PDBsum entry 3gxr

Hydrolase

PDB id

3gxr

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Contents

			Protein chains

					185 a.a. *


					174 a.a. *

			Ligands

					NAG-NAG ×2


					NAG-NAG-NAG ×3

			Waters ×293

* Residue conservation analysis

PDB id:

3gxr

Links

Name:

Hydrolase

Title:

The crystal structure of g-type lysozyme from atlantic cod (gadus morhua l.) In complex with NAG oligomers sheds new light on substrate binding and the catalytic mechanism. Structure with NAG to 1.7

Structure:

Goose-type lysozyme 1. Chain: a, b, c, d. Fragment: unp residues 31-217. Engineered: yes

Source:

Gadus morhua. Atlantic cod. Organism_taxid: 8049. Gene: lysozyme. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.70Å

R-factor:

0.206

R-free:

0.252

Authors:

R.Helland,R.L.Larsen,S.Finstad,P.Kyomuhendo,A.N.Larsen

Key ref:

R.Helland et al. (2009). Crystal structures of g-type lysozyme from Atlantic cod shed new light on substrate binding and the catalytic mechanism. Cell Mol Life Sci, 66, 2585-2598. PubMed id: 19543850

Date:

02-Apr-09

Release date:

20-Oct-09

PROCHECK

	Headers

	References

Protein chains

B9TU22 (B9TU22_GADMO) - Lysozyme g from Gadus morhua

Seq: Struc:					217 a.a. 185 a.a.*

Protein chain

B9TU22 (B9TU22_GADMO) - Lysozyme g from Gadus morhua

Seq: Struc:					217 a.a. 174 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 2 residue positions (black crosses)



		Enzyme reactions

Enzyme class:

Chains A, B, C, D: 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.

	Cell Mol Life Sci 66:2585-2598 (2009)
PubMed id: 19543850

Crystal structures of g-type lysozyme from Atlantic cod shed new light on substrate binding and the catalytic mechanism.
R.Helland, R.L.Larsen, S.Finstad, P.Kyomuhendo, A.N.Larsen.

ABSTRACT

Crystal structures of Atlantic cod lysozyme have been solved with and without ligand bound in the active site to 1.7 and 1.9 A resolution, respectively. The structures reveal the presence of NAG in the substrate binding sites at both sides of the catalytic Glu73, hence allowing the first crystallographic description of the goose-type (g-type) lysozyme E-G binding sites. In addition, two aspartic acid residues suggested to participate in catalysis (Asp101 and Asp90) were mutated to alanine. Muramidase activity data for two single mutants and one double mutant demonstrates that both residues are involved in catalysis, but Asp101 is the more critical of the two. The structures and activity data suggest that a water molecule is the nucleophile completing the catalytic reaction, and the roles of the aspartic acids are to ensure proper positioning of the catalytic water.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20734102

L.Vanderkelen, J.M.Van Herreweghe, K.G.Vanoirbeek, G.Baggerman, B.Myrnes, P.J.Declerck, I.W.Nilsen, C.W.Michiels, and L.Callewaert (2011).
Identification of a bacterial inhibitor against g-type lysozyme.

Cell Mol Life Sci, 68, 1053-1064.

21085702

A.Wohlkönig, J.Huet, Y.Looze, and R.Wintjens (2010).
Structural relationships in the lysozyme superfamily: significant evidence for glycoside hydrolase signature motifs.

PLoS One, 5, e15388.

20413917

L.Callewaert, and C.W.Michiels (2010).
Lysozymes in the animal kingdom.

J Biosci, 35, 127-160.

20586063

Y.Maruyama, A.Ochiai, T.Itoh, B.Mikami, W.Hashimoto, and K.Murata (2010).
Mutational studies of the peptidoglycan hydrolase FlgJ of Sphingomonas sp. strain A1.

J Basic Microbiol, 50, 311-317.

PDB code:

3k3t

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 code is shown on the right.