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

 

 

 

 

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Contents
Protein chain
129 a.a. *
Waters ×79
* Residue conservation analysis
PDB id:
1lzd
Name: Hydrolase (o-glycosyl)
Title: Dissection of protein-carbohydrate interactions in mutant hen egg- white lysozyme complexes and their hydrolytic activity
Structure: Hen egg white lysozyme. Chain: a. Engineered: yes
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Organ: egg
Resolution:
1.80Å     R-factor:   0.167    
Authors: K.Maenaka,M.Matsushima,H.Song,K.Watanabe,I.Kumagai
Key ref:
K.Maenaka et al. (1995). Dissection of protein-carbohydrate interactions in mutant hen egg-white lysozyme complexes and their hydrolytic activity. J Mol Biol, 247, 281-293. PubMed id: 7707375 DOI: 10.1006/jmbi.1994.0139
Date:
10-Feb-95     Release date:   08-May-95    
PROCHECK
Go to PROCHECK summary
 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 1 residue position (black cross)

 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.

 

 
DOI no: 10.1006/jmbi.1994.0139 J Mol Biol 247:281-293 (1995)
PubMed id: 7707375  
 
 
Dissection of protein-carbohydrate interactions in mutant hen egg-white lysozyme complexes and their hydrolytic activity.
K.Maenaka, M.Matsushima, H.Song, F.Sunada, K.Watanabe, I.Kumagai.
 
  ABSTRACT  
 
Trp62 in the binding subsite B of hen egg-white lysozyme shows general features often observed in protein-carbohydrate interactions including a stacking interaction and a hydrogen bonding network with water molecules. A previous report by our group showed that the perturbation of these interactions by substitution of Trp62 with tyrosine or phenylalanine affects the substrate binding modes and also enhances the hydrolytic activity. In order to elucidate the relationship between structural and functional changes of these protein-carbohydrate interactions, the Trp62Tyr and Trp62Phe mutants complexed with the substrate analogue, (GlcNAc)3, were analyzed at 1.8 A resolution by X-ray crystallography. The overall structures of the mutant enzymes are indistinguishable from that of the wild type enzyme. Although the wild-type enzyme binds (GlcNAc)3 in only one binding mode (A-B-C), the Trp62Tyr mutant binds (GlcNAc)3 in two binding modes (A-B-C, B-C-D) and the Trp62Phe mutant has an even weaker binding mode. The aromatic rings of Tyr62 and Phe62 maintain their interactions with the carbohydrate molecules, but make fewer stacking interactions with the GlcNAc in the B site than the wild-type enzyme does. The hydroxyl group of Tyr62 interacts weakly with a water molecule which mediates hydrogen bonding in the GlcNAc residues in the B and C sites. The C-6 hydroxyl group of the GlcNAc residue in the C site rotates around the C-5-C-6 bond to complete the hydrogen bond network in the Trp62Tyr mutant-(GlcNAc)3 complex. On the other hand, this hydrogen bonding network does not form in the Trp62Phe mutant-(GlcNAc)3. In addition to these structural studies, the kinetic parameters of the hydrolysis of 4-methylumbelliferyl N-acetyl-chitotriose, ((GlcNAc)3-MeU), have been determined in order to further characterize the enzymatic properties of these mutant lysozymes. This demonstrates that the modulation of the hydrogen bonding network, including the flexible part of the carbohydrate and water molecules and/or the slight reduction of stacking interaction in the B site, alters the binding mode toward the carbohydrate and induces an enhancement of the hydrolytic activity.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. The GlcNAc oligomer binding modes toward the subsites of the hen egg-white lysozyme and its mutants are shown together with the average temperature factors for each GlcNAc residue (numbers under the GlcNAc residues). The Trp62Tyr mutant had a (GlcNAc)3 in 2 binding modes, A-B-C and B-C-D (see the text). 		Figure 8.
Figure 8. Schematic Figures of the interactions between lysozyme and the GlcNAc oligomer molecule: (a) WT3, (b) W62Y3 and (c) W62F3. The dotted lines and numbers indicate the hydrogen bonds and their distances (in Å ), respectively.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1995, 247, 281-293) copyright 1995.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19543850 R.Helland, R.L.Larsen, S.Finstad, P.Kyomuhendo, and A.N.Larsen (2009).
Crystal structures of g-type lysozyme from Atlantic cod shed new light on substrate binding and the catalytic mechanism.
  Cell Mol Life Sci, 66, 2585-2598.
PDB codes: 3gxk 3gxr
18845568 H.Hirakawa, A.Ochi, Y.Kawahara, S.Kawamura, T.Torikata, and S.Kuhara (2008).
Catalytic Reaction Mechanism of Goose Egg-white Lysozyme by Molecular Modelling of Enzyme-Substrate Complex.
  J Biochem, 144, 753-761.  
17636570 N.Kamiya, Y.Yonezawa, H.Nakamura, and J.Higo (2008).
Protein-inhibitor flexible docking by a multicanonical sampling: native complex structure with the lowest free energy and a free-energy barrier distinguishing the native complex from the others.
  Proteins, 70, 41-53.  
18776207 T.Goto, T.Ohkuri, S.Shioi, Y.Abe, T.Imoto, and T.Ueda (2008).
Crystal structures of k33 mutant hen lysozymes with enhanced activities.
  J Biochem, 144, 619-623.  
18214981 Y.Nonaka, T.Aizawa, D.Akieda, M.Yasui, M.Watanabe, N.Watanabe, I.Tanaka, M.Kamiya, M.Mizuguchi, M.Demura, and K.Kawano (2008).
Spontaneous asparaginyl deamidation of canine milk lysozyme under mild conditions.
  Proteins, 72, 313-322.
PDB code: 2z2e
15645473 S.Zameo, B.Vauzeilles, and J.M.Beau (2005).
Dynamic combinatorial chemistry: lysozyme selects an aromatic motif that mimics a carbohydrate residue.
  Angew Chem Int Ed Engl, 44, 965-969.  
15162493 A.Berchanski, B.Shapira, and M.Eisenstein (2004).
Hydrophobic complementarity in protein-protein docking.
  Proteins, 56, 130-142.  
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.  
12493836 E.García-Hernández, R.A.Zubillaga, E.A.Chavelas-Adame, E.Vázquez-Contreras, A.Rojo-Domínguez, and M.Costas (2003).
Structural energetics of protein-carbohydrate interactions: Insights derived from the study of lysozyme binding to its natural saccharide inhibitors.
  Protein Sci, 12, 135-142.  
11847280 A.Heifetz, E.Katchalski-Katzir, and M.Eisenstein (2002).
Electrostatics in protein-protein docking.
  Protein Sci, 11, 571-587.  
11752774 E.Girard, L.Chantalat, J.Vicat, and R.Kahn (2002).
Gd-HPDO3A, a complex to obtain high-phasing-power heavy-atom derivatives for SAD and MAD experiments: results with tetragonal hen egg-white lysozyme.
  Acta Crystallogr D Biol Crystallogr, 58, 1-9.
PDB code: 1h87
12005440 S.C.Garman, L.Hannick, A.Zhu, and D.N.Garboczi (2002).
The 1.9 A structure of alpha-N-acetylgalactosaminidase: molecular basis of glycosidase deficiency diseases.
  Structure, 10, 425-434.
PDB codes: 1ktb 1ktc
  11890617 E.Lund, I.B.Rasmussen, K.H.Western, J.K.Eidem, I.Sandlie, and B.Bogen (2001).
"Troy-bodies": recombinant antibodies that target T cell epitopes to antigen presenting cells.
  Int Rev Immunol, 20, 647-673.  
11517321 I.B.Rasmussen, E.Lunde, T.E.Michaelsen, B.Bogen, and I.Sandlie (2001).
The principle of delivery of T cell epitopes to antigen-presenting cells applied to peptides from influenza virus, ovalbumin, and hen egg lysozyme: implications for peptide vaccination.
  Proc Natl Acad Sci U S A, 98, 10296-10301.  
10737939 D.W.Ritchie, and G.J.Kemp (2000).
Protein docking using spherical polar Fourier correlations.
  Proteins, 39, 178-194.  
10873861 F.A.Saul, P.Rovira, G.Boulot, E.J.Damme, W.J.Peumans, P.Truffa-Bachi, and G.A.Bentley (2000).
Crystal structure of Urtica dioica agglutinin, a superantigen presented by MHC molecules of class I and class II.
  Structure, 8, 593-603.
PDB codes: 1eis 1en2 1enm
10866795 J.F.Espinosa, J.L.Asensio, J.L.García, J.Laynez, M.Bruix, C.Wright, H.C.Siebert, H.J.Gabius, F.J.Cañada, and J.Jiménez-Barbero (2000).
NMR investigations of protein-carbohydrate interactions binding studies and refined three-dimensional solution structure of the complex between the B domain of wheat germ agglutinin and N,N', N"-triacetylchitotriose.
  Eur J Biochem, 267, 3965-3978.  
10842338 J.L.Asensio, H.C.Siebert, C.W.von Der Lieth, J.Laynez, M.Bruix, U.M.Soedjanaamadja, J.J.Beintema, F.J.Cañada, H.J.Gabius, and J.Jiménez-Barbero (2000).
NMR investigations of protein-carbohydrate interactions: studies on the relevance of Trp/Tyr variations in lectin binding sites as deduced from titration microcalorimetry and NMR studies on hevein domains. Determination of the NMR structure of the complex between pseudohevein and N,N',N"-triacetylchitotriose.
  Proteins, 40, 218-236.  
10328272 G.Moont, H.A.Gabb, and M.J.Sternberg (1999).
Use of pair potentials across protein interfaces in screening predicted docked complexes.
  Proteins, 35, 364-373.  
10417410 U.Samanta, D.Pal, and P.Chakrabarti (1999).
Packing of aromatic rings against tryptophan residues in proteins.
  Acta Crystallogr D Biol Crystallogr, 55, 1421-1427.  
9714162 H.G.Nagendra, N.Sukumar, and M.Vijayan (1998).
Role of water in plasticity, stability, and action of proteins: the crystal structures of lysozyme at very low levels of hydration.
  Proteins, 32, 229-240.
PDB codes: 1xei 1xej 1xek
9062927 E.Liepinsh, and G.Otting (1997).
Organic solvents identify specific ligand binding sites on protein surfaces.
  Nat Biotechnol, 15, 264-268.  
  9307874 P.K.Qasba, and S.Kumar (1997).
Molecular divergence of lysozymes and alpha-lactalbumin.
  Crit Rev Biochem Mol Biol, 32, 255-306.  
9242666 R.Kuroki, Y.Ito, Y.Kato, and T.Imoto (1997).
A covalent enzyme-substrate adduct in a mutant hen egg white lysozyme (D52E).
  J Biol Chem, 272, 19976-19981.  
8955089 K.Tsumoto, K.Ogasahara, Y.Ueda, K.Watanabe, K.Yutani, and I.Kumagai (1996).
Role of salt bridge formation in antigen-antibody interaction. Entropic contribution to the complex between hen egg white lysozyme and its monoclonal antibody HyHEL10.
  J Biol Chem, 271, 32612-32616.  
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 codes are shown on the right.

 

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