ISDA

Deposition Date 2001-06-19

Release Date 2001-08-30

Last Version Date 2024-05-01

Entry Detail

PDB ID:

1H6M

Keywords:

HYDROLASE

Title:

Covalent glycosyl-enzyme intermediate of hen egg white lysozyme

Biological Source:

Source Organism:

GALLUS GALLUS (Taxon ID: 9031)

Host Organism:

SACCHAROMYCES CEREVISIAE

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.64 Å

R-Value Free:

0.22

R-Value Work:

0.17

R-Value Observed:

0.17

Space Group:

P 43 21 2

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:LYSOZYME C
Gene (Uniprot):LYZ
Mutations:YES
Chain IDs:A
Chain Length:129
Number of Molecules:1
Biological Source:GALLUS GALLUS

UniProt ID:P00698 Pfam ID:PF00062 EC:3.2.1.17

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
ASN	A	ASN	GLYCOSYLATION SITE

Ligand Molecules

Primary Citation

Catalysis by Hen Egg-White Lysozyme Proceeds Via a Covalent Intermediate

Vocadlo, D.J, Davies, G.J, Laine, R, Withers, S.G, Strydnaka, N.C.J, James, M.N.G, Malcolm, B.A, Rosenberg, S, Corey, M.J, Allen, J.S, Debaetselier, A, Kirsch, J.F, Blake, C.C.F, Koenig, D.F, Mair, G.A, North, A.C.T, Phillips, D.C, Sarma, V.R.Show

Nature 412 835 ? (2001)

PMID: 11518970 DOI: 10.1038/35090602

Abstact

Hen egg-white lysozyme (HEWL) was the first enzyme to have its three-dimensional structure determined by X-ray diffraction techniques. A catalytic mechanism, featuring a long-lived oxocarbenium-ion intermediate, was proposed on the basis of model-building studies. The 'Phillips' mechanism is widely held as the paradigm for the catalytic mechanism of beta-glycosidases that cleave glycosidic linkages with net retention of configuration of the anomeric centre. Studies with other retaining beta-glycosidases, however, provide strong evidence pointing to a common mechanism for these enzymes that involves a covalent glycosyl-enzyme intermediate, as previously postulated. Here we show, in three different cases using electrospray ionization mass spectrometry, a catalytically competent covalent glycosyl-enzyme intermediate during the catalytic cycle of HEWL. We also show the three-dimensional structure of this intermediate as determined by X-ray diffraction. We formulate a general catalytic mechanism for all retaining beta-glycosidases that includes substrate distortion, formation of a covalent intermediate, and the electrophilic migration of C1 along the reaction coordinate.

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Disease

Primary Citation of related structures