PDBsum entry 2gdv

Transferase

PDB id: 2gdv

Contents

Protein chains

504 a.a. *

Ligands

BGC ×2

Waters ×1006

* Residue conservation analysis

PDB id:

2gdv

Name:

Transferase

Title:

Sucrose phosphorylase from bifidobacterium adolescentis reacted with sucrose

Structure:

Sucrose phosphorylase. Chain: a, b. Engineered: yes

Source:

Bifidobacterium adolescentis. Organism_taxid: 1680. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.00Å R-factor: 0.198 R-free: 0.237

Authors:

L.K.Skov,O.Mirza,M.Gajhede,J.S.Katsrup

Key ref:

O.Mirza et al. (2006). Structural rearrangements of sucrose phosphorylase from Bifidobacterium adolescentis during sucrose conversion. J Biol Chem, 281, 35576-35584. PubMed id: 16990265 DOI: 10.1074/jbc.M605611200

Date:

17-Mar-06 Release date: 26-Sep-06

Protein chains

A0ZZH6  (SUCP_BIFAA) -  Sucrose phosphorylase from Bifidobacterium adolescentis (strain ATCC 15703 / DSM 20083 / NCTC 11814 / E194a)

Seq: 504 a.a.

Struc: 504 a.a.

Enzyme reactions

• Enzyme class: E.C.2.4.1.7 - sucrose phosphorylase.
• Reaction: sucrose + phosphate = D-fructose + alpha-D-glucose 1-phosphate

sucrose + phosphate = D-fructose + alpha-D-glucose 1-phosphate (Bound ligand (Het Group name = BGC) matches with 91.67% similarity)

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

reference

DOI no: 10.1074/jbc.M605611200

J Biol Chem 281:35576-35584 (2006)

PubMed id: 16990265

Structural rearrangements of sucrose phosphorylase from Bifidobacterium adolescentis during sucrose conversion.

O.Mirza, L.K.Skov, D.Sprogøe, L.A.van den Broek, G.Beldman, J.S.Kastrup, M.Gajhede.

ABSTRACT

The reaction mechanism of sucrose phosphorylase from Bifidobacterium adolescentis (BiSP) was studied by site-directed mutagenesis and x-ray crystallography. An inactive mutant of BiSP (E232Q) was co-crystallized with sucrose. The structure revealed a substrate-binding mode comparable with that seen in other related sucrose-acting enzymes. Wild-type BiSP was also crystallized in the presence of sucrose. In the dimeric structure, a covalent glucosyl intermediate was formed in one molecule of the BiSP dimer, and after hydrolysis of the glucosyl intermediate, a beta-D-glucose product complex was formed in the other molecule. Although the overall structure of the BiSP-glucosyl intermediate complex is similar to that of the BiSP(E232Q)-sucrose complex, the glucose complex discloses major differences in loop conformations. Two loops (residues 336-344 and 132-137) in the proximity of the active site move up to 16 and 4 A, respectively. On the basis of these findings, we have suggested a reaction cycle that takes into account the large movements in the active-site entrance loops.

Selected figure(s)

Figure 1.
FIGURE 1. Schematic representation of the domain organization of the mixed dimer of BiSP. The glucosyl intermediate (molecule A; left) and the glucose hydrolysis product (molecule B; right) are shown as red spheres. domains A, B, B', and C are colored green, yellow, blue, and orange, respectively. N and C correspond to the N and C termini, respectively, whereas A and B indicate the positions of loops A and B.

Figure 4.
FIGURE 4. Structural changes occurring during the enzyme reaction. A, close-up view of loops A and B of the wild-type BiSP covalent intermediate (molecule A; cyan) superimposed on the glucose product-bound form (molecule B; yellow). The bound glucose of molecule B is shown for clarity. B, close-up view of loops A and B and the noncovalently bound glucose molecule of the wild-type BiSP-glucose complex. Glucose 1-phosphate (yellow) has been modeled based on the position of the glucose interacting with Arg^135 and Tyr^344. C, proposed intermolecular phosphate-binding site created by two Arg^135 residues. The distances indicated by dashed lines are 3.9 Å. The bound sucrose molecules are shown as red van der Waals spheres.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 35576-35584) copyright 2006.

Figures were selected by an automated process.