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)

Biological Assembly 2  

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

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 134.88 kDa 
• Atom Count: 10379 
• Modelled Residue Count: 1171 
• Deposited Residue Count: 1197 
• Unique protein chains: 1

3OT9

Phosphopentomutase from Bacillus cereus bound to glucose-1,6-bisphosphate

• PDB DOI: 10.2210/pdb3OT9/pdb

• Classification: ISOMERASE
• Organism(s): Bacillus cereus ATCC 14579
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-09-10 Released: 2010-12-29 
• Deposition Author(s): Panosian, T.D., Nannemann, D.P., Watkins, G., Phalen, V., Wadzinski, B., Bachmann, B.O., Iverson, T.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.190 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 

Literature

Bacillus cereus Phosphopentomutase Is an Alkaline Phosphatase Family Member That Exhibits an Altered Entry Point into the Catalytic Cycle.

Panosian, T.D., Nannemann, D.P., Watkins, G.R., Phelan, V.V., McDonald, W.H., Wadzinski, B.E., Bachmann, B.O., Iverson, T.M.

(2011) J Biol Chem 286: 8043-8054

• PubMed: 21193409 
• DOI: 10.1074/jbc.M110.201350
• Primary Citation of Related Structures:  
  3M8W, 3M8Y, 3M8Z, 3OT9


• PubMed Abstract: 
  

Bacterial phosphopentomutases (PPMs) are alkaline phosphatase superfamily members that interconvert α-D-ribose 5-phosphate (ribose 5-phosphate) and α-D-ribose 1-phosphate (ribose 1-phosphate). We investigated the reaction mechanism of Bacillus cereus PPM using a combination of structural and biochemical studies. Four high resolution crystal structures of B. cereus PPM revealed the active site architecture, identified binding sites for the substrate ribose 5-phosphate and the activator α-D-glucose 1,6-bisphosphate (glucose 1,6-bisphosphate), and demonstrated that glucose 1,6-bisphosphate increased phosphorylation of the active site residue Thr-85. The phosphorylation of Thr-85 was confirmed by Western and mass spectroscopic analyses. Biochemical assays identified Mn(2+)-dependent enzyme turnover and demonstrated that glucose 1,6-bisphosphate treatment increases enzyme activity. These results suggest that protein phosphorylation activates the enzyme, which supports an intermolecular transferase mechanism. We confirmed intermolecular phosphoryl transfer using an isotope relay assay in which PPM reactions containing mixtures of ribose 5-[(18)O(3)]phosphate and [U-(13)C(5)]ribose 5-phosphate were analyzed by mass spectrometry. This intermolecular phosphoryl transfer is seemingly counter to what is anticipated from phosphomutases employing a general alkaline phosphatase reaction mechanism, which are reported to catalyze intramolecular phosphoryl transfer. However, the two mechanisms may be reconciled if substrate encounters the enzyme at a different point in the catalytic cycle.

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Organizational Affiliation: 

Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphopentomutase	A, B, C	399	Bacillus cereus ATCC 14579	Mutation(s): 0  Gene Names: BC_4087, deoB EC: 5.4.2.7
UniProt
Find proteins for Q818Z9 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)) Explore Q818Z9  Go to UniProtKB:  Q818Z9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G16	I [auth A]	1,6-di-O-phosphono-alpha-D-glucopyranose C6 H13 O12 P2 RWHOZGRAXYWRNX-VFUOTHLCSA-M
GOL	G [auth A], H [auth A], M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	D [auth A], E [auth A], F [auth A], J [auth B], K [auth B], L [auth B], N [auth C], O [auth C], P [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A, B, C	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.190 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.871	α = 90
b = 76.582	β = 108.73
c = 107.051	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-09-10 
• Released Date: 2010-12-29 
Deposition Author(s): Panosian, T.D., Nannemann, D.P., Watkins, G., Phalen, V., Wadzinski, B., Bachmann, B.O., Iverson, T.M.

Revision History  

• Version 1.0: 2010-12-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary