1U11 | pdb_00001u11

PurE (N5-carboxyaminoimidazole Ribonucleotide Mutase) from the acidophile Acetobacter aceti

• PDB DOI: https://doi.org/10.2210/pdb1U11/pdb

• Classification: LYASE
• Organism(s): Acetobacter aceti
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-07-14 Released: 2004-09-28 
• Deposition Author(s): Settembre, E.C., Chittuluru, J.R., Mill, C.P., Kappock, T.J., Ealick, S.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.199 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

Acidophilic adaptations in the structure of Acetobacter aceti N5-carboxyaminoimidazole ribonucleotide mutase (PurE).

Settembre, E.C., Chittuluru, J.R., Mill, C.P., Kappock, T.J., Ealick, S.E.

(2004) Acta Crystallogr D Biol Crystallogr 60: 1753-1760

• PubMed: 15388921 
• DOI: https://doi.org/10.1107/S090744490401858X
• Primary Citation Related Structures: 
  1U11


• PubMed Abstract: 
  

  The crystal structure of Acetobacter aceti PurE was determined to a resolution of 1.55 A and is compared with the known structures of the class I PurEs from a mesophile, Escherichia coli, and a thermophile, Thermotoga maritima. Analyses of the general factors that increase protein stability are examined as potential explanations for the acid stability of A. aceti PurE. Increased inter-subunit hydrogen bonding and an increased number of arginine-containing salt bridges appear to account for the bulk of the increased acid stability. A chain of histidines linking two active sites is discussed in the context of the proton transfers catalyzed by the enzyme.

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Organizational Affiliation: 
• Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 16-mer - A16 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 37.89 kDa 
• Atom Count: 2,698 
• Modeled Residue Count: 322 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PurE (N5-carboxyaminoimidazole Ribonucleotide Mutase)	A, B	182	Acetobacter aceti	Mutation(s): 0  Gene Names: PurE EC: 5.4.99.18
UniProt
Find proteins for Q2QJL3 (Acetobacter aceti) Explore Q2QJL3  Go to UniProtKB:  Q2QJL3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A], D [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.199 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.25	α = 90
b = 99.25	β = 90
c = 164.81	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-28 
Deposition Author(s): Settembre, E.C., Chittuluru, J.R., Mill, C.P., Kappock, T.J., Ealick, S.E.

Revision History  

• Version 1.0: 2004-09-28
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations