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

Harata, Kazuaki

doi:10.1107/s0907444993005542

Cited by 27 publications

(23 citation statements)

References 16 publications

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“…1. The backbone structure of TEL is essentially the same as the structure of native TEL (Harata, 1993). The r.m.s.…”

Section: Structure Of Telmentioning

confidence: 52%

“…When the NAG2 molecule is adopted in the cleft, the sugar molecule excludes the water molecules, some of which are hydrogen bonded to residues, Glu35, Gln57, Asn59, Trp63, Alal07, Vail09, etc. (Harata, 1993). The two lobes of the cleft are so moved that these residues form hydrogen bonds with NAG2 and are found to be in favorable van der Waals contacts.…”

Section: Discussionmentioning

confidence: 92%

“…The carboxyl group of Aspl01 forms a hydrogen bond with a sugar residue of NAG3 (Blake et al, 1967;Ford, Johnson, Machin, Phillips & Tjian, 1974;Strynadka & James, 1991;Cheetham, Artymiuk & Phillips, 1992). In the previous paper, we have reported the structure of a monoclinic form of TEL at 1.3 A resolution and demonstrated that the conformation of the region of residues 100-104 differs between TEL and HEL (Harata, 1993). The structural difference in the subsite A may affect the binding geometry of the substrate saccharide.…”

Section: Introductionmentioning

confidence: 99%

“…Crystals of TEL were prepared according to the previously reported method (Harata, 1993). The complex with NAG2 was prepared by the soaking method.…”

Section: Crystallization and Data Collectionmentioning

confidence: 99%

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X-ray structure of turkey egg lysozyme complex with di-N-acetyl-chitobiose. Recognition and binding of α-anomeric form

Harata¹,

Muraki²

1995

Acta Cryst D

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The crystalline complex of turkey-egg lysozyme (TEL) with di-N-acetylchitobiose (NAG2) was prepared by a soaking method and the structure was determined by Xray analysis at 1.55/~, resolution. The structure was refined to an R value of 0.175 by simulated annealing and energy minimization. The a-anomer of NAG2 is located at subsite D with the orientation perpendicular to the direction of the active-site cleft. The anomeric residue is deeply inserted into the cleft and the O1 --H hydroxyl group is hydrogen bonded to the carboxyl group of Glu35 which is a catalytic residue. The other sugar residue protrudes outside the cleft and is in van der Waals contact with the E-sheet region comprising of residues 43-53. The binding of NAG2 makes the activesite cleft 0.3-0.5 ,~ narrower and supresses the thermal motion of two lobes constructing the cleft. The NAG2 molecule is bound in a manner not assumed in the catalytic action of the enzyme and the geometry of binding indicates that the a-anomer blocks the active center and acts only as an inhibitor.

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“…1. The backbone structure of TEL is essentially the same as the structure of native TEL (Harata, 1993). The r.m.s.…”

Section: Structure Of Telmentioning

confidence: 52%

Section: Discussionmentioning

confidence: 92%

Section: Introductionmentioning

confidence: 99%

“…Crystals of TEL were prepared according to the previously reported method (Harata, 1993). The complex with NAG2 was prepared by the soaking method.…”

Section: Crystallization and Data Collectionmentioning

confidence: 99%

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X-ray structure of turkey egg lysozyme complex with di-N-acetyl-chitobiose. Recognition and binding of α-anomeric form

Harata¹,

Muraki²

1995

Acta Cryst D

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“…TEWL has also been crystallized in a monoclinic space group and the structure solved at 1.3 A resolution (Harata, 1993). Turkey egg-white lysozyme belongs to the type C class of lysozymes which have been studied extensively using X-ray crystallographic techniques (Blake et al, 1965;Moult et al, 1976;Aschaffenburg et al, 1980;Artymiuk & Blake, 1981;Artymiuk, Blake, Rice & Wilson, 1982;Berthou, Lifchitz, Artymiuk & Joll6s, 1983;Kundrot & Richards, 1987;Kodandapani, Suresh & Vijayan, 1990;Ramanadham, Sieker & Jensen, 1989;Rao, Hogle & Sundaralingam, 1983;Parsons & Phillips, 1988;Howell, Almo, Parsons, Hajdu & Petsko, 1992;Harata, 1993;Lescar, Souchon & Alzari, 1994;Turner & Howell, 1995a).…”

Section: Introductionmentioning

confidence: 99%

Structure of hexagonal turkey egg-white lysozyme at 1.65Å resolution

Howell¹

1995

Acta Cryst D

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The structure of hexagonal turkey egg-white lysozyme (TEWL) has been determined and refined at 1.65 A resolution. The crystals were grown from a 150mM potassium thiocyanate solution at pH 4.5 and belong to space group P6122 with unit-cell dimensions a = b = 70.96, c = 83.01 ~, ot = ~ = 90, 3' = 120 °. The crystals were isomorphous with those of hexagonal pH 8.0 TEWL. The coordinates of PDB entry code 3LZ2 were therefore used as the initial model and subjected to rigidbody refinement, simulated annealing and least-squares refinement to a final residual of 0.20. The root-meansquare deviations from the ideal bond distances and angles were 0.016/~, and 2.2 °, respectively. During the refinement, 86 water molecules and one thiocyanate ion were located in the structure. The thiocyanate ion lies close to the interface between two symmetry-related molecules. The S atom of the ion forms two direct intermolecular contacts with Argl4 and interacts indirectly via a network of water molecules to Arg5 of a symmetryrelated molecule. The structure provides direct evidence for the mode of thiocyanate binding to arginine residues and suggests a possible mechanism for the efficiency of thiocyanate in crystallizing basic proteins.

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Full-matrix least-squares refinement of lysozymes and analysis of anisotropic thermal motion

1998

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Crystal structures of turkey egg lysozyme (TEL) and human lysozyme (HL) were refined by full-matrix least-squares method using anisotropic temperature factors. The refinement converged at the conventional R-values of 0.104 (TEL) and 0.115 (HL) for reflections with Fo > 0 to the resolution of 1.12 A and 1.15 A, respectively. The estimated r.m.s. coordinate errors for protein atoms were 0.031 A (TEL) and 0.034 A (HL). The introduction of anisotropic temperature factors markedly reduced the R-value but did not significantly affect the main chain coordinates. The degree of anisotropy of atomic thermal motion has strong positive correlation with the square of distance from the molecular centroid. The ratio of the radial component of thermal ellipsoid to the r.m.s. magnitude of three principal components has negative correlation with the distance from the molecular centroid, suggesting the domination of libration rather than breathing motion. The TLS model was applied to elucidate the characteristics of the rigid-body motion. The TLS tensors were determined by the least-squares fit to observed temperature factors. The profile of the magnitude of reproduced temperature factors by the TLS method well fitted to that of observed B(eqv). However, considerable disagreement was observed in the shape and orientation of thermal ellipsoid for atoms with large temperature factors, indicating the large contribution of local motion. The upper estimate of the external motion, 67% (TEL) and 61% (HL) of B(eqv), was deduced from the plot of the magnitude of TLS tensors determined for main chain atoms which were grouped into shells according to the distance from the center of libration. In the external motion, the translational portion is predominant and the contribution of libration and screw motion is relatively small. The internal motion, estimated by subtracting the upper estimate of the external motion from the observed temperature factor, is very similar between TEL and HL in spite of the difference in 54 of 130 amino acid residues and in crystal packing, being suggested to reflect the intrinsic internal motion of chicken-type lysozymes.

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

Cited by 27 publications

References 16 publications

X-ray structure of turkey egg lysozyme complex with di-N-acetyl-chitobiose. Recognition and binding of α-anomeric form

X-ray structure of turkey egg lysozyme complex with di-N-acetyl-chitobiose. Recognition and binding of α-anomeric form

Structure of hexagonal turkey egg-white lysozyme at 1.65Å resolution

Full-matrix least-squares refinement of lysozymes and analysis of anisotropic thermal motion

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