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PDBsum entry 1l77
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Hydrolase (o-glycosyl) PDB id
1l77

 

 

 

 

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Contents
Protein chain
162 a.a. *
Ligands
BME-BME
Metals
_CL ×2
Waters ×99
* Residue conservation analysis
PDB id:
1l77
Name: Hydrolase (o-glycosyl)
Title: Design and structural analysis of alternative hydrophobic core packing arrangements in bacteriophage t4 lysozyme
Structure: T4 lysozyme. Chain: a. Engineered: yes
Source: Enterobacteria phage t4. Organism_taxid: 10665.
Biol. unit: Dimer (from PQS)
Resolution:
2.05Å     R-factor:   0.159    
Authors: J.H.Hurley,B.W.Matthews
Key ref: J.H.Hurley et al. (1992). Design and structural analysis of alternative hydrophobic core packing arrangements in bacteriophage T4 lysozyme. J Mol Biol, 224, 1143-1159. PubMed id: 1569571
Date:
12-Nov-91     Release date:   15-Apr-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00720  (ENLYS_BPT4) -  Endolysin from Enterobacteria phage T4
Seq:
Struc: 		164 a.a.
162 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.17  - lysozyme.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of the 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.

 

 
J Mol Biol 224:1143-1159 (1992)
PubMed id: 1569571  
 
 
Design and structural analysis of alternative hydrophobic core packing arrangements in bacteriophage T4 lysozyme.
J.H.Hurley, W.A.Baase, B.W.Matthews.
 
  ABSTRACT  
 
An attempt has been made to design modified core-packing arrangements in bacteriophage T4 lysozyme. Alternative replacements of the buried residues Leu99, Met102, Val111 and Phe153 were selected using packing calculations and energy minimization. To test the design procedure, a series of multiple mutants was constructed culminating in the replacement L99F/M102L/V111I/F153L. These variants decrease the stability of T4 lysozyme by approximately 0 to 2 kcal/mol. The crystal structures of a number of the variants were determined. In the variant in which Val111 was replaced by Ile, alpha-helix 107-114 moved by approximately 1.5 A, breaking the hydrogen bond between the backbone carbonyl group of Thr109 and the backbone amide group of Gly113. This conformational change was not anticipated by the design procedure. Compensating interactions of magnitude up to 1.1 kcal/mol occur for some sets of mutations, while other sets display nearly additive stability changes. Within experimental error, the stability of the double mutant V111F/F153L is additive, with delta delta G different by only 0.1 kcal/mol from the sum of the two single mutants. The quadruple mutant L99F/M102L/V111I/F153L is destabilized by 0.5 kcal/mol, compared to delta delta G = -1.6 kcal/mol for the sum of the four single mutants. Multiple mutants show smaller overall structural changes from wild-type than M102L or V111I alone. Co-operative changes in structure and stability can be rationalized in terms of specific structural differences between single and multiple mutants. Genuine repacking of the hydrophobic core of T4 lysozyme with minimal effects on structure, stability and activity thus appears to have been achieved.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20422176 C.M.Theriot, X.Du, S.R.Tove, and A.M.Grunden (2010).
Improving the catalytic activity of hyperthermophilic Pyrococcus prolidases for detoxification of organophosphorus nerve agents over a broad range of temperatures.
  Appl Microbiol Biotechnol, 87, 1715-1726.  
20095051 W.A.Baase, L.Liu, D.E.Tronrud, and B.W.Matthews (2010).
Lessons from the lysozyme of phage T4.
  Protein Sci, 19, 631-641.  
19324680 M.Suárez, and A.Jaramillo (2009).
Challenges in the computational design of proteins.
  J R Soc Interface, 6, S477-S491.  
18780783 L.Liu, M.L.Quillin, and B.W.Matthews (2008).
Use of experimental crystallographic phases to examine the hydration of polar and nonpolar cavities in T4 lysozyme.
  Proc Natl Acad Sci U S A, 105, 14406-14411.
PDB code: 3dke
17208969 A.Ghosh, K.V.Brinda, and S.Vishveshwara (2007).
Dynamics of lysozyme structure network: probing the process of unfolding.
  Biophys J, 92, 2523-2535.  
17222055 K.B.Zeldovich, I.N.Berezovsky, and E.I.Shakhnovich (2007).
Protein and DNA sequence determinants of thermophilic adaptation.
  PLoS Comput Biol, 3, e5.  
18029422 K.L.Schweiker, A.Zarrine-Afsar, A.R.Davidson, and G.I.Makhatadze (2007).
Computational design of the Fyn SH3 domain with increased stability through optimization of surface charge charge interactions.
  Protein Sci, 16, 2694-2702.  
16120678 I.N.Berezovsky, and E.I.Shakhnovich (2005).
Physics and evolution of thermophilic adaptation.
  Proc Natl Acad Sci U S A, 102, 12742-12747.  
15313244 S.Park, X.Yang, and J.G.Saven (2004).
Advances in computational protein design.
  Curr Opin Struct Biol, 14, 487-494.  
15162481 S.Ventura, and L.Serrano (2004).
Designing proteins from the inside out.
  Proteins, 56, 1.  
12634013 S.A.Marshall, G.A.Lazar, A.J.Chirino, and J.R.Desjarlais (2003).
Rational design and engineering of therapeutic proteins.
  Drug Discov Today, 8, 212-221.  
14627732 S.R.Brych, J.Kim, T.M.Logan, and M.Blaber (2003).
Accommodation of a highly symmetric core within a symmetric protein superfold.
  Protein Sci, 12, 2704-2718.
PDB codes: 1jy0 1m16 1nzk 1p63
12142453 A.L.Lomize, M.Y.Reibarkh, and I.D.Pogozheva (2002).
Interatomic potentials and solvation parameters from protein engineering data for buried residues.
  Protein Sci, 11, 1984-2000.  
11173468 C.Qu, S.Akanuma, N.Tanaka, H.Moriyama, and T.Oshima (2001).
Design, X-ray crystallography, molecular modelling and thermal stability studies of mutant enzymes at site 172 of 3-isopropylmalate dehydrogenase from Thermus thermophilus.
  Acta Crystallogr D Biol Crystallogr, 57, 225-232.
PDB codes: 1g2u 1gc8 1gc9
11714927 S.R.Brych, S.I.Blaber, T.M.Logan, and M.Blaber (2001).
Structure and stability effects of mutations designed to increase the primary sequence symmetry within the core region of a beta-trefoil.
  Protein Sci, 10, 2587-2599.
PDB codes: 1jqz 1jt3 1jt4 1jt5 1jt7 1jtc
  11152136 J.M.Word, R.C.Bateman, B.K.Presley, S.C.Lovell, and D.C.Richardson (2000).
Exploring steric constraints on protein mutations using MAGE/PROBE.
  Protein Sci, 9, 2251-2259.  
10449321 B.I.Dahiyat (1999).
In silico design for protein stabilization.
  Curr Opin Biotechnol, 10, 387-390.  
10467150 E.C.Johnson, G.A.Lazar, J.R.Desjarlais, and T.M.Handel (1999).
Solution structure and dynamics of a designed hydrophobic core variant of ubiquitin.
  Structure, 7, 967-976.
PDB code: 1ud7
10097082 M.G.Mateu, and A.R.Fersht (1999).
Mutually compensatory mutations during evolution of the tetramerization domain of tumor suppressor p53 lead to impaired hetero-oligomerization.
  Proc Natl Acad Sci U S A, 96, 3595-3599.  
10666571 N.C.Gassner, and B.W.Matthews (1999).
Use of differentially substituted selenomethionine proteins in X-ray structure determination.
  Acta Crystallogr D Biol Crystallogr, 55, 1967-1970.
PDB codes: 1cx7 1d2w 1d2y 1d3f 1d3j 1d3m 1d3n
  10417229 Y.Korkhin, A.J.Kalb (Gilboa), M.Peretz, O.Bogin, Y.Burstein, and F.Frolow (1999).
Oligomeric integrity--the structural key to thermal stability in bacterial alcohol dehydrogenases.
  Protein Sci, 8, 1241-1249.  
9770481 C.Vetriani, D.L.Maeder, N.Tolliday, K.S.Yip, T.J.Stillman, K.L.Britton, D.W.Rice, H.H.Klump, and F.T.Robb (1998).
Protein thermostability above 100 degreesC: a key role for ionic interactions.
  Proc Natl Acad Sci U S A, 95, 12300-12305.  
9914192 G.A.Lazar, and T.M.Handel (1998).
Hydrophobic core packing and protein design.
  Curr Opin Chem Biol, 2, 675-679.  
9665160 H.W.Hellinga (1998).
Computational protein engineering.
  Nat Struct Biol, 5, 525-527.  
9729739 J.R.Desjarlais, and N.D.Clarke (1998).
Computer search algorithms in protein modification and design.
  Curr Opin Struct Biol, 8, 471-475.  
  9541409 L.A.Lipscomb, N.C.Gassner, S.D.Snow, A.M.Eldridge, W.A.Baase, D.L.Drew, and B.W.Matthews (1998).
Context-dependent protein stabilization by methionine-to-leucine substitution shown in T4 lysozyme.
  Protein Sci, 7, 765-773.
PDB codes: 230l 231l 232l 233l 234l
9484240 V.De Filippis, F.De Antoni, M.Frigo, P.Polverino de Laureto, and A.Fontana (1998).
Enhanced protein thermostability by Ala-->Aib replacement.
  Biochemistry, 37, 1686-1696.  
9228039 A.Akasako, M.Haruki, M.Oobatake, and S.Kanaya (1997).
Conformational stabilities of Escherichia coli RNase HI variants with a series of amino acid substitutions at a cavity within the hydrophobic core.
  J Biol Chem, 272, 18686-18693.  
9384561 A.Motta, P.Amodeo, P.Fucile, M.A.Castiglione Morelli, B.Bremnes, and O.Bakke (1997).
A new triple-stranded alpha-helical bundle in solution: the assembling of the cytosolic tail of MHC-associated invariant chain.
  Structure, 5, 1453-1464.  
  9260282 A.Su, and S.L.Mayo (1997).
Coupling backbone flexibility and amino acid sequence selection in protein design.
  Protein Sci, 6, 1701-1707.  
  9194194 B.I.Dahiyat, D.B.Gordon, and S.L.Mayo (1997).
Automated design of the surface positions of protein helices.
  Protein Sci, 6, 1333-1337.  
  9194177 G.A.Lazar, J.R.Desjarlais, and T.M.Handel (1997).
De novo design of the hydrophobic core of ubiquitin.
  Protein Sci, 6, 1167-1178.  
9294154 H.W.Hellinga (1997).
Rational protein design: combining theory and experiment.
  Proc Natl Acad Sci U S A, 94, 10015-10017.  
  8732761 B.I.Dahiyat, and S.L.Mayo (1996).
Protein design automation.
  Protein Sci, 5, 895-903.  
8672470 H.S.Mchaourab, M.A.Lietzow, K.Hideg, and W.L.Hubbell (1996).
Motion of spin-labeled side chains in T4 lysozyme. Correlation with protein structure and dynamics.
  Biochemistry, 35, 7692-7704.  
8611545 W.Colón, G.A.Elöve, L.P.Wakem, F.Sherman, and H.Roder (1996).
Side chain packing of the N- and C-terminal helices plays a critical role in the kinetics of cytochrome c folding.
  Biochemistry, 35, 5538-5549.  
  8763950 X.Zhu, C.D.Amsler, K.Volz, and P.Matsumura (1996).
Tyrosine 106 of CheY plays an important role in chemotaxis signal transduction in Escherichia coli.
  J Bacteriol, 178, 4208-4215.  
7749923 B.W.Matthews (1995).
Can proteins be turned inside-out?
  Nat Struct Biol, 2, 85-86.  
  8535237 J.R.Desjarlais, and T.M.Handel (1995).
De novo design of the hydrophobic cores of proteins.
  Protein Sci, 4, 2006-2018.  
7667303 P.B.Harbury, B.Tidor, and P.S.Kim (1995).
Repacking protein cores with backbone freedom: structure prediction for coiled coils.
  Proc Natl Acad Sci U S A, 92, 8408-8412.  
7615544 S.Ganguli, H.Wang, P.Matsumura, and K.Volz (1995).
Uncoupled phosphorylation and activation in bacterial chemotaxis. The 2.1-A structure of a threonine to isoleucine mutant at position 87 of CheY.
  J Biol Chem, 270, 17386-17393.
PDB code: 1vlz
7765172 E.P.Baldwin, and B.W.Matthews (1994).
Core-packing constraints, hydrophobicity and protein design.
  Curr Opin Biotechnol, 5, 396-402.  
8278404 W.A.Lim, A.Hodel, R.T.Sauer, and F.M.Richards (1994).
The crystal structure of a mutant protein with altered but improved hydrophobic core packing.
  Proc Natl Acad Sci U S A, 91, 423-427.
PDB code: 1lli
  8401213 D.E.Anderson, J.H.Hurley, H.Nicholson, W.A.Baase, and B.W.Matthews (1993).
Hydrophobic core repacking and aromatic-aromatic interaction in the thermostable mutant of T4 lysozyme Ser 117-->Phe.
  Protein Sci, 2, 1285-1290.
PDB code: 1tla
8058892 F.M.Richards, and W.A.Lim (1993).
An analysis of packing in the protein folding problem.
  Q Rev Biophys, 26, 423-498.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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