Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 112.81 kDa 
• Atom Count: 9393 
• Modelled Residue Count: 1008 
• Deposited Residue Count: 1008 
• Unique protein chains: 1

1R7A

Sucrose Phosphorylase from Bifidobacterium adolescentis

• PDB DOI: 10.2210/pdb1R7A/pdb

• Classification: TRANSFERASE
• Organism(s): Bifidobacterium adolescentis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-10-21 Released: 2004-02-10 
• Deposition Author(s): Sprogoe, D., van den Broek, L.A.M., Mirza, O., Kastrup, J.S., Voragen, A.G.J., Gajhede, M., Skov, L.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.195 
• R-Value Work: 0.164 
• R-Value Observed: 0.164 

Literature

Crystal structure of sucrose phosphorylase from Bifidobacterium adolescentis.

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

(2004) Biochemistry 43: 1156-1162

• PubMed: 14756551 
• DOI: 10.1021/bi0356395
• Primary Citation of Related Structures:  
  1R7A


• PubMed Abstract: 
  

Around 80 enzymes are implicated in the generic starch and sucrose pathways. One of these enzymes is sucrose phosphorylase, which reversibly catalyzes the conversion of sucrose and orthophosphate to d-Fructose and alpha-d-glucose 1-phosphate. Here, we present the crystal structure of sucrose phosphorylase from Bifidobacterium adolescentis (BiSP) refined at 1.77 A resolution. It represents the first 3D structure of a sucrose phosphorylase and is the first structure of a phosphate-dependent enzyme from the glycoside hydrolase family 13. The structure of BiSP is composed of the four domains A, B, B', and C. Domain A comprises the (beta/alpha)(8)-barrel common to family 13. The catalytic active-site residues (Asp192 and Glu232) are located at the tips of beta-sheets 4 and 5 in the (beta/alpha)(8)-barrel, as required for family 13 members. The topology of the B' domain disfavors oligosaccharide binding and reduces the size of the substrate access channel compared to other family 13 members, underlining the role of this domain in modulating the function of these enzymes. It is remarkable that the fold of the C domain is not observed in any other known hydrolases of family 13. BiSP was found as a homodimer in the crystal, and a dimer contact surface area of 960 A(2) per monomer was calculated. The majority of the interactions are confined to the two B domains, but interactions between the loop 8 regions of the two barrels are also observed. This results in a large cavity in the dimer, including the entrance to the two active sites.

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Organizational Affiliation: 

Structural Biology Group, Department of Medicinal Chemistry, The Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK-2100 Copenhagen, Denmark.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
sucrose phosphorylase	A, B	504	Bifidobacterium adolescentis	Mutation(s): 1  EC: 2.4.1.7
UniProt
Find proteins for A0ZZH6 (Bifidobacterium adolescentis (strain ATCC 15703 / DSM 20083 / NCTC 11814 / E194a)) Explore A0ZZH6  Go to UniProtKB:  A0ZZH6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	C [auth A], D [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A, B	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.195 
• R-Value Work: 0.164 
• R-Value Observed: 0.164 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.04	α = 90
b = 123.36	β = 90
c = 151.481	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-10-21 
• Released Date: 2004-02-10 
Deposition Author(s): Sprogoe, D., van den Broek, L.A.M., Mirza, O., Kastrup, J.S., Voragen, A.G.J., Gajhede, M., Skov, L.K.

Revision History  

• Version 1.0: 2004-02-10
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2014-11-19
  Changes: Non-polymer description