Refined structure of human carbonic anhydrase II at 2.0 Å resolution

Eriksson, Anders; Jones, T. Alwyn; Liljas, Anders

doi:10.1002/prot.340040406

Cited by 548 publications

(569 citation statements)

References 25 publications

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“…Wilson plots (Wilson, 1942) revealed that the data for inhibitors l a and Ib were usable to 2.1 A, while the IC complex was usable to 1.6 A. Model building was started using the refined native structure (Eriksson et al, 1988) as taken from the Protein Data Bank (Bernstein et al, 1977). To begin the refine- …”

Section: Methodsmentioning

confidence: 99%

“…Movement of the side chain of His-64 has also been implicated in the enzyme mechanism (Tu et al, 1989;Krebs et al, 1991;Nair & Christianson, 1991). Therefore, the observation of a change in the position of the side chain of His-64 between the native enzyme (Eriksson et al, 1988) and that inhibited by I C (Baldwin et al, 1992) (Fig. 1) led us to the question of whether inhibitors l a and Ib, with shorter side chains on the nitrogen, would also alter the position of His-64 and the adjacent water.…”

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confidence: 99%

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Positions of His‐64 and a bound water in human carbonic anhydrase II upon binding three structurally related inhibitors

et al. 1994

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The 3-dimensional structure of human carbonic anhydrase I1 (HCAII; EC 4.2.1.1) complexed with 3 structurally related inhibitors, l a , l b , and I C , has been determined by X-ray crystallographic methods. The 3 inhibitors ( l a = C8H,2N204S3) vary only in the length of the substituent on the 4-amino group: l a , proton; Ib, methyl; and IC, ethyl. The binding constants (Ki's) for la, Ib, and I C to HCAII are 1.52, 1.88, and 0.37 nM, respectively. These structures were solved to learn if any structural cause could be found for the difference in binding. In the complex with inhibitors l a and l b , electron density can be observed for His-64 and a bound water molecule in the native positions. When inhibitor IC is bound, the side chain attached to the 4-amino group is positioned so that His-64 can only occupy the alternate position and the bound water is absent. While a variety of factors contribute to the observed binding constants, the major reason IC binds tighter to HCAII than does l a or l b appears to be entropy: the increase in entropy when the bound water molecule is released contributes to the increase in binding and overcomes the small penalty for putting the His-64 side chain in a higher energy state.

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Section: Methodsmentioning

confidence: 99%

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confidence: 99%

Positions of His‐64 and a bound water in human carbonic anhydrase II upon binding three structurally related inhibitors

et al. 1994

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“…The X-ray structure determinations indicate that these isoenzymes are essentially identical with respect to tertiary and secondary structures (Kannan et al, 1975;Eriksson et al, 1988; Hkkansson et al, 1992;Eriksson & Liljas, 1993), but differ in 2479…”

Section: Introductionmentioning

confidence: 97%

A comparative CD study of carbonic anhydrase isoenzymes with different number of tryptophans: Impact on calculation of secondary structure content

Borén¹,

Freskgård²,

Carlsson³

1996

Protein Science

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The CD spectra of human carbonic anhydrase I and I1 and bovine carbonic anhydrase 111 were recorded and analyzed. The 3D structures of these isoenzymes are known, showing very similar secondary structure and polypeptide-chain fold. The tryptophan content, however, differs between the isoenzymes, i.e., isoenzymes I, 11, and 111 possess 6, 7, and 8 tryptophans, respectively. All of the tryptophans except the additional tryptophans in isoenzymes I1 and 111, i.e., W245 and W47, are conserved. Despite the fact that X-ray structure determinations showed that the isoenzymes had highly similar secondary structure, the contents of a-helix and p-sheet structure differed considerably when using different CD algorithms for estimation of the fractions of various secondary structural elements. This shows that aromatic amino acids also interfere in the wavelength region (far-UV) used to calculate the amount of secondary structure. Such interference is especially problematic when analyzing proteins like carbonic anhydrase, which consist mainly of p-structure that gives rise to weak ellipticity bands, compared to the bands arising from a-helical structure.Keywords: aromatic amino acids; bovine carbonic anhydrase 111; p-structure; human carbonic anhydrase I and I1Proteins exhibit characteristic CD spectra in the far-UV region and the appearance of these spectra are related to the presence of secondary structure (Greenfield & Fasman, 1969 Compton & Johnson, 1986;Manavalan &Johnson, 1987;Perczel et al., 1991). Knowledge of the secondary structure is of great importance in the understanding of the function, stability, and folding of a protein, and CD estimations of the amount of a-helices have been particularly accurate for many proteins. On the other hand, it has been more difficult to predict the contents of p-structure (Sreerama & Woody, 1994). One obvious reason for this is that the a-helix spectrum dominates the protein far-UV CD spectrum (Johnson, 1990;Sreerama & Woody, 1993), and the CD signal arising from p-structure is of lower intensity. This means that calculations of the amount of this type of secondary structure are more sensitive to perturbations from other contributing structural elements. Based on theoretical calculations and experimental evidence from peptide models, it has been suggested that aromatic amino acids make contributions to the far-UV CD spectrum (Strickland, 1974; ManReprint ning & Woody, 1989;Manning et al., 1992). Because this wavelength region is used. for estimation of the amount of secondary structure and the models used do not consider aromatic contributions explicitly, aromatic amino acids could seriously interfere with such calculations. In a recent study, we used site-directed mutagenesis to replace one Trp at a time in human carbonic anhydrase I1 (HCA 11) in order to assign the contribution of each of the Trp residues to the CD spectrum (Freskgkd et al., 1994). We found that the individual Trp residues contributed to the CD spectrum not only in the near-UV wavelength region, but also...

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“…Hydroxide ion, which is the catalytic nucleophile in the CO 2 hydration mechanism, completes a tetrahedral metal coordination polyhedron. Zinc-bound hydroxide donates a hydrogen bond to the hydroxyl group of Thr-199, which in turn donates a hydrogen bond to Glu-106 (Eriksson et al, 1986(Eriksson et al, , 1988aHåkansson et al, 1992). The binding of sulfonamide inhibitors displaces zinc-bound hydroxide and maintains the tetrahedral metal coordination polyhedron by the coordination of an ionized sulfonamide NH group, which also maintains the hydrogen bond interaction with Thr-199 (e.g.…”

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confidence: 99%

Unexpected Binding Mode of the Sulfonamide Fluorophore 5-Dimethylamino-1-naphthalene Sulfonamide to Human Carbonic Anhydrase II

Nair¹,

Elbaum²,

Christianson³

1996

Journal of Biological Chemistry

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The three-dimensional structure of human carbonic anhydrase II (CAII) complexed with the sulfonamide fluorophore 5-dimethylamino-1-naphthalene sulfonamide (dansylamide) has been determined to 2.1-Å resolution by x-ray crystallographic methods. Unlike other arylsulfonamide inhibitors of CAII, the naphthyl ring of dansylamide binds in a hydrophobic pocket in the active site, making van der Waals contacts with Val-121, Phe-131, Val-143, Leu-198, and Trp-209. Interestingly, a conformational change of Leu-198 is required to accommodate dansylamide binding, which rationalizes the enhanced dansylamide affinity measured for certain Sensors based upon biological macromolecules are increasingly used for the selective detection of numerous chemical entities, including the detection of trace quantities of metal ions. The advantages of metalloprotein-based biosensors over classical fluorometric chemical indicators for such applications include greater recognition and affinity for the target metal ion, exquisite discrimination among transition metals, and kinetically rapid biosensor-analyte association and dissociation. Recently, Thompson and Jones (1993) have exploited the selective recognition of zinc by the metalloenzyme carbonic anhydrase II (CAII) 1 in the design of an enzyme-based zinc biosensor. The physical basis of this sensor is the binding of zinc to the CAII apoenzyme, followed by binding of the fluorophore inhibitor 5-dimethylamino-1-naphthalene sulfonamide (dansylamide, K d ϭ 0.93 M (Nair et al., 1995); see Fig. 1) to the zinccontaining CAII holoenzyme. This leads to a titratable change in the fluorescence emission wavelength and intensity (Chen and Kernohan, 1967); nanomolar concentrations of zinc can be detected and quantified by ratiometric methods by measuring the emission of free dansylamide at 580 nm and the emission of bound dansylamide at 470 nm when excited at 290 nm.The zinc ion of CAII resides at the base of a 15-Å deep cleft, where it is liganded by the imidazole side chains of His-94, His-96, and His-119 (Håkansson et al., 1992). Hydroxide ion, which is the catalytic nucleophile in the CO 2 hydration mechanism, completes a tetrahedral metal coordination polyhedron. Zinc-bound hydroxide donates a hydrogen bond to the hydroxyl group of Thr-199, which in turn donates a hydrogen bond to Glu-106 (Eriksson et al., 1986, 1988aHåkansson et al., 1992). The binding of sulfonamide inhibitors displaces zinc-bound hydroxide and maintains the tetrahedral metal coordination polyhedron by the coordination of an ionized sulfonamide NH group, which also maintains the hydrogen bond interaction with Thr-199 (e.g. see Eriksson et al. (1988b) and Vidgren et al.

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Refined structure of human carbonic anhydrase II at 2.0 Å resolution

Cited by 548 publications

References 25 publications

Positions of His‐64 and a bound water in human carbonic anhydrase II upon binding three structurally related inhibitors

Positions of His‐64 and a bound water in human carbonic anhydrase II upon binding three structurally related inhibitors

A comparative CD study of carbonic anhydrase isoenzymes with different number of tryptophans: Impact on calculation of secondary structure content

Unexpected Binding Mode of the Sulfonamide Fluorophore 5-Dimethylamino-1-naphthalene Sulfonamide to Human Carbonic Anhydrase II

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