4EX9

Crystal structure of the prealnumycin C-glycosynthase AlnA in complex with ribulose 5-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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.USA 110: 1291-1296

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

  • 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 th ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AlnA
A
316Streptomyces sp. CM020Gene Names: alnA
Find proteins for B6SEG5 (Streptomyces sp. CM020)
Go to UniProtKB:  B6SEG5
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
5RP
Query on 5RP

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Download CCD File 
A
RIBULOSE-5-PHOSPHATE
C5 H11 O8 P
FNZLKVNUWIIPSJ-UHNVWZDZSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.220 
  • Space Group: I 41 3 2
Unit Cell:
Length (Å)Angle (°)
a = 168.790α = 90.00
b = 168.790β = 90.00
c = 168.790γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
DNAdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2013-02-13
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Structure summary