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PDBsum entry 1ja2

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protein links
Hydrolase PDB id
1ja2
Jmol PyMol
Contents
Protein chain
129 a.a. *
* Residue conservation analysis
PDB id:
1ja2
Name: Hydrolase
Title: Binding of n-acetylglucosamine to chicken egg lysozyme: a powder diffraction study
Structure: Lysozyme. Chain: a. Synonym: 1,4-beta-n-acetylmuramidasE C. Allergen gal d 4. Gal d iv. Engineered: yes
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Cellular_location: cytoplasm. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Authors: R.B.Von Dreele
Key ref:
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. PubMed id: 11717496 DOI: 10.1107/S0907444901015748
Date:
29-May-01     Release date:   15-Jun-01    
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  

 

 
DOI no: 10.1107/S0907444901015748 Acta Crystallogr D Biol Crystallogr 57:1836-1842 (2001)
PubMed id: 11717496  
 
 
Binding of N-acetylglucosamine to chicken egg lysozyme: a powder diffraction study.
R.B.Von Dreele.
 
  ABSTRACT  
 
The binding of N-acetylglucosamine (NAG) to chicken egg lysozyme (E.C. 3.2.1.17) was investigated by high-resolution X-ray powder diffraction at room temperature. NAG was found to bind to lysozyme in a rapid precipitation preparation with 0.05 M NaCl buffer pH 6.0, but not 0.05 M NaCl buffer pH 5.0. Binding was indicated by significant and readily apparent changes in the diffraction pattern from that of the apo protein precipitated from the same solvent. The location of NAG bound to lysozyme was easily found from a difference Fourier map generated from structure factors extracted during a preliminary combined Rietveld and stereochemical restraint refinement. Full protein and protein-NAG structures were refined with these techniques (R(wp) = 2.22-2.49%, R(p) = 1.79-1.95%, R(F)(2) = 4.95-6.35%) and revealed a binding mode for NAG which differed from that found in an earlier single-crystal study and probably represents a precursor trapped by rapid precipitation.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 Stereographic representation of the F map at 1.5 . The map was developed from structure factors extracted during the Rietveld refinement of the lysozyme structure using the diffraction data obtained from the 0.5 M NaCl pH 6.0 NAG-lysozyme material. Superimposed are the NAG molecule (shown in red) found by the final Rietveld refinement of the NAG-lysozyme complex and the NAG molecule (shown in green) found by the single-crystal analysis of Perkins et al. (1978[Perkins, S. J., Johnson, L. N., Machin, P. A. & Phillips, D. C. (1978). Biochem. J. 173, 607-616.]).
Figure 6.
Figure 6 Steroscopic view of molecular surface of lysozyme with a CPK representation of the bound N-acetylglucosamine. The protein surface is colored according to the electrostatic potential, where blue is positive and red negative.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 1836-1842) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21382498 K.Fujii, M.T.Young, and K.D.Harris (2011).
Exploiting powder X-ray diffraction for direct structure determination in structural biology: The P2X4 receptor trafficking motif YEQGL.
  J Struct Biol, 174, 461-467.  
18156682 I.Margiolaki, and J.P.Wright (2008).
Powder crystallography on macromolecules.
  Acta Crystallogr A, 64, 169-180.  
17691895 B.Y.Chen, V.Y.Fofanov, D.H.Bryant, B.D.Dodson, D.M.Kristensen, A.M.Lisewski, M.Kimmel, O.Lichtarge, and L.E.Kavraki (2007).
The MASH pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifs.
  J Comput Biol, 14, 791-816.  
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.

 

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