PDBsum entry: 4pbg

Hydrolase

PDB id: 4pbg

Contents

Protein chains

468 a.a. *

Ligands

BGP ×2

Waters ×359

* Residue conservation analysis

PDB id:

4pbg

Name:

Hydrolase

Title:

6-phospho-beta-galactosidase form-cst

Structure:

6-phospho-beta-d-galactosidase. Chain: a, b. Synonym: pgal. Engineered: yes. Mutation: yes

Source:

Lactococcus lactis. Organism_taxid: 1358. Strain: subsp. Lactis 712. Gene: lacg. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.50Å R-factor: 0.202

Authors:

C.Wiesmann,G.E.Schulz

Key ref:

C.Wiesmann et al. (1997). Crystal structures and mechanism of 6-phospho-beta-galactosidase from Lactococcus lactis. J Mol Biol, 269, 851-860. PubMed id: 9223646 DOI: 10.1006/jmbi.1997.1084

Date:

21-Feb-97 Release date: 23-Jul-97

Protein chains

P11546  (LACG_LACLA) -  6-phospho-beta-galactosidase

Seq: 468 a.a.

Struc: 468 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.2.1.85 - 6-phospho-beta-galactosidase.
• Reaction: A 6-phospho-beta-D-galactoside + H₂O = 6-phospho-D-galactose + an alcohol

6-phospho-beta-D-galactoside + H(2)O = 6-phospho-D-galactose (Bound ligand (Het Group name = BGP) corresponds exactly) + alcohol

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

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (3 terms)
• Biochemical function: catalytic activity (6 terms)

reference

DOI no: 10.1006/jmbi.1997.1084

J Mol Biol 269:851-860 (1997)

PubMed id: 9223646

Crystal structures and mechanism of 6-phospho-beta-galactosidase from Lactococcus lactis.

C.Wiesmann, W.Hengstenberg, G.E.Schulz.

ABSTRACT

The initial structural model of 6-phospho-beta-galactosidase from Lactococcus = 23.6%) to 2.3 A resolution (1 A = 0.1 nm), and the structures of three other crystal forms were solved by molecular replacement. The four structural models are essentially identical. The catalytic center of the enzyme is approximately at the mass center of the molecule and can only be reached through a 20 A long channel, which is observed with an "open" or "closed" entrance. The closed entrance is probably too small for the educt lactose-6-phosphate to enter, but large enough for the first product glucose to leave. Among the presented structures is a complex between an almost inactive mutant and the second product galactose-6-phosphate, which is exclusively bound at side-chains. A superposition (onto the native enzyme) of galactose-6-phosphate as bound to the mutant suggests the geometry of a postulated covalent intermediate. The binding mode of the educt was modeled, starting from the bound galactose-6-phosphate. A tightly fixed tryptophan is used as a chopping-board for splitting the disaccharide, and several other aromatic residues in the active center cavity are likely to participate in substrate transport/binding.

Selected figure(s)

Figure 3.
Figure 3. View of the active center cavity/channel containing the bound Gal-6P produced as a cut surface representation of program GRASP [Nicholls et al 1991]. The positions of acid/base Glu160, phosphate-binding Lys435 and the mobile loops at the channel entrance (mouth) are indicated. Furthermore, the molecular “horn” at the top is identified by one residue label.

Figure 8.
Figure 8. Galactose-6-phosphate bound to enzyme mutant Glu375→Cys in crystal form C* as superimposed onto the native enzyme structure in crystal form C. The hydrogen bonds are marked by broken lines. The short distance between the nucleophile Glu375 and the C1-atom of Gal-6P is emphasized. The arrangement is likely to show an intermediate of the reaction.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1997, 269, 851-860) copyright 1997.

Figures were selected by an automated process.