PDBsum entry 2zut

Transferase

PDB id: 2zut

Contents

Protein chains

744 a.a. *

Ligands

A2G ×4

GOL ×9

NO3

Metals

_MG ×6

Waters ×3114

* Residue conservation analysis

PDB id:

2zut

Name:

Transferase

Title:

Crystal structure of galacto-n-biose/lacto-n-biose i phosphorylase in complex with galnac

Structure:

Lacto-n-biose phosphorylase. Chain: a, b, c, d. Synonym: galacto-n-biose/lacto-n-biose i phosphorylase. Engineered: yes

Source:

Bifidobacterium longum. Organism_taxid: 216816. Strain: jcm1217. Gene: lnpa. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.163 R-free: 0.204

Authors:

M.Hidaka,M.Nishimoto,M.Kitaoka,T.Wakagi,H.Shoun,S.Fushinobu

Key ref:

M.Hidaka et al. (2009). The crystal structure of galacto-N-biose/lacto-N-biose I phosphorylase: a large deformation of a TIM barrel scaffold. J Biol Chem, 284, 7273-7283. PubMed id: 19124470 DOI: 10.1074/jbc.M808525200

Date:

28-Oct-08 Release date: 30-Dec-08

Protein chains

E8MF13  (LNPA_BIFL2) -  1,3-beta-galactosyl-N-acetylhexosamine phosphorylase from Bifidobacterium longum subsp. longum (strain ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194b)

Seq: 751 a.a.

Struc: 744 a.a.

Enzyme reactions

• Enzyme class: E.C.2.4.1.211 - 1,3-beta-galactosyl-N-acetylhexosamine phosphorylase.
• Reaction: beta-D-galactosyl-(1->3)-N-acetyl-D-glucosamine + phosphate = alpha-D- galactose 1-phosphate + N-acetyl-D-glucosamine

beta-D-galactosyl-(1->3)-N-acetyl-D-glucosamine + phosphate = alpha-D- galactose 1-phosphate + N-acetyl-D-glucosamine (Bound ligand (Het Group name = A2G) corresponds exactly)

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

reference

DOI no: 10.1074/jbc.M808525200

J Biol Chem 284:7273-7283 (2009)

PubMed id: 19124470

The crystal structure of galacto-N-biose/lacto-N-biose I phosphorylase: a large deformation of a TIM barrel scaffold.

M.Hidaka, M.Nishimoto, M.Kitaoka, T.Wakagi, H.Shoun, S.Fushinobu.

ABSTRACT

Galacto-N-biose/lacto-N-biose I phosphorylase (GLNBP) from Bifidobacterium longum, a key enzyme for intestinal growth, phosphorolyses galacto-N-biose and lacto-N-biose I with anomeric inversion. GLNBP homologues are often found in human pathogenic and commensal bacteria, and their substrate specificities potentially define the nutritional acquisition ability of these microbes in their habitat. We report the crystal structures of GLNBP in five different ligand-binding forms. This is the first three-dimensional structure of glycoside hydrolase (GH) family 112. The GlcNAc- and GalNAc-bound forms provide structural insights into distinct substrate preferences of GLNBP and its homologues from pathogens. The catalytic domain consists of a partially broken TIM barrel fold that is structurally similar to a thermophilic beta-galactosidase, strongly supporting the current classification of GLNBP homologues as one of the GH families. Anion binding induces a large conformational change by rotating a half-unit of the barrel. This is an unusual example of molecular adaptation of a TIM barrel scaffold to substrates.

Selected figure(s)

Figure 1.
Schematic representation of the reaction catalyzed by GalHexNAcP.

Figure 2.
Overall structure of GLNBP. The TIM barrel fold domain (blue), Ig-like fold domain (green), α/β fold domain (yellow), and C-terminal domain (red) are shown. A, dimeric structure of GlcNAc-NO[3]-EG crystal form. Subunits in the closed and semiclosed states are shown in a ribbon model. The semiclosed state subunit is shown with a different color code (TIM barrel domain in light blue, Ig-like domain in light green, α/β domain in brown, and C-terminal domain in pink). The ligand-free form in the open state (subunit A) (B) and GlcNAc-NO[3]-EG in the closed state (subunit A) (C) are shown from the same view as A. Ligands in the active site (GlcNAc, ethylene glycol, and ) are shown as a space-filling model. Asp-313 and Trp-233 are shown as a stick model (cyan), and the Cα atom of Gly-371 is shown as a red sphere.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 7273-7283) copyright 2009.

Figures were selected by an automated process.