Refinement of human lysozyme at 1.5 Å resolution analysis of non-bonded and hydrogen-bond interactions

Artymiuk, Peter J.; Blake, C. C. F.

doi:10.1016/0022-2836(81)90125-x

Cited by 279 publications

(126 citation statements)

References 40 publications

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“…On the contrary, some amyloidogenic proteins retain their native structures before undergoing conformational transition and eventual fibril formation (55). This group of proteins include prion (56), β2-microglobulin (β2m) (57,58), lysozyme (59,60), transthyretin (TTR) (61), and the variable region of immunoglobulin lightchain (VL) (62), which are responsible for mad cow disease (63), dialysis-related amyloidosis (64), hereditary systemic amyloidosis http://bmbreports.org BMB reports (65), senile systemic amyloidosis (61) and light-chain amyloidosis (62), respectively. In addition, apomyoglobin prepared by phase separation using the acid methylethylketone method (66) formed amyloid-like structures upon denaturation in 50 mM sodium borate, pH 9.0, at 65 o C, suggesting that amyloid fibril formation could be considered a generic phenomena of proteins as they experience misfolded structures (67,68).…”

Section: Various Amyloidogenic Proteinsmentioning

confidence: 99%

Mechanism of amyloidogenesis: nucleation-dependent fibrillation versus double-concerted fibrillation

Bhak

Choe²,

Paik

2009

BMB Reports

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Section: Various Amyloidogenic Proteinsmentioning

confidence: 99%

Mechanism of amyloidogenesis: nucleation-dependent fibrillation versus double-concerted fibrillation

Bhak

Choe²,

Paik

2009

BMB Reports

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“…Several structures of chicken-type lysozymes (Moult et al, 1976;Aschaffenburg et al, 1980;Hogle et al, 1981;Artymiuk & Blake, 1981;Artymiuk, Blake, Rice & Wilson, 1982;Berthou, Lifchitz, Artymiuk & Jolles, 1983;Kundrot & Richards, 1987;Kodandapani, Suresh & Vijayan, 1990), including antigen-antibody complexes (Amit, Mariuzza, Phillips & Poljak, 1986;Sheriff et al, 1987), have been reported. The active site of HEL consists of six subsites designated A to F and binds not only substrate polysaccharides but also mono-and oligosaccharides of substrate analogues (Blake et al, 1967;Kelly, Sielecki, Sykes, James & Phillips, 1979).…”

Section: Introductionmentioning

confidence: 99%

X-ray structure of monoclinic turkey egg lysozyme at 1.3 Å resolution

Harata

1993

Acta Cryst D

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Monoclinic crystals of turkey egg lysozyme (TEL, E.C. 3.2.1.17) were obtained from 2.2 M ammonium sulfate solution at pH 4.2. They belong to space group P2~ with unit-cell dimensions a = 38.07, b = 33.20, c = 46.12 A and 13 = 110.1 °, and contain one molecule in the asymmetric unit (V,,, = 1.91 A 3 Da-I). The three-dimensional structure of TEL was solved by the method of multiple isomorphous replacement with anomalous scattering. Area detector data to !.5 A resolution from native and heavy-atom derivatives were used for the structure determination. The structure was refined by the simulated-annealing method with diffraction data of 10-1.30 A resolution. The conventional R factor was 0.189. The root-mean-square deviations from ideal bond distances and angles were 0.016 A and 2.9 '~, respectively. The backbone structure of TEL is very similar to that of hen egg lysozyme (HEL) and the difference in seven amino-acid residues does not affect the basic folding of the polypeptide chain. Except for the region from Glyl01 to Glyl04, the geometry of the active-site cleft is conserved between TEL and HEL. The Glyl01 residue is located at the end of the sugar-binding site and the structural change in this region between TEL and HEL is considered to be responsible for the difference in their enzymatic properties.

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“…"Omit maps" (30) were calculated to remove potential bias from the model phases. The current R factor at 2.8 A is 38.3%.…”

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confidence: 99%

Three-dimensional structure of the bifunctional enzyme N-(5'-phosphoribosyl)anthranilate isomerase-indole-3-glycerol-phosphate synthase from Escherichia coli.

Priestle¹,

Grütter²,

White³

et al. 1987

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

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N-(5'-Phosphoribosyl)anthranilate isomerase-indole-3-glycerol-phosphate synthase from Escherichia coli is a monomeric bifunctional enzyme ofMr 49,500 that catalyzes two sequential reactions in the biosynthesis of tryptophan. The three-dimensional structure ofthe enzyme has been determined at 2.8-A resolution by x-ray crystallography. The two catalytic activities reside on distinct functional domains of similar folding, that of an eightfold parallel ,8-barrel with a-helices on the outside connecting the f8-strands. Both active sites were located with an iodinated substrate analogue and found to be in depressions on the surface of the domains created by the outward-curving loops between the carboxyl termini of the ,8-sheet strands and the subsequent a-helices. They do not face each other, making "channeling" of the substrate between active sites virtually impossible. Despite the structural similarity of the two domains, no significant sequence homology was found when topologically equivalent residues were compared. MATERIALS AND METHODS Crystals of PRAI-IGPS were obtained as described (14,15). They belong to space group P41 with unit cell parameters a = b = 104.7 A, c = 68.0 A, and one molecule per asymmetric unit (67% solvent content). Screening of heavy atom derivatives was done by soaking crystals in a buffered solution of the appropriate heavy atom compound in 3 M ammonium sulfate (Table 1). For potentially useful derivatives, a low-resolution diffractometer data set was collected, while oscillation data sets to 2.5-A resolution were collected for the three best derivatives. One derivative was prepared by diffusing an iodinated form of the substrate analogue N-(5'-phosphoribit-1-yl)anthranilate (rCdRP) into the crystals. 5-Iodo-rCdRP was prepared as described for rCdRP (16) except that 5-iodoanthranilate (Fluka) was used in place of anthranilate as starting material and was dissolved in dioxane instead of in 50% aqueous ethanol.The crystals were mounted in thin-walled glass capillaries. Diffractometer data were collected as described elsewhere (17) with the following modifications: after crystal alignment, a single test reflection was used to determine the direction of the c-axis of the crystal; several crystals were required per data set due to strong radiation sensitivity; a maximum intensity loss of about 30% was accepted; and intensities were measured by c-scan over 0.8-1.5°, depending on mosaic spread.Oscillation data were collected and processed as described elsewhere (18) with the following modifications: a cooling device kept the crystal at about 40C; data were collected over 900; two sheets of film per film pack were used; crystal orientation was checked by still photographs at the beginning and end of data collection; and the films were digitized, using a 3.0 OD scale.The oscillation and diffractometer data sets (Table 1) were not merged at this point. Heavy atom sites were accepted only if found with both sets of data. They were located by difference Patterson and difference Fourier techniqu...

show abstract

Refinement of human lysozyme at 1.5 Å resolution analysis of non-bonded and hydrogen-bond interactions

Cited by 279 publications

References 40 publications

Mechanism of amyloidogenesis: nucleation-dependent fibrillation versus double-concerted fibrillation

Mechanism of amyloidogenesis: nucleation-dependent fibrillation versus double-concerted fibrillation

X-ray structure of monoclinic turkey egg lysozyme at 1.3 Å resolution

Three-dimensional structure of the bifunctional enzyme N-(5'-phosphoribosyl)anthranilate isomerase-indole-3-glycerol-phosphate synthase from Escherichia coli.

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