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PDBsum entry 1hew

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Hydrolase(o-glycosyl) PDB id
1hew
Jmol PyMol
Contents
Protein chain
129 a.a. *
Ligands
NAG-NAG-NAG
Waters ×103
* Residue conservation analysis
PDB id:
1hew
Name: Hydrolase(o-glycosyl)
Title: Refinement of an enzyme complex with inhibitor bound at part occupancy. Hen egg-white lysozyme and tri-n-acetylchitotrio angstroms resolution
Structure: Hen egg white lysozyme. Chain: a. Engineered: yes
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Tissue: egg white
Resolution:
1.75Å     R-factor:   0.229    
Authors: J.C.Cheetham,P.J.Artymiuk,D.C.Phillips
Key ref: J.C.Cheetham et al. (1992). Refinement of an enzyme complex with inhibitor bound at partial occupancy. Hen egg-white lysozyme and tri-N-acetylchitotriose at 1.75 A resolution. J Mol Biol, 224, 613-628. PubMed id: 1569548
Date:
20-Jan-92     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00698  (LYSC_CHICK) -  Lysozyme C
Seq:
Struc:
147 a.a.
129 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   4 terms 
  Biological process     metabolic process   5 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
J Mol Biol 224:613-628 (1992)
PubMed id: 1569548  
 
 
Refinement of an enzyme complex with inhibitor bound at partial occupancy. Hen egg-white lysozyme and tri-N-acetylchitotriose at 1.75 A resolution.
J.C.Cheetham, P.J.Artymiuk, D.C.Phillips.
 
  ABSTRACT  
 
The structure of the tri-N-acetylchitotriose inhibitor complex of hen egg-white lysozyme has been refined at 1.75 A resolution, using data collected from a complex crystal with ligand bound at less than full occupancy. To determine the exact value of the inhibitor occupancy, a model comprising unliganded and sugar-bound protein molecules was generated and refined against the 1.75 A data, using a modified version of the Hendrickson & Konnert least-squares procedure. The crystallographic R-factor for the model was found to fall to a minimum at 55% bound sugar. Conventional refinement assuming unit occupancy was found to yield incorrect thermal and positional parameters. Application of the same refinement procedures to an earlier 2.0 A data set, collected independently on different complex crystals by Blake et al. gave less consistent results than the 1.75 A refinement. From an analysis of the high resolution structure a detailed picture of the protein-carbohydrate interactions in the non-productive complex has emerged, together with the conformation and mobility changes that accompany ligand binding. The specificity of interaction between the protein and inhibitor, bound in subsites A to C of the active site, is seen to be generated primarily by an extensive network of hydrogen bonds, both to the protein itself and to bound solvent molecules. The latter also play an important role in maintaining the structural integrity of the active site cleft in the apo-protein.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22505256 P.V.Afonine, R.W.Grosse-Kunstleve, N.Echols, J.J.Headd, N.W.Moriarty, M.Mustyakimov, T.C.Terwilliger, A.Urzhumtsev, P.H.Zwart, and P.D.Adams (2012).
Towards automated crystallographic structure refinement with phenix.refine.
  Acta Crystallogr D Biol Crystallogr, 68, 352-367.  
21084280 L.Ito, K.Shiraki, T.Matsuura, M.Okumura, K.Hasegawa, S.Baba, H.Yamaguchi, and T.Kumasaka (2011).
High-resolution X-ray analysis reveals binding of arginine to aromatic residues of lysozyme surface: implication of suppression of protein aggregation by arginine.
  Protein Eng Des Sel, 24, 269-274.
PDB codes: 3agg 3agh 3agi
19823947 H.M.Zhang, B.P.Tang, and Y.Q.Wang (2010).
The interaction of lysozyme with caffeine, theophylline and theobromine in solution.
  Mol Biol Rep, 37, 3127-3136.  
20413917 L.Callewaert, and C.W.Michiels (2010).
Lysozymes in the animal kingdom.
  J Biosci, 35, 127-160.  
19279191 R.Suzuki, Z.Fujimoto, S.Ito, S.Kawahara, S.Kaneko, K.Taira, T.Hasegawa, and A.Kuno (2009).
Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86.
  J Biochem, 146, 61-70.
PDB codes: 2d1z 2d20 2d22 2d23 2d24
19343485 Z.Wang, X.Tan, D.Chen, Q.Yue, and Z.Song (2009).
Study on the binding behavior of lysozyme with cephalosporin analogues by fluorescence spectroscopy.
  J Fluoresc, 19, 801-808.  
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.  
17631496 T.Goto, Y.Abe, Y.Kakuta, K.Takeshita, T.Imoto, and T.Ueda (2007).
Crystal structure of Tapes japonica Lysozyme with substrate analogue: structural basis of the catalytic mechanism and manifestation of its chitinase activity accompanied by quaternary structural change.
  J Biol Chem, 282, 27459-27467.
PDB code: 2dqa
17187178 M.Setou, D.Radostin, K.Atsuzawa, I.Yao, Y.Fukuda, N.Usuda, and K.Nagayama (2006).
Mammalian cell nano structures visualized by cryo Hilbert differential contrast transmission electron microscopy.
  Med Mol Morphol, 39, 176-180.  
  16880547 S.R.Marana, F.C.Cançado, A.A.Valério, C.Ferreira, W.R.Terra, and J.A.Barbosa (2006).
Crystallization, data collection and phasing of two digestive lysozymes from Musca domestica.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 750-752.
PDB codes: 2fbd 2h5z
16794868 V.M.Ioffe, G.P.Gorbenko, A.L.Tatarets, L.D.Patsenker, and E.A.Terpechnig (2006).
Examining protein-lipid interactions in model systems with a new squarylium fluorescent dye.
  J Fluoresc, 16, 547-554.  
15805597 I.Margiolaki, J.P.Wright, A.N.Fitch, G.C.Fox, and R.B.Von Dreele (2005).
Synchrotron X-ray powder diffraction study of hexagonal turkey egg-white lysozyme.
  Acta Crystallogr D Biol Crystallogr, 61, 423-432.
PDB code: 1xft
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
15608372 R.B.Von Dreele (2005).
Binding of N-acetylglucosamine oligosaccharides to hen egg-white lysozyme: a powder diffraction study.
  Acta Crystallogr D Biol Crystallogr, 61, 22-32.
PDB codes: 1sf4 1sf6 1sf7 1sfb 1sfg
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.  
12606493 A.Mandal, K.L.Klotz, J.Shetty, F.L.Jayes, M.J.Wolkowicz, L.C.Bolling, S.A.Coonrod, M.B.Black, A.B.Diekman, T.A.Haystead, C.J.Flickinger, and J.C.Herr (2003).
SLLP1, a unique, intra-acrosomal, non-bacteriolytic, c lysozyme-like protein of human spermatozoa.
  Biol Reprod, 68, 1525-1537.  
14730141 T.Araki, G.Toshima, T.Kusao, Y.Chijiiwa, S.Kawamura, and T.Torikata (2003).
The amino acid sequence of satyr tragopan lysozyme and its activity.
  Biosci Biotechnol Biochem, 67, 2621-2626.  
11717496 R.B.Von Dreele (2001).
Binding of N-acetylglucosamine to chicken egg lysozyme: a powder diffraction study.
  Acta Crystallogr D Biol Crystallogr, 57, 1836-1842.
PDB codes: 1ja2 1ja4 1ja6 1ja7
11679726 S.Datta, B.K.Biswal, and M.Vijayan (2001).
The effect of stabilizing additives on the structure and hydration of proteins: a study involving tetragonal lysozyme.
  Acta Crystallogr D Biol Crystallogr, 57, 1614-1620.
PDB codes: 1jis 1jit 1jiy 1jj0 1jj1 1jj3
10957630 B.K.Biswal, N.Sukumar, and M.Vijayan (2000).
Hydration, mobility and accessibility of lysozyme: structures of a pH 6.5 orthorhombic form and its low-humidity variant and a comparative study involving 20 crystallographically independent molecules.
  Acta Crystallogr D Biol Crystallogr, 56, 1110-1119.
PDB codes: 1f0w 1f10
10924902 L.I.Krishtalik, and V.V.Topolev (2000).
Effects of medium polarization and pre-existing field on activation energy of enzymatic charge-transfer reactions.
  Biochim Biophys Acta, 1459, 88.  
  11045614 S.Mine, T.Ueda, Y.Hashimoto, and T.Imoto (2000).
Analysis of the internal motion of free and ligand-bound human lysozyme by use of 15N NMR relaxation measurement: a comparison with those of hen lysozyme.
  Protein Sci, 9, 1669-1684.  
10089395 V.B.Vollan, E.Hough, and S.Karlsen (1999).
Structural studies on the binding of 4-methylumbelliferone glycosides of chitin to rainbow trout lysozyme.
  Acta Crystallogr D Biol Crystallogr, 55, 60-66.
PDB codes: 1bb6 1bb7
9813287 A.Kristiansen, K.M.Vårum, and H.Grasdalen (1998).
Quantitative studies of the non-productive binding of lysozyme to partially N-acetylated chitosans. Binding of large ligands to a one-dimensional binary lattice studied by a modified McGhee and von Hippel model.
  Biochim Biophys Acta, 1425, 137-150.  
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
9147134 C.S.Tsai (1997).
Molecular modelling studies of lysozyme catalysed hydrolysis of synthetic substrates.
  Int J Biochem Cell Biol, 29, 325-334.  
9062927 E.Liepinsh, and G.Otting (1997).
Organic solvents identify specific ligand binding sites on protein surfaces.
  Nat Biotechnol, 15, 264-268.  
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.  
  9260288 H.Jóhannesson, V.P.Denisov, and B.Halle (1997).
Dimethyl sulfoxide binding to globular proteins: a nuclear magnetic relaxation dispersion study.
  Protein Sci, 6, 1756-1763.  
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.  
9451786 Y.Amo, and I.Karube (1997).
Dielectric measurements of lysozyme and tri-N-acetyl-D-glucosamine association at radio and microwave frequencies.
  Biosens Bioelectron, 12, 953-958.  
9222937 Y.Inoue, N.Nakamura, and T.Inagami (1997).
A review of mutagenesis studies of angiotensin II type 1 receptor, the three-dimensional receptor model in search of the agonist and antagonist binding site and the hypothesis of a receptor activation mechanism.
  J Hypertens, 15, 703-714.  
8619952 B.C.Braden, B.A.Fields, and R.J.Poljak (1995).
Conservation of water molecules in an antibody-antigen interaction.
  J Mol Recognit, 8, 317-325.  
7493989 P.Kuhn, C.Guan, T.Cui, A.L.Tarentino, T.H.Plummer, and P.Van Roey (1995).
Active site and oligosaccharide recognition residues of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F.
  J Biol Chem, 270, 29493-29497.
PDB code: 1pnf
  8535242 P.Shih, and J.F.Kirsch (1995).
Design and structural analysis of an engineered thermostable chicken lysozyme.
  Protein Sci, 4, 2063-2072.  
8444153 I.Kumagai, K.Maenaka, F.Sunada, S.Takeda, and K.Miura (1993).
Effects of subsite alterations on substrate-binding mode in the active site of hen egg-white lysozyme.
  Eur J Biochem, 212, 151-156.  
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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