PDBsum entry 4lzm

Hydrolase (o-glycosyl)

PDB id: 4lzm

Contents

Protein chain

162 a.a.

Ligands

BME

Metals

_CL ×2

Waters ×139

References listed in PDB file

Key reference

Title

Comparison of the crystal structure of bacteriophage t4 lysozyme at low, Medium, And high ionic strengths.

Authors

J.A.Bell, K.P.Wilson, X.J.Zhang, H.R.Faber, H.Nicholson, B.W.Matthews.

Ref.

Proteins, 1991, 10, 10-21.

PubMed id

2062826

Abstract

Crystals of bacteriophage T4 lysozyme used for structural studies are routinely grown from concentrated phosphate solutions. It has been found that crystals in the same space group can also be grown from solutions containing 0.05 M imidazole chloride, 0.4 M sodium choride, and 30% polyethylene glycol 3500. These crystals, in addition, can also be equilibrated with a similar mother liquor in which the sodium chloride concentration is reduced to 0.025 M. The availability of these three crystal variants has permitted the structure of T4 lysozyme to be compared at low, medium, and high ionic strength. At the same time the X-ray structure of phage T4 lysozyme crystallized from phosphate solutions has been further refined against a new and improved X-ray diffraction data set. The structures of T4 lysozyme in the crystals grown with polyethylene glycol as a precipitant, regardless of the sodium chloride concentration, were very similar to the structure in crystals grown from concentrated phosphate solutions. The main differences are related to the formation of mixed disulfides between cysteine residues 54 and 97 and 2-mercaptoethanol, rather than to the differences in the salt concentration in the crystal mother liquor. Formation of the mixed disulfide at residue 54 resulted in the displacement of Arg-52 and the disruption of the salt bridge between this residue and Glu-62. Other than this change, no obvious alterations in existing salt bridges in T4 lysozyme were observed. Neither did the reduction in the ionic strength of the mother liquor result in the formation of new salt bridge interactions. These results are consistent with the ideas that a crystal structure determined at high salt concentrations is a good representation of the structure at lower ionic strengths, and that models of electrostatic interactions in proteins that are based on crystal structures determined at high salt concentrations are likely to be relevant at physiological ionic strengths.

Secondary reference #1

Title

Authors

H.Nicholson, W.Becktel, B.W.Matthews.

Ref.

TO BE PUBLISHED ...

Secondary reference #2

Title

Structural and thermodynamic consequences of burying a charged residue within the hydrophobic core of t4 lysozyme.

Authors

S.Dao-Pin, D.E.Anderson, W.A.Baase, F.W.Dahlquist, B.W.Matthews.

Ref.

Biochemistry, 1991, 30, 11521-11529. [DOI no: 10.1021/bi00113a006]

PubMed id

1747370

Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a percentage match of 96%.

Secondary reference #3

Title

Structure of a hinge-Bending bacteriophage t4 lysozyme mutant, Ile3-->Pro.

Authors

M.M.Dixon, H.Nicholson, L.Shewchuk, W.A.Baase, B.W.Matthews.

Ref.

J Mol Biol, 1992, 227, 917-933. [DOI no: 10.1016/0022-2836(92)90231-8]

PubMed id

1404394

Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a percentage match of 72%.

Figure 2.
GLU S

Figure 9.
Figure 9. (a) Comparison of the backbones f the 4 independent molecules of M6I (Faber & Matthews, 1990) and of WT lysozyme with molecule 13P,. The alignment of the different lysozymes is based on their amino-terminal domams, residues 15 to 60. The Figure shows that 13P, is most similar to M61,. (b) Comparison of the 4 molecules of mutant M61 an of WT with molecule 13Pk. The Figure shows that I3Ps is most similar to M61,.

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #4

Title

Similar hydrophobic replacements of leu99 and phe153 within the core of t4 lysozyme have different structural and thermodynamic consequences.

Authors

A.E.Eriksson, W.A.Baase, B.W.Matthews.

Ref.

J Mol Biol, 1993, 229, 747-769.

PubMed id

8433369

Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a percentage match of 80%.

Secondary reference #5

Title

Folding and function of a t4 lysozyme containing 10 consecutive alanines illustrate the redundancy of information in an amino acid sequence.

Authors

D.W.Heinz, W.A.Baase, B.W.Matthews.

Ref.

Proc Natl Acad Sci U S A, 1992, 89, 3751-3755. [DOI no: 10.1073/pnas.89.9.3751]

PubMed id

1570293

Secondary reference #6

Title

Response of a protein structure to cavity-Creating mutations and its relation to the hydrophobic effect.

Authors

A.E.Eriksson, W.A.Baase, X.J.Zhang, D.W.Heinz, M.Blaber, E.P.Baldwin, B.W.Matthews.

Ref.

Science, 1992, 255, 178-183. [DOI no: 10.1126/science.1553543]

PubMed id

1553543

Secondary reference #7

Title

A cavity-Containing mutant of t4 lysozyme is stabilized by buried benzene.

Authors

A.E.Eriksson, W.A.Baase, J.A.Wozniak, B.W.Matthews.

Ref.

Nature, 1992, 355, 371-373.

PubMed id

1731252

Secondary reference #8

Title

Tolerance of t4 lysozyme to proline substitutions within the long interdomain alpha-Helix illustrates the adaptability of proteins to potentially destabilizing lesions.

Authors

U.H.Sauer, D.P.San, B.W.Matthews.

Ref.

J Biol Chem, 1992, 267, 2393-2399.

PubMed id

1733941

Secondary reference #9

Title

Cumulative site-Directed charge-Change replacements in bacteriophage t4 lysozyme suggest that long-Range electrostatic interactions contribute little to protein stability.

Authors

S.Dao-Pin, E.Söderlind, W.A.Baase, J.A.Wozniak, U.Sauer, B.W.Matthews.

Ref.

J Mol Biol, 1991, 221, 873-887.

PubMed id

1942034

Secondary reference #10

Title

Analysis of the interaction between charged side chains and the alpha-Helix dipole using designed thermostable mutants of phage t4 lysozyme.

Authors

H.Nicholson, D.E.Anderson, S.Dao-Pin, B.W.Matthews.

Ref.

Biochemistry, 1991, 30, 9816-9828. [DOI no: 10.1021/bi00105a002]

PubMed id

1911773

Secondary reference #11

Title

Structural and thermodynamic analysis of the packing of two alpha-Helices in bacteriophage t4 lysozyme.

Authors

S.Daopin, T.Alber, W.A.Baase, J.A.Wozniak, B.W.Matthews.

Ref.

J Mol Biol, 1991, 221, 647-667.

PubMed id

1920439

Secondary reference #12

Title

Contributions of engineered surface salt bridges to the stability of t4 lysozyme determined by directed mutagenesis.

Authors

D.P.Sun, U.Sauer, H.Nicholson, B.W.Matthews.

Ref.

Biochemistry, 1991, 30, 7142-7153. [DOI no: 10.1021/bi00243a015]

PubMed id

1854726

Secondary reference #13

Title

Toward a simplification of the protein folding problem: a stabilizing polyalanine alpha-Helix engineered in t4 lysozyme.

Authors

X.J.Zhang, W.A.Baase, B.W.Matthews.

Ref.

Biochemistry, 1991, 30, 2012-2017. [DOI no: 10.1021/bi00222a001]

PubMed id

1998663

Secondary reference #14

Title

Structure of a thermostable disulfide-Bridge mutant of phage t4 lysozyme shows that an engineered cross-Link in a flexible region does not increase the rigidity of the folded protein.

Authors

P.E.Pjura, M.Matsumura, J.A.Wozniak, B.W.Matthews.

Ref.

Biochemistry, 1990, 29, 2592-2598. [DOI no: 10.1021/bi00462a023]

PubMed id

2334683

Secondary reference #15

Title

Structural studies of mutants of t4 lysozyme that alter hydrophobic stabilization.

Authors

M.Matsumura, J.A.Wozniak, D.P.Sun, B.W.Matthews.

Ref.

J Biol Chem, 1989, 264, 16059-16066.

PubMed id

2674124

Secondary reference #16

Title

High-Resolution structure of the temperature-Sensitive mutant of phage lysozyme, Arg 96----His.

Authors

L.H.Weaver, T.M.Gray, M.G.Grütter, D.E.Anderson, J.A.Wozniak, F.W.Dahlquist, B.W.Matthews.

Ref.

Biochemistry, 1989, 28, 3793-3797. [DOI no: 10.1021/bi00435a025]

PubMed id

2665808

Secondary reference #17

Title

Contributions of left-Handed helical residues to the structure and stability of bacteriophage t4 lysozyme.

Authors

H.Nicholson, E.Söderlind, D.E.Tronrud, B.W.Matthews.

Ref.

J Mol Biol, 1989, 210, 181-193.

PubMed id

2511328

Secondary reference #18

Title

Hydrophobic stabilization in t4 lysozyme determined directly by multiple substitutions of ile 3.

Authors

M.Matsumura, W.J.Becktel, B.W.Matthews.

Ref.

Nature, 1988, 334, 406-410.

PubMed id

3405287

Secondary reference #19

Title

Enhanced protein thermostability from designed mutations that interact with alpha-Helix dipoles.

Authors

H.Nicholson, W.J.Becktel, B.W.Matthews.

Ref.

Nature, 1988, 336, 651-656.

PubMed id

3200317

Secondary reference #20

Title

Replacements of pro86 in phage t4 lysozyme extend an alpha-Helix but do not alter protein stability.

Authors

T.Alber, J.A.Bell, D.P.Sun, H.Nicholson, J.A.Wozniak, S.Cook, B.W.Matthews.

Ref.

Science, 1988, 239, 631-635. [DOI no: 10.1126/science.3277275]

PubMed id

3277275

Secondary reference #21

Title

Enhanced protein thermostability from site-Directed mutations that decrease the entropy of unfolding.

Authors

B.W.Matthews, H.Nicholson, W.J.Becktel.

Ref.

Proc Natl Acad Sci U S A, 1987, 84, 6663-6667. [DOI no: 10.1073/pnas.84.19.6663]

PubMed id

3477797

Secondary reference #22

Title

Structural analysis of the temperature-Sensitive mutant of bacteriophage t4 lysozyme, Glycine 156----Aspartic acid.

Authors

T.M.Gray, B.W.Matthews.

Ref.

J Biol Chem, 1987, 262, 16858-16864.

PubMed id

3680274

Secondary reference #23

Title

Contributions of hydrogen bonds of thr 157 to the thermodynamic stability of phage t4 lysozyme.

Authors

T.Alber, D.P.Sun, K.Wilson, J.A.Wozniak, S.P.Cook, B.W.Matthews.

Ref.

Nature, 1987, 330, 41-46.

PubMed id

3118211

Secondary reference #24

Title

Structural studies of mutants of the lysozyme of bacteriophage t4. The temperature-Sensitive mutant protein thr157----Ile.

Authors

M.G.Grütter, T.M.Gray, L.H.Weaver, T.A.Wilson, B.W.Matthews.

Ref.

J Mol Biol, 1987, 197, 315-329.

PubMed id

3681997

Secondary reference #25

Title

Structure of bacteriophage t4 lysozyme refined at 1.7 a resolution.

Authors

L.H.Weaver, B.W.Matthews.

Ref.

J Mol Biol, 1987, 193, 189-199.

PubMed id

3586019

Secondary reference #26

Title

Temperature-Sensitive mutations of bacteriophage t4 lysozyme occur at sites with low mobility and low solvent accessibility in the folded protein.

Authors

T.Alber, D.P.Sun, J.A.Nye, D.C.Muchmore, B.W.Matthews.

Ref.

Biochemistry, 1987, 26, 3754-3758. [DOI no: 10.1021/bi00387a002]

PubMed id

3651410

Secondary reference #27

Title

Common precursor of lysozymes of hen egg-White and bacteriophage t4.

Authors

B.W.Matthews, M.G.Grütter, W.F.Anderson, S.J.Remington.

Ref.

Nature, 1981, 290, 334-335.

PubMed id

7207627

Secondary reference #28

Title

Crystallographic determination of the mode of binding of oligosaccharides to t4 bacteriophage lysozyme: implications for the mechanism of catalysis.

Authors

W.F.Anderson, M.G.Grütter, S.J.Remington, L.H.Weaver, B.W.Matthews.

Ref.

J Mol Biol, 1981, 147, 523-543. [DOI no: 10.1016/0022-2836(81)90398-3]

PubMed id

7277499

Figure 4.
FIN. 4. (a) Stereo drawing showing the diterence density (lcNAc,,-native) (b) Elert,ron density ap ith coeficients (4F,,,,.,,,,-3Fx,, 1.

Figure 6.
FIG. 6. View of the presumed binding of a pentasaccharide in the active sik of phage Iq'sozyme.

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #29

Title

Relation between hen egg white lysozyme and bacteriophage t4 lysozyme: evolutionary implications.

Authors

B.W.Matthews, S.J.Remington, M.G.Grütter, W.F.Anderson.

Ref.

J Mol Biol, 1981, 147, 545-558. [DOI no: 10.1016/0022-2836(81)90399-5]

PubMed id

7277500

Figure 5.
FIG. 5. Schematic drawing comparing the saccharie-protein interaction in phage lysozyme (names in parentheses) and hen egg white lyszyme. The hatched line illustrat,es the apparent close contact that owu~`s hen saccharide D is in the normal chair conformat.ion.

Figure 6.
FIG:. 6. Superosition of common elements of the phage lysozyme active site (solid bonds and names nderlined) onto hen egg white lysozyme. (a) Mono view looking into the active site cleft. (b) Stereo vie along z. i.e. approximately at right angles to that shown in (a).

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #30

Title

Structure of the lysozyme from bacteriophage t4: an electron density map at 2.4 a resolution.

Authors

S.J.Remington, W.F.Anderson, J.Owen, L.F.Ten eyck, C.T.Grainger, B.W.Matthews.

Ref.

J Mol Biol, 1978, 118, 81-98. [DOI no: 10.1016/0022-2836(78)90245-0]

PubMed id

625058

Figure 5.
FIG. 5. Schemaic illustration of the p-sheet region of T4 phage lysozyme.

Figure 6.
FIG. 6. Conformation angls for T4 phage lysozyme; glycine residues are indicated by open circles. he allowed regions for a hard-sphere model (Ramachandran & Sasisekharan, 1968) are indicated by solid lines, and those preicted by a quantum mechanical method (Pullman et ~1.. 1970) are indicated by a broken line.

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #31

Title

Atomic coordinates for t4 phage lysozyme.

Authors

S.J.Remington, L.F.Eyck, B.W.Matthews.

Ref.

Biochem Biophys Res Commun, 1977, 75, 265-270.

PubMed id

322662

Secondary reference #32

Title

Comparison of the predicted and observed secondary structure of t4 phage lysozyme.

Author

B.W.Matthews.

Ref.

Biochim Biophys Acta, 1975, 405, 442-451.

PubMed id

1180967

Secondary reference #33

Title

The three dimensional structure of the lysozyme from bacteriophage t4.

Authors

B.W.Matthews, S.J.Remington.

Ref.

Proc Natl Acad Sci U S A, 1974, 71, 4178-4182. [DOI no: 10.1073/pnas.71.10.4178]

PubMed id

4530293

Secondary reference #34

Title

Letter: crystallographic data fro lysoxyme from bacteriophage t4.

Authors

B.W.Matthews, F.W.Dahlquist, A.Y.Maynard.

Ref.

J Mol Biol, 1973, 78, 575-576.

PubMed id

4754847