PDBsum entry: 1bb6

Hydrolase

PDB id: 1bb6

Contents

Protein chain

129 a.a. *

Ligands

UMG

Waters ×142

* Residue conservation analysis

PDB id:

1bb6

Name:

Hydrolase

Title:

Lysozyme complex with 4-methyl-umbelliferyl chitotriose

Structure:

Lysozyme. Chain: a. Synonym: n-acetyl-muramidase. Ec: 3.2.1.17

Source:

Oncorhynchus mykiss. Rainbow trout. Organism_taxid: 8022. Organ: kidney

Resolution:

2.00Å R-factor: 0.211 R-free: 0.271

Authors:

V.B.Vollan,E.Hough,S.Karlsen

Key ref:

V.B.Vollan et al. (1999). Structural studies on the binding of 4-methylumbelliferone glycosides of chitin to rainbow trout lysozyme. Acta Crystallogr D Biol Crystallogr, 55, 60-66. PubMed id: 10089395 DOI: 10.1107/S0907444998006623

Date:

29-Apr-98 Release date: 04-May-99

Protein chain

P11941  (LYSC2_ONCMY) -  Lysozyme C II

Seq: 144 a.a.

Struc: 129 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.2.1.17 - Lysozyme.
• 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 

• Cellular component: extracellular region (1 term)
• Biological process: metabolic process (4 terms)
• Biochemical function: catalytic activity (4 terms)

DOI no: 10.1107/S0907444998006623

Acta Crystallogr D Biol Crystallogr 55:60-66 (1999)

PubMed id: 10089395

Structural studies on the binding of 4-methylumbelliferone glycosides of chitin to rainbow trout lysozyme.

V.B.Vollan, E.Hough, S.Karlsen.

ABSTRACT

Two complexes between rainbow trout lysozyme (RBTL) and 4-methylumbelliferyl chitobioside, 4MeU-(GlcNAc)2, and chitotrioside, 4MeU-(GlcNAc)3, were produced by co-crystallization and soaking, respectively, and the crystal structures were solved at 2.0 A resolution. The results show that 4-MeU-(GlcNAc)3 binds in subsites A-D and that 4-MeU-(GlcNAc)2 binds in subsites B-D in the active-site cleft of RBTL. This agrees well with earlier crystallographic studies on the binding of oligosaccharides of chitin to RBTL, which showed that (GlcNAc)3 binds to sites B-D in RBTL and not to A-C as seen in the human and turkey egg-white lysozymes. For both complexes the 4-MeU moiety in site D has diffuse electron density and is flexible, as it is only bound to water molecules and not to the protein. Since no electron density was observed in site E, the solved structures give views of nonproductive enzyme-substrate complexes.

Selected figure(s)

Figure 4.
Figure 4 Hydrogen-bonding interactions between (a) 4-MeU-(GlcNAc)[2] and (b) 4-MeU-(GlcNAc)[3] and RBTL. The complexes are illustrated with ball-and-stick models and the hydrogen bonds are shown by dotted lines. The figures were generated by using the program BOBSCRIPT (Esnouf, 1997[Esnouf, R. M. (1997). J. Mol. Graph. 15, 133-138.]).

Figure 5.
Figure 5 All figures were generated using BOBSCRIPT (Esnouf, 1997[Esnouf, R. M. (1997). J. Mol. Graph. 15, 133-138.]). (a) A superimposition of 4-MeU-(GlcNAc)[2] (blue) on 4-MeU-(GlcNAc)[3] (red) in the active-site cleft of RBTL. The protein models in the former and latter complexes are coloured green and purple, respectively. (b) A superimposition of RBTL-4-MeU-(GlcNAc)[3] (purple/red) and RBTL-(GlcNAc)[4] (green/blue) (Karlsen & Hough, 1995[Karlsen, S. & Hough, E. (1995). Acta Cryst. D51, 962-978.]). (c) A superimposition of RBTL-4-MeU-(GlcNAc)[3] (purple/red) and RBTL-bulgecin (green/blue) (Karlsen & Hough, 1996[Karlsen, S. & Hough, E. (1996). Acta Cryst. D52, 115-123.]).

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1999, 55, 60-66) copyright 1999.

Figures were selected by an automated process.