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

 

 

 

 

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Contents
Protein chain
129 a.a. *
Waters ×185
* Residue conservation analysis
PDB id:
1hep
Name: Hydrolase(o-glycosyl)
Title: Structural and thermodynamic analysis of compensating mutations within the core of chicken egg white lysozyme
Structure: Hen egg white lysozyme. Chain: a. Engineered: yes
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Organ: egg
Resolution:
1.80Å     R-factor:   0.153    
Authors: K.P.Wilson,B.A.Malcolm,B.W.Matthews
Key ref: K.P.Wilson et al. (1992). Structural and thermodynamic analysis of compensating mutations within the core of chicken egg white lysozyme. J Biol Chem, 267, 10842-10849. PubMed id: 1587860
Date:
10-Jan-92     Release date:   31-Oct-93    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00698  (LYSC_CHICK) -  Lysozyme C from Gallus gallus
Seq:
Struc: 		147 a.a.
129 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 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 Biol Chem 267:10842-10849 (1992)
PubMed id: 1587860  
 
 
Structural and thermodynamic analysis of compensating mutations within the core of chicken egg white lysozyme.
K.P.Wilson, B.A.Malcolm, B.W.Matthews.
 
  ABSTRACT  
 
High resolution crystal structures have been determined for six chicken-type lysozymes that were constructed to investigate putative intermediates in the evolution of the lysozymes of modern game birds (Malcolm, B. A., Wilson, K. P., Matthews, B. W., Kirsch, J. F., and Wilson, A. C. (1990) Nature 345, 86-89). The amino acid replacements include Thr-40----Ser, Ile-55----Val, and Ser-91----Thr, as well as combinations of these substitutions. Residues 40, 55, and 91 are buried within the core of chicken lysozyme. The replacements therefore involve the insertion and/or removal of methyl groups from the protein interior. The mutant proteins have normal activities, and their thermal stabilities span a range of 7 degrees C, with some variants more stable and some less stable than the naturally occurring forms. Comparison of the crystal structures shows the overall structures to be very similar, but there are differences in the packing of side chains in the region of the replacements. The x-ray coordinates were used to evaluate the repacking of side chains in the protein interior and to attempt to evaluate the contributions of the different energetic interactions toward the overall stability of each variant. The results illustrate how proteins can compensate for potentially destabilizing substitutions in different ways and underscore the importance of high resolution structural data if changes in protein thermostability due to changes in protein sequence are to be understood. The findings also suggest that protein stability can be increased by mutations that lower strain in the protein interior while maintaining total buried hydrophobic surface area.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20975933 M.Lunzer, G.B.Golding, and A.M.Dean (2010).
Pervasive cryptic epistasis in molecular evolution.
  PLoS Genet, 6, e1001162.  
19523237 L.Azevedo, J.Carneiro, B.van Asch, A.Moleirinho, F.Pereira, and A.Amorim (2009).
Epistatic interactions modulate the evolution of mammalian mitochondrial respiratory complex components.
  BMC Genomics, 10, 266.  
19006167 A.Vinu, N.Gokulakrishnan, V.V.Balasubramanian, S.Alam, M.P.Kapoor, K.Ariga, and T.Mori (2008).
Three-dimensional ultralarge-pore ia3d mesoporous silica with various pore diameters and their application in biomolecule immobilization.
  Chemistry, 14, 11529-11538.  
18186466 K.Fukushima, M.Wada, and M.Sakurai (2008).
An insight into the general relationship between the three dimensional structures of enzymes and their electronic wave functions: Implication for the prediction of functional sites of enzymes.
  Proteins, 71, 1940-1954.  
18687682 R.Perez-Jimenez, A.P.Wiita, D.Rodriguez-Larrea, P.Kosuri, J.A.Gavira, J.M.Sanchez-Ruiz, and J.M.Fernandez (2008).
Force-clamp spectroscopy detects residue co-evolution in enzyme catalysis.
  J Biol Chem, 283, 27121-27129.  
18641079 Z.Hu, and J.Jiang (2008).
Electrophoresis in protein crystal: nonequilibrium molecular dynamics simulations.
  Biophys J, 95, 4148-4156.  
18071253 A.Harada, H.Yagi, A.Saito, H.Azakami, and A.Kato (2007).
Relationship between the stability of hen egg-white lysozymes mutated at sites designed to interact with alpha-helix dipoles and their secretion amounts in yeast.
  Biosci Biotechnol Biochem, 71, 2952-2961.  
17186526 T.Imai, R.Hiraoka, A.Kovalenko, and F.Hirata (2007).
Locating missing water molecules in protein cavities by the three-dimensional reference interaction site model theory of molecular solvation.
  Proteins, 66, 804-813.  
16929100 J.Ondrácek, and J.R.Mesters (2006).
An ensemble of crystallographic models enables the description of novel bromate-oxoanion species trapped within a protein crystal.
  Acta Crystallogr D Biol Crystallogr, 62, 996.
PDB code: 2d6b
17003964 S.Pricl, M.Ferrone, M.Fermeglia, F.Amato, C.Cosentino, M.M.Cheng, R.Walczak, and M.Ferrari (2006).
Multiscale modeling of protein transport in silicon membrane nanochannels. Part 1. Derivation of molecular parameters from computer simulations.
  Biomed Microdevices, 8, 277-290.  
15778956 D.Segal, and M.Eisenstein (2005).
The effect of resolution-dependent global shape modifications on rigid-body protein-protein docking.
  Proteins, 59, 580-591.  
16131750 J.Ondrácek, M.S.Weiss, J.Brynda, J.Fiala, F.Jursík, P.Rezácová, L.B.Jenner, and J.Sedlácek (2005).
Regular arrangement of periodates bound to lysozyme.
  Acta Crystallogr D Biol Crystallogr, 61, 1181-1189.
PDB code: 1hc0
16074985 M.A.DePristo, D.M.Weinreich, and D.L.Hartl (2005).
Missense meanderings in sequence space: a biophysical view of protein evolution.
  Nat Rev Genet, 6, 678-687.  
15754058 V.A.Higman, J.Boyd, L.J.Smith, and C.Redfield (2004).
Asparagine and glutamine side-chain conformation in solution and crystal: a comparison for hen egg-white lysozyme using residual dipolar couplings.
  J Biomol NMR, 30, 327-346.  
12784363 E.Ben-Zeev, and M.Eisenstein (2003).
Weighted geometric docking: incorporating external information in the rotation-translation scan.
  Proteins, 52, 24-27.  
12740607 Y.Li, H.Li, F.Yang, S.J.Smith-Gill, and R.A.Mariuzza (2003).
X-ray snapshots of the maturation of an antibody response to a protein antigen.
  Nat Struct Biol, 10, 482-488.
PDB codes: 1ndg 1ndm
11847280 A.Heifetz, E.Katchalski-Katzir, and M.Eisenstein (2002).
Electrostatics in protein-protein docking.
  Protein Sci, 11, 571-587.  
12324397 R.E.Georgescu, E.G.Alexov, and M.R.Gunner (2002).
Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins.
  Biophys J, 83, 1731-1748.  
11506221 P.Hvelplund, S.B.Nielsen, M.Sørensen, J.U.Andersen, and T.J.Jørgensen (2001).
Electron loss from multiply protonated lysozyme ions in high energy collisions with molecular oxygen.
  J Am Soc Mass Spectrom, 12, 889-893.  
10944331 M.S.Weiss, G.J.Palm, and R.Hilgenfeld (2000).
Crystallization, structure solution and refinement of hen egg-white lysozyme at pH 8.0 in the presence of MPD.
  Acta Crystallogr D Biol Crystallogr, 56, 952-958.
PDB codes: 1dpw 1dpx
10828942 Y.Li, H.Li, S.J.Smith-Gill, and R.A.Mariuzza (2000).
Three-dimensional structures of the free and antigen-bound Fab from monoclonal antilysozyme antibody HyHEL-63(,).
  Biochemistry, 39, 6296-6309.
PDB codes: 1dqj 1dqm 1dqq
10388736 E.L.Mehler, and F.Guarnieri (1999).
A self-consistent, microenvironment modulated screened coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins.
  Biophys J, 77, 3.  
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.  
9779784 H.W.van Vlijmen, M.Schaefer, and M.Karplus (1998).
Improving the accuracy of protein pKa calculations: conformational averaging versus the average structure.
  Proteins, 33, 145-158.  
9145111 G.Otting, E.Liepinsh, B.Halle, and U.Frey (1997).
NMR identification of hydrophobic cavities with low water occupancies in protein structures using small gas molecules.
  Nat Struct Biol, 4, 396-404.  
  9307874 P.K.Qasba, and S.Kumar (1997).
Molecular divergence of lysozymes and alpha-lactalbumin.
  Crit Rev Biochem Mol Biol, 32, 255-306.  
  8535241 P.Shih, D.R.Holland, and J.F.Kirsch (1995).
Thermal stability determinants of chicken egg-white lysozyme core mutants: hydrophobicity, packing volume, and conserved buried water molecules.
  Protein Sci, 4, 2050-2062.
PDB codes: 1lsm 1lsn
  8535242 P.Shih, and J.F.Kirsch (1995).
Design and structural analysis of an engineered thermostable chicken lysozyme.
  Protein Sci, 4, 2063-2072.  
7763513 V.V.Mozhaev (1993).
Mechanism-based strategies for protein thermostabilization.
  Trends Biotechnol, 11, 88-95.  
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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