that the SH3BGRL gene is missing in a mentally retarded male patient, the exact functional role of h-SH3BGRL is still needed to be defined. Here we report the crystal structure of h-SH3BGRL protein determined by the SIRAS method. The structure indicates that SH3BGRL can not bind to the SH3 or Homer EVH1 domain as previously expected due to our finding that the binding motif (PLPPQIF) is buried in the tertiary structure. As the first structure of the human SH3BGR protein family, the tertiary structure of h-SH3BGRL shows a typical thioredoxin fold at the Nterminal part and a helix-loop-helix motif at the Cterminal lobe. Sequence and structure comparisons show that h-SH3BGRL belongs to the thioredoxin fold protein family but it is distinct from all five classes of the thioredoxin fold proteins identified thus far. According to the unique structural and functional characterizations, h-SH3BGRL represents a novel class of the thioredoxin fold proteins.

A Novel Induced-fit Reaction Mechanism of Asymmetric Hot Dog Thioesterase PaaI

Hot dog fold proteins sharing the characteristic "hot dog" fold are known to involve certain coenzyme A binding enzymes with various oligomeric states. In order to elucidate the oligomerization-function relationship of the hot dog fold proteins, crystal structures of the phenylacetate degradation protein PaaI from Thermus thermophilus HB8 (TtPaaI), a tetrameric acyl-CoA thioesterase with the hot dog fold, have been determined and compared with those of other family members. In the liganded crystal forms with coenzyme A derivatives, only two of four intersubunit catalytic pockets of the TtPaaI tetramer are occupied by the ligands. A detailed structural comparison between several liganded and unliganded forms reveals that a subtle rigid-body rearrangement of subunits within 2 degrees upon binding of the first two ligand molecules can induce a strict negative cooperativity to prevent further binding at the remaining two pockets, indicating that the so-called "half-of-the-sites reactivity" of oligomeric enzymes is visualized for the first time. Considering kinetic and mutational analyses together, a possible reaction mechanism of TtPaaI is proposed; one tetramer binds only two acyl-CoA molecules with a novel asymmetric induced-fit mechanism and carries out the hydrolysis according to a base-catalyzed reaction through activation of a water molecule by Asp48. From a structural comparison with other family members, it is concluded that a subgroup of the hot dog fold protein family, referred to as "asymmetric hot dog thioesterases" including medium chain acyl-CoA thioesterase II from Escherichia coli and human thioesterase III, might share the same oligomerization mode and the asymmetric induced-fit mechanism as observed in TtPaaI.

Characterization of human glutaredoxin 2 as iron–sulfur protein: A possible role as redox sensor

Human mitochondrial glutaredoxin 2 (Grx2) is a glutathione-dependent oxidoreductase (active site: Cys-Ser-Tyr-Cys) that facilitates the maintenance of mitochondrial redox homeostasis upon induction of apoptosis by oxidative stress. Here, we have characterized Grx2 as an iron-sulfur center-containing member of the thioredoxin fold protein family. Mossbauer spectroscopy revealed the presence of a four cysteine-coordinated nonoxidizable [2Fe-2S]2+ cluster that bridges two Grx2 molecules via two structural Cys residues to form dimeric holo Grx2. Coimmunoprecipitation of radiolabeled iron with Grx2 from human cell lines indicated the presence of the cluster in vivo. The [2Fe-2S]-bridged dimer was enzymatically inactive, but degradation of the cluster and the resulting monomerization of Grx2 activated the protein. Slow degradation under aerobic conditions was prevented by the presence of glutathione, whereas glutathione disulfide as well as one-electron oxidants or reductants promoted monomerization of Grx2. We propose that the iron-sulfur cluster serves as a redox sensor for the activation of Grx2 during conditions of oxidative stress when free radicals are formed and the glutathione pool becomes oxidized.

Optimization of factor VIII replacement therapy: can structural studies help in evading antibody inhibitors?

Optimization of factor VIII replacement therapy: can structural studies help in evading antibody inhibitors?

Thermodynamics and Folding Kinetics Analysis of the SH3 Domain form Discrete Molecular Dynamics

We perform a detailed analysis of the thermodynamics and folding kinetics of the SH3 domain fold with discrete molecular dynamic simulations. We propose a protein model that reproduces some of the experimentally observed thermodynamic and folding kinetic properties of proteins. Specifically, we use our model to study the transition state ensemble of the SH3 fold family of proteins, a set of unstable conformations that fold to the protein native state with probability 1/2. We analyze the participation of each secondary structure element formed at the transition state ensemble. We also identify the folding nucleus of the SH3 fold and test extensively its importance for folding kinetics. We predict that a set of amino acid contacts between the RT-loop and the distal hairpin are the critical folding nucleus of the SH3 fold and propose a hypothesis that explains this result.

Detailed analysis of the atrial natriuretic factor receptor hormone-binding domain crystal structure

The X-ray crystal structure of the dimerized atrial natriuretic factor (ANF) receptor hormone-binding domain has provided a first structural view of this anti-hypertensive receptor. The structure reveals a surprising evolutionary link to the periplasmic-binding protein fold family. Furthermore, the presence of a chloride ion in the membrane distal domain and the presence of a second putative effector pocket suggests that the extracellular domain of this receptor is allosterically regulated. The scope of this article is to extensively review the data published on this receptor and to correlate it with the hormone-binding domain structure. In addition, a more detailed description is provided of the important features of this structure including the different binding sites for the ANF hormone, chloride ion, putative effector pocket, glycosylation sites, and dimer interface.Key words: crystal structure, periplasmic-binding protein fold, guanylyl cyclase, hormone receptor.

Crystal structure of cis-prenyl chain elongating enzyme, undecaprenyl diphosphate synthase.

Undecaprenyl diphosphate synthase (UPS) catalyzes the cis-prenyl chain elongation onto trans, trans-farnesyl diphosphate (FPP) to produce undecaprenyl diphosphate (UPP), which is indispensable for the biosynthesis of bacterial cell walls. We report here the crystal structure of UPS as the only three-dimensional structure among cis-prenyl chain elongating enzymes. The structure is classified into a protein fold family and is completely different from the so-called "isoprenoid synthase fold" that is believed to be a common structure for the enzymes relating to isoprenoid biosynthesis. Conserved amino acid residues among cis-prenyl chain elongating enzymes are located around a large hydrophobic cleft in the UPS structure. A structural P-loop motif, which frequently appears in the various kinds of phosphate binding site, is found at the entrance of this cleft. The catalytic site is determined on the basis of these structural features, from which a possible reaction mechanism is proposed.

Detailed analysis of the atrial natriuretic factor receptor hormone-binding domain crystal structure

The X-ray crystal structure of the dimerized atrial natriuretic factor (ANF) receptor hormone-binding domain has provided a first structural view of this anti-hypertensive receptor. The structure reveals a surprising evolutionary link to the periplasmic-binding protein fold family. Furthermore, the presence of a chloride ion in the membrane distal domain and the presence of a second putative effector pocket suggests that the extracellular domain of this receptor is allosterically regulated. The scope of this article is to extensively review the data published on this receptor and to correlate it with the hormone-binding domain structure. In addition, a more detailed description is provided of the important features of this structure including the different binding sites for the ANF hormone, chloride ion, putative effector pocket, glycosylation sites, and dimer interface.

Proteins with Similar Architecture Exhibit Similar Large-Scale Dynamic Behavior

We have investigated the similarities and differences in the computed dynamic fluctuations exhibited by six members of a protein fold family with a coarse-grained Gaussian network model. Specifically, we consider the cofactor binding fragment of CysB; the lysine/arginine/ornithine-binding protein (LAO); the enzyme porphobilinogen deaminase (PBGD); the ribose-binding protein (RBP); the N-terminal lobe of ovotransferrin in apo-form (apo-OVOT); and the leucine/isoleucine/valine-binding protein (LIVBP). All have domains that resemble a Rossmann fold, but there are also some significant differences. Results indicate that similar global dynamic behavior is preserved for the members of a fold family, and that differences usually occur in regions only where specific function is localized. The present work is a computational demonstration that the scaffold of a protein fold may be utilized for diverse purposes. LAO requires a bound ligand before it conforms to the large-scale fluctuation behavior of the three other members of the family, CysB, PBGD, and RBP, all of which contain a substrate (cofactor) at the active site cleft. The dynamics of the ligand-free enzymes LIVBP and apo-OVOT, on the other hand, concur with that of unliganded LAO. The present results suggest that it is possible to construct structure alignments based on dynamic fluctuation behavior.

Common EF-hand motifs in cholinesterases and neuroligins suggest a role for Ca2+ binding in cell surface associations.

Comparisons of protein sequence via cyclic training of Hidden Markov Models (HMMs) in conjunction with alignments of three-dimensional structure, using the Combinatorial Extension (CE) algorithm, reveal two putative EF-hand metal binding domains in acetylcholinesterase. Based on sequence similarity, putative EF-hands are also predicted for the neuroligin family of cell surface proteins. These predictions are supported by experimental evidence. In the acetylcholinesterase crystal structure from Torpedo californica, the first putative EF-hand region binds the Zn2+ found in the heavy metal replacement structure. Further, the interaction of neuroligin 1 with its cognate receptor neurexin depends on Ca2+. Thus, members of the alpha,beta hydrolase fold family of proteins contain potential Ca2+ binding sites, which in some family members may be critical for heterologous cell associations.

ACHEdb: the database system for ESTHER, the alpha/beta fold family of proteins and the Cholinesterase gene server.

Acetylcholinesterase belongs to a family of proteins, the alpha/beta hydrolase fold family, whose constituents evolutionarily diverged from a common ancestor and share a similar structure of a central beta sheet surrounded by alpha helices. These proteins fulfil a wide range of physiological functions (hydrolases, adhesion molecules, hormone precursors) [Krejci,E., Duval,N., Chatonnet,A., Vincens,P. and Massoulié,J. (1991) Proc. Natl. Acad. Sci. USA , 88, 6647-6651]. ESTHER (for esterases, alpha/beta hydrolase enzymes and relatives) is a database aimed at collecting in one information system, sequence data together with biological annotations and experimental biochemical results related to the structure-function analysis of the enzymes of the family. The major upgrade of the database comes from the use of a new database management system: aCHEdb which uses the ACeDB program designed by Richard Durbin and Jean Thierry-Mieg. It can be found at http://www.ensam.inra.fr/cholinesterase

Hydroxynitrile lyase from Hevea brasiliensis: Molecular characterization and mechanism of enzyme catalysis

(S)-Hydroxynitrile lyase (Hnl) from the tropical rubber tree Hevea brasiliensis is a 29 kDa single chain protein that catalyses the breakdown or formation of a C--C bond by reversible addition of hydrocyanic acid to aldehydes or ketones. The primary sequence of Hnl has no significant homology to known proteins. Detailed homology investigations employing PROFILESEARCH and secondary structure prediction algorithms suggest that Hnl is a member of the alpha/beta hydrolase fold protein family and contains a catalytic triad as functional residues for catalysis. The significance of predicted catalytic residues was tested and confirmed by site-directed mutagenesis and expression of mutant and wild-type proteins in the yeast, Saccharomyces cerevisiae. Based on these data we suggest a mechanistic model for the (S)-cyanohydrin synthesis catalyzed by hydroxynitrile lyase from Hevea brasiliensis.

Hydroxynitrile lyase from Hevea brasiliensis: Molecular characterization and mechanism of enzyme catalysis

(S)-Hydroxynitrile lyase (Hnl) from the tropical rubber tree Hevea brasiliensis is a 29 kDa single chain protein that catalyses the breakdown or formation of a C--C bond by reversible addition of hydrocyanic acid to aldehydes or ketones. The primary sequence of Hnl has no significant homology to known proteins. Detailed homology investigations employing PROFILESEARCH and secondary structure prediction algorithms suggest that Hnl is a member of the alpha/beta hydrolase fold protein family and contains a catalytic triad as functional residues for catalysis. The significance of predicted catalytic residues was tested and confirmed by site-directed mutagenesis and expression of mutant and wild-type proteins in the yeast, Saccharomyces cerevisiae. Based on these data we suggest a mechanistic model for the (S)-cyanohydrin synthesis catalyzed by hydroxynitrile lyase from Hevea brasiliensis.