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PDBsum entry 135l

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Hydrolase(o-glycosyl) PDB id
135l
Jmol
Contents
Protein chain
129 a.a. *
Waters ×114
* Residue conservation analysis
PDB id:
135l
Name: Hydrolase(o-glycosyl)
Title: X-ray structure of monoclinic turkey egg lysozyme at 1.3 angstroms resolution
Structure: Turkey egg white lysozyme. Chain: a. Engineered: yes
Source: Meleagris gallopavo. Turkey. Organism_taxid: 9103. Tissue: egg white
Resolution:
1.30Å     R-factor:   0.189    
Authors: K.Harata
Key ref:
K.Harata (1993). X-ray structure of monoclinic turkey egg lysozyme at 1.3 A resolution. Acta Crystallogr D Biol Crystallogr, 49, 497-504. PubMed id: 15299509 DOI: 10.1107/S0907444993005542
Date:
10-Jun-93     Release date:   31-Oct-93    
Supersedes: 1lz3
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00703  (LYSC_MELGA) -  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   3 terms 
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
DOI no: 10.1107/S0907444993005542 Acta Crystallogr D Biol Crystallogr 49:497-504 (1993)
PubMed id: 15299509  
 
 
X-ray structure of monoclinic turkey egg lysozyme at 1.3 A resolution.
K.Harata.
 
  ABSTRACT  
 
Monoclinic crystals of turkey egg lysozyme (TEL, E.C. 3.2.1.17) were obtained from 2.2 M ammonium sulfate solution at pH 4.2. They belong to space group P2(1) with unit-cell dimensions a = 38.07, b = 33.20, c = 46.12 A and beta = 110.1 degrees, and contain one molecule in the asymmetric unit (V(m) = 1.91 A(3) Da(-1)). The three-dimensional structure of TEL was solved by the method of multiple isomorphous replacement with anomalous scattering. Area detector data to 1.5 A resolution from native and heavy-atom derivatives were used for the structure determination. The structure was refined by the simulated-annealing method with diffraction data of 10-1.30 A resolution. The conventional R factor was 0.189. The root-mean-square deviations from ideal bond distances and angles were 0.016 A and 2.9 degrees, respectively. The backbone structure of TEL is very similar to that of hen egg lysozyme (HEL) and the difference in seven amino-acid residues does not affect the basic folding of the polypeptide chain. Except for the region from Gly101 to Gly104, the geometry of the active-site cleft is conserved between TEL and HEL. The Gly101 residue is located at the end of the sugar-binding site and the structural change in this region between TEL and HEL is considered to be responsible for the difference in their enzymatic properties.
 
  Selected figure(s)  
 
Figure 7.
Fig. 7. Structure of the active-site region. Water molecules are shown by shaded circles. Inter- molecular distances less than 3.2 A, involving side-chain atoms and water molecules, are shown by thin lines. Subsites for the binding of sugar residues arc denoted A--E.
Figure 8.
Fig. 8. Hydrogen-bond network in the active-site cleft. Distances less than 3.3 A are denoted by dashed lines. Water molecules are shown by full circles.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1993, 49, 497-504) copyright 1993.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19558703 R.Alterovitz, A.Arvey, S.Sankararaman, C.Dallett, Y.Freund, and K.Sjölander (2009).
ResBoost: characterizing and predicting catalytic residues in enzymes.
  BMC Bioinformatics, 10, 197.  
16231289 H.Li, A.D.Robertson, and J.H.Jensen (2005).
Very fast empirical prediction and rationalization of protein pKa values.
  Proteins, 61, 704-721.  
15185334 A.D.Mackerell, M.Feig, and C.L.Brooks (2004).
Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations.
  J Comput Chem, 25, 1400-1415.  
10620274 E.Banachowicz, J.GapiƄski, and A.Patkowski (2000).
Solution structure of biopolymers: a new method of constructing a bead model.
  Biophys J, 78, 70-78.  
8805552 A.C.Pike, K.Brew, and K.R.Acharya (1996).
Crystal structures of guinea-pig, goat and bovine alpha-lactalbumin highlight the enhanced conformational flexibility of regions that are significant for its action in lactose synthase.
  Structure, 4, 691-703.
PDB codes: 1hfx 1hfy 1hfz
8816770 M.Gerstein, and C.Chothia (1996).
Packing at the protein-water interface.
  Proc Natl Acad Sci U S A, 93, 10167-10172.  
  8535242 P.Shih, and J.F.Kirsch (1995).
Design and structural analysis of an engineered thermostable chicken lysozyme.
  Protein Sci, 4, 2063-2072.  
  8061608 J.Lescar, H.Souchon, and P.M.Alzari (1994).
Crystal structures of pheasant and guinea fowl egg-white lysozymes.
  Protein Sci, 3, 788-798.
PDB codes: 1ghl 1hhl
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.