PDBsum entry 4jaw

Hydrolase

PDB id: 4jaw

Contents

Protein chains

633 a.a.

Ligands

GAL-NGT ×2

SO4 ×7

Waters ×403

PDB id:

4jaw

Name:

Hydrolase

Title:

Crystal structure of lacto-n-biosidase from bifidobacterium bifidum complexed with lnb-thiazoline

Structure:

Lacto-n-biosidase. Chain: a, b. Fragment: unp residue 41-663. Engineered: yes

Source:

Bifidobacterium bifidum. Organism_taxid: 398514. Strain: jcm1254. Gene: lnbb. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.80Å R-factor: 0.183 R-free: 0.213

Authors:

T.Ito,T.Katayama,K.A.Stubbs,S.Fushinobu

Key ref:

T.Ito et al. (2013). Crystal structures of a glycoside hydrolase family 20 lacto-N-biosidase from Bifidobacterium bifidum. J Biol Chem, 288, 11795-11806. PubMed id: 23479733 DOI: 10.1074/jbc.M112.420109

Date:

19-Feb-13 Release date: 20-Mar-13

Protein chains

B3TLD6  (LNBB_BIFB1) -  Lacto-N-biosidase from Bifidobacterium bifidum (strain DSM 20082 / JCM 1254 / BCRC 11844 / KCTC 3440 / E319f (Variant a))

Seq: 1112 a.a.

Struc: 633 a.a.*

* PDB and UniProt seqs differ at 10 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.2.1.140 - lacto-N-biosidase.
• Reaction: beta-D-Gal-(1->3)-beta-D-GlcNAc-(1->3)-beta-D-Gal-(1->4)-D-Glc + H2O = beta-D-galactosyl-(1->3)-N-acetyl-D-glucosamine + lactose

beta-D-Gal-(1->3)-beta-D-GlcNAc-(1->3)-beta-D-Gal-(1->4)-D-Glc + H2O = beta-D-galactosyl-(1->3)-N-acetyl-D-glucosamine + lactose (Bound ligand (Het Group name = GAL) matches with 47.83% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1074/jbc.M112.420109

J Biol Chem 288:11795-11806 (2013)

PubMed id: 23479733

Crystal structures of a glycoside hydrolase family 20 lacto-N-biosidase from Bifidobacterium bifidum.

T.Ito, T.Katayama, M.Hattie, H.Sakurama, J.Wada, R.Suzuki, H.Ashida, T.Wakagi, K.Yamamoto, K.A.Stubbs, S.Fushinobu.

ABSTRACT

Human milk oligosaccharides contain a large variety of oligosaccharides, of which lacto-N-biose I (Gal-β1,3-GlcNAc; LNB) predominates as a major core structure. A unique metabolic pathway specific for LNB has recently been identified in the human commensal bifidobacteria. Several strains of infant gut-associated bifidobacteria possess lacto-N-biosidase, a membrane-anchored extracellular enzyme, that liberates LNB from the nonreducing end of human milk oligosaccharides and plays a key role in the metabolic pathway of these compounds. Lacto-N-biosidase belongs to the glycoside hydrolase family 20, and its reaction proceeds via a substrate-assisted catalytic mechanism. Several crystal structures of GH20 β-N-acetylhexosaminidases, which release monosaccharide GlcNAc from its substrate, have been determined, but to date, a structure of lacto-N-biosidase is unknown. Here, we have determined the first three-dimensional structures of lacto-N-biosidase from Bifidobacterium bifidum JCM1254 in complex with LNB and LNB-thiazoline (Gal-β1,3-GlcNAc-thiazoline) at 1.8-Å resolution. Lacto-N-biosidase consists of three domains, and the C-terminal domain has a unique β-trefoil-like fold. Compared with other β-N-acetylhexosaminidases, lacto-N-biosidase has a wide substrate-binding pocket with a -2 subsite specific for β-1,3-linked Gal, and the residues responsible for Gal recognition were identified. The bound ligands are recognized by extensive hydrogen bonds at all of their hydroxyls consistent with the enzyme's strict substrate specificity for the LNB moiety. The GlcNAc sugar ring of LNB is in a distorted conformation near (4)E, whereas that of LNB-thiazoline is in a (4)C1 conformation. A possible conformational pathway for the lacto-N-biosidase reaction is discussed.