Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.34 kDa 
• Atom Count: 2024 
• Modelled Residue Count: 219 
• Deposited Residue Count: 237 
• Unique protein chains: 1

4EX6

Crystal structure of the alnumycin P phosphatase AlnB

• PDB DOI: 10.2210/pdb4EX6/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces sp. CM020
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-30 Released: 2013-01-16 
• Deposition Author(s): Oja, T., Niiranen, L., Sandalova, T., Klika, K.D., Niemi, J., Mantsala, P., Schneider, G., Metsa-Ketela, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.153 
• R-Value Work: 0.119 
• R-Value Observed: 0.121 

Literature

Structural basis for C-ribosylation in the alnumycin A biosynthetic pathway.

Oja, T., Niiranen, L., Sandalova, T., Klika, K.D., Niemi, J., Mantsala, P., Schneider, G., Metsa-Ketela, M.

(2013) Proc Natl Acad Sci U S A 110: 1291-1296

• PubMed: 23297194 
• DOI: 10.1073/pnas.1207407110
• Primary Citation of Related Structures:  
  4EX6, 4EX7, 4EX8, 4EX9


• PubMed Abstract: 
  

Alnumycin A is an exceptional aromatic polyketide that contains a carbohydrate-like 4'-hydroxy-5'-hydroxymethyl-2',7'-dioxane moiety attached to the aglycone via a carbon-carbon bond. Recently, we have identified the D-ribose-5-phosphate origin of the dioxane unit and demonstrated that AlnA and AlnB are responsible for the overall C-ribosylation reaction. Here, we provide direct evidence that AlnA is a natural C-glycosynthase, which catalyzes the attachment of D-ribose-5-phosphate to prealnumycin by formation of the C(8)-C(1') bond as demonstrated by the structure of the intermediate alnumycin P. This compound is subsequently dephosphorylated by AlnB, an enzyme of the haloacid dehalogenase superfamily. Structure determination of the native trimeric AlnA to 2.1-Å resolution revealed a highly globular fold encompassing an α/β/α sandwich. The crystal structure of the complex with D-ribose-5-phosphate indicated that the phosphosugar is bound in the open-chain configuration. Identification of residues E29, K86, and K159 near the C-1 carbonyl of the ligand led us to propose that the carbon-carbon bond formation proceeds through a Michael-type addition. Determination of the crystal structure of the monomeric AlnB in the open conformation to 1.25-Å resolution showed that the protein consists of core and cap domains. Modeling of alnumycin P inside the cap domain positioned the phosphate group next to a Mg(2+) ion present at the junction of the domains. Mutagenesis data were consistent with the canonical reaction mechanism for this enzyme family revealing the importance of residues D15 and D17 for catalysis. The characterization of the prealnumycin C-ribosylation illustrates an alternative means for attachment of carbohydrates to natural products.

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Organizational Affiliation: 

Department of Biochemistry and Food Chemistry, University of Turku, FIN-20014 Turku, Finland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AlnB	A	237	Streptomyces sp. CM020	Mutation(s): 0  Gene Names: alnB
UniProt
Find proteins for B6SEG4 (Streptomyces sp. CM020) Explore B6SEG4  Go to UniProtKB:  B6SEG4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BO3	C [auth A]	BORIC ACID B H3 O3 KGBXLFKZBHKPEV-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.153 
• R-Value Work: 0.119 
• R-Value Observed: 0.121 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.929	α = 90
b = 62.378	β = 90
c = 62.873	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-04-30 
• Released Date: 2013-01-16 
Deposition Author(s): Oja, T., Niiranen, L., Sandalova, T., Klika, K.D., Niemi, J., Mantsala, P., Schneider, G., Metsa-Ketela, M.

Revision History  

• Version 1.0: 2013-01-16
  Type: Initial release
  
• Version 1.1: 2013-02-13
  Changes: Database references