PDBsum entry: 1bb7

Hydrolase

PDB-id: 1bb7

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PROCHECK

Protein chain

129 a.a. *

Ligands

GUM

Waters ×133

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

1bb7

Name:

Hydrolase

Title:

Lysozyme complex with 4-methyl-umbelliferyl chitobiose

Structure:

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

Source:

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

UniProt:

P11941 (LYSC2_ONCMY)

Seq:

144 a.a.

Struc:

129 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

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

Enzyme class:

E.C.3.2.1.17   [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.

Resolution:

2.00Å

R-factor:

0.175

R-free:

0.243

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

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Clefts

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Key reference

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.