3DEZ

Crystal structure of Orotate phosphoribosyltransferase from Streptococcus mutans

• PDB DOI: https://doi.org/10.2210/pdb3DEZ/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus mutans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2008-06-11 Released: 2009-06-16 
• Deposition Author(s): Liu, C.P., Gao, Z.Q., Hou, H.F., Li, L.F., Su, X.D., Dong, Y.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.249 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 

Starting Model: experimental

Literature

Structure of orotate phosphoribosyltransferase from the caries pathogen Streptococcus mutans

Liu, C.P., Xu, R., Gao, Z.Q., Xu, J.H., Hou, H.F., Li, L.Q., She, Z., Li, L.F., Su, X.D., Liu, P., Dong, Y.H.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 498-502

• PubMed: 20445243 
• DOI: https://doi.org/10.1107/S1744309110009243
• Primary Citation of Related Structures:  
  3DEZ


• PubMed Abstract: 
  

  Orotate phosphoribosyltransferase (OPRTase) catalyzes the OMP-forming step in de novo pyrimidine-nucleotide biosynthesis. Here, the crystal structure of OPRTase from the caries pathogen Streptococcus mutans is reported at 2.4 A resolution. S. mutans OPRTase forms a symmetric dimer and each monomer binds two sulfates at the active sites. The structural symmetry of the sulfate-binding sites and the missing loops in this structure are consistent with a symmetric catalysis mechanism.

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Organizational Affiliation: 

Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 53.11 kDa 
• Atom Count: 3,198 
• Modelled Residue Count: 400 
• Deposited Residue Count: 486 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotate phosphoribosyltransferase	A, B	243	Streptococcus mutans	Mutation(s): 1  Gene Names: pyrE EC: 2.4.2.10
UniProt
Find proteins for Q8DTV2 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DTV2  Go to UniProtKB:  Q8DTV2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth B], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.249 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.798	α = 90
b = 73.798	β = 90
c = 184.779	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-16 
Deposition Author(s): Liu, C.P., Gao, Z.Q., Hou, H.F., Li, L.F., Su, X.D., Dong, Y.H.

Revision History  

• Version 1.0: 2009-06-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.3: 2023-11-01
  Changes: Data collection, Refinement description