Modes of binding substrates and their analogues to the enzyme D-xylose isomerase

Carrell, H. L.; Hoier, Helga; Glusker, Jenny P.

doi:10.1107/s0907444993009345

Cited by 60 publications

(56 citation statements)

References 5 publications

(5 reference statements)

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“…2c shows the structure and some of the presumed active-site residues for PMI. Experimental evidence supports a proton transfer mechanism by means of a cis ene-diol intermediate (35), rather than by a hydride shift as for xylose isomerase (36,37).…”

Section: Resultsmentioning

confidence: 86%

THEMATICS: A simple computational predictor of enzyme function from structure

Ondrechen

Clifton

Ringe

2001

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

213

203

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We show that theoretical microscopic titration curves (THEMATICS) can be used to identify active-site residues in proteins of known structure. Results are featured for three enzymes: triosephosphate isomerase (TIM), aldose reductase (AR), and phosphomannose isomerase (PMI). We note that TIM and AR have similar structures but catalyze different kinds of reactions, whereas TIM and PMI have different structures but catalyze similar reactions. Analysis of the theoretical microscopic titration curves for all of the ionizable residues of these proteins shows that a small fraction (3-7%) of the curves possess a flat region where the residue is partially protonated over a wide pH range. The preponderance of residues with such perturbed curves occur in the active site. Additional results are given in summary form to show the success of the method for proteins with a variety of different chemistries and structures.T here is a need to develop methods to predict protein function from structure; this need becomes particularly acute as novel protein folds are discovered for which there are no proteins of similar structure with known function. We show that theoretical microscopic titration curves (THEMATICS) can be used to identify active-site residues in enzymes of known structure. This information will prove to be important in the current challenging quest to predict protein function from sequence and structure.Knowledge of protein sequences and structures has burgeoned very recently as a result of genome sequencing (1) and structural genomics efforts. To translate such information into tangible benefits to humankind, the next step is to develop methods that enable one to predict and to establish function from structure. Techniques used to predict function from sequence or function from structure are in their infancy and rely either on analogies to related proteins of known function (2-8) or on computational searches for binding sites by docking (9) of selected sets of small molecules onto the structure. For instance, recent work has searched the Protein Data Bank (PDB; ref. 10; http:͞͞ www.rcsb.org͞pdb͞) for previously unrecognized cation-binding sites (11).However, there is as yet no reliable method to identify active sites of enzymes or other interaction sites of proteins in the absence of biochemical data, even when the structure is known. There is a wealth of biochemical data that demonstrates that active-site residues involved in specific kinds of chemistry possess predictable chemical properties that enable one to identify them as active-site residues. The most important of these properties is a perturbed pK a that can be determined experimentally by pH titrations of the activity of the enzyme. Herein we demonstrate that theoretical titration functions can identify active-site residues that are involved in Brønsted acid-base chemistry for a variety of proteins, thereby identifying the active site from the location of the residues.In an experimental titration curve, one typically plots pH as a function of the volume of...

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Section: Resultsmentioning

confidence: 86%

THEMATICS: A simple computational predictor of enzyme function from structure

Ondrechen

Clifton

Ringe

2001

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

213

203

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“…The third pattern found in small organic compounds, R:(6), was found so far in protein-protein interactions, for example, in D-xylose isomerase (Carrell et al, 1994) crystal structure solved to a resolution of 1.6 A. In this protein, arginine side chains are the main residues involved in protein-protein interactions.…”

Section: Resultsmentioning

confidence: 99%

Hydrogen bonding motifs of protein side chains: Descriptions of binding of arginine and amide groups

Shimoni

Glusker

1995

Protein Science

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The modes of hydrogen bonding of arginine, asparagine, and glutamine side chains and of urea have been examined in small-molecule crystal structures in the Cambridge Structural Database and in crystal structures of proteinnucleic acid and protein-protein complexes. Analysis of the hydrogen bonding patterns of each by graph-set theory shows three patterns of rings (R) with one or two hydrogen bond acceptors and two donors and with eight, nine, or six atoms in the ring, designated R:(8), R$(9), and Rk(6). These three patterns are found for arginine-like groups and for urea, whereas only the first two patterns R:(8) and Ri(9) are found for asparagine-and glutaminelike groups. In each case, the entire system is planar within 0.7 A or less. On the other hand, in macromolecular crystal structures, the hydrogen bonding patterns in protein-nucleic acid complexes between the nucleic acid base and the protein are all R:(9), whereas hydrogen bonding between Watson-Crick-like pairs of nucleic acid bases is R$(8). These two hydrogen bonding arrangements [R:(9) and R: (8)] are predetermined by the nature of the groups available for hydrogen bonding. The third motif identified, Rl(6), involves hydrogen bonds that are less linear than in the other two motifs and is found in proteins.

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“…It has good stability properties overtime and to radiation. Although, as a tetramer of 173 kDa it is quite large compared to many proteins of interest [13]. We therefore propose the use of monomeric enhanced green fluorescent protein (m-eGFP).…”

Section: Introductionmentioning

confidence: 99%

Monomeric green fluorescent protein as a protein standard for small angle scattering

Myatt

Hatter

Rogers

et al. 2017

BSI

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Abstract. Protein small angle scattering (SAS) has become increasing important in structural biochemistry, due to the increased performance and specification of new instruments and advances in the software and hardware used to analyse the data. Whilst all of this is encouraging, there is a lack of standardised experimental methodology within the community. Although a number of protein standards are currently used in SAS experiments to allow accurate molecular weight determination, each has specific advantages and disadvantages. We therefore propose the use of a mutated monomeric enhanced green fluorescent protein, as a protein standard, abbreviated to m-eGFP. It has a number of advantages over the currently used protein standards, for example it is cheap and easy to produce. It can be expressed in large amounts (>40 mg/L) in both hydrogenated and deuterated form. The mutation means it is highly monodisperse and GFP being a beta-barrel structure is thermodynamically stable over a number of days, giving highly reproducible results. We therefore believe m-eGFP is a good protein standard for small angle scattering (SAS).

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Modes of binding substrates and their analogues to the enzyme D-xylose isomerase

Cited by 60 publications

References 5 publications

THEMATICS: A simple computational predictor of enzyme function from structure

THEMATICS: A simple computational predictor of enzyme function from structure

Hydrogen bonding motifs of protein side chains: Descriptions of binding of arginine and amide groups

Monomeric green fluorescent protein as a protein standard for small angle scattering

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