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 and generated by PISA (software)

Biological Assembly 2  

 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 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 61.54 kDa 
• Atom Count: 2718 
• Modelled Residue Count: 354 
• Deposited Residue Count: 528 
• Unique protein chains: 1

4JEN

Structure of Clostridium botulinum CMP N-glycosidase, BcmB

• PDB DOI: 10.2210/pdb4JEN/pdb

• Classification: HYDROLASE
• Organism(s): Clostridium botulinum A str. ATCC 19397
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-02-27 Released: 2013-09-11 
• Deposition Author(s): Sikowitz, M.D., Cooper, L.E., Begley, T.P., Kaminski, P.A., Ealick, S.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.250 
• R-Value Work: 0.234 
• R-Value Observed: 0.235 

Literature

Reversal of the substrate specificity of CMP N-glycosidase to dCMP.

Sikowitz, M.D., Cooper, L.E., Begley, T.P., Kaminski, P.A., Ealick, S.E.

(2013) Biochemistry 52: 4037-4047

• PubMed: 23659472 
• DOI: 10.1021/bi400316p
• Primary Citation of Related Structures:  
  4JEL, 4JEM, 4JEN


• PubMed Abstract: 
  

MilB is a CMP hydrolase involved in the early steps of biosynthesis of the antifungal compound mildiomycin. An enzyme from the bacimethrin biosynthetic pathway, BcmB, is closely related to MilB in both sequence and function. These two enzymes belong to the nucleoside 2'-deoxyribosyltransferase (NDT) superfamily. NDTs catalyze N-glycosidic bond cleavage of 2'-deoxynucleosides via a covalent 2-deoxyribosyl-enzyme intermediate. Conservation of key active site residues suggests that members of the NDT superfamily share a common mechanism; however, the enzymes differ in their substrate preferences. Substrates vary in the type of nucleobase, the presence or absence of a 2'-hydroxyl group, and the presence or absence of a 5'-phosphate group. We have determined the structures of MilB and BcmB and compared them to previously determined structures of NDT superfamily members. The comparisons reveal how these enzymes differentiate between ribosyl and deoxyribosyl nucleotides or nucleosides and among different nucleobases. The 1.6 Å structure of the MilB-CMP complex reveals an active site feature that is not obvious from comparisons of sequence alone. MilB and BcmB that prefer substrates containing 2'-ribosyl groups have a phenylalanine positioned in the active site, whereas NDT family members with a preference for 2'-deoxyribosyl groups have a tyrosine residue. Further studies show that the phenylalanine is critical for the specificity of MilB and BcmB toward CMP, and mutation of this phenylalanine residue to tyrosine results in a 1000-fold reversal of substrate specificity from CMP to dCMP.

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Organizational Affiliation: 

Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CMP N-GLYCOSIDASE	A, B, C	176	Clostridium botulinum A str. ATCC 19397	Mutation(s): 0  Gene Names: CLB_0809

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth A], E [auth B], F [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.250 
• R-Value Work: 0.234 
• R-Value Observed: 0.235 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 177.948	α = 90
b = 104.006	β = 97.98
c = 40.225	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-02-27 
• Released Date: 2013-09-11 
Deposition Author(s): Sikowitz, M.D., Cooper, L.E., Begley, T.P., Kaminski, P.A., Ealick, S.E.

Revision History  

• Version 1.0: 2013-09-11
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description