5I2A | pdb_00005i2a

1,2-propanediol Dehydration in Roseburia inulinivorans; Structural Basis for Substrate and Enantiomer Selectivity

• PDB DOI: https://doi.org/10.2210/pdb5I2A/pdb

• Classification: LYASE
• Organism(s): Roseburia inulinivorans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-02-08 Released: 2016-06-01 
• Deposition Author(s): LaMattina, J.W., Reitzer, P., Kapoor, S., Galzerani, F., Koch, D.J., Gouvea, I.E., Lanzilotta, W.N.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.183 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Literature

1,2-Propanediol Dehydration in Roseburia inulinivorans: STRUCTURAL BASIS FOR SUBSTRATE AND ENANTIOMER SELECTIVITY.

LaMattina, J.W., Keul, N.D., Reitzer, P., Kapoor, S., Galzerani, F., Koch, D.J., Gouvea, I.E., Lanzilotta, W.N.

(2016) J Biological Chem 291: 15515-15526

• PubMed: 27252380 
• DOI: https://doi.org/10.1074/jbc.M116.721142
• Primary Citation Related Structures: 
  5I2A, 5I2G


• PubMed Abstract: 
  

  Glycyl radical enzymes (GREs) represent a diverse superfamily of enzymes that utilize a radical mechanism to catalyze difficult, but often essential, chemical reactions. In this work we present the first biochemical and structural data for a GRE-type diol dehydratase from the organism Roseburia inulinivorans (RiDD). Despite high sequence (48% identity) and structural similarity to the GRE-type glycerol dehydratase from Clostridium butyricum, we demonstrate that the RiDD is in fact a diol dehydratase. In addition, the RiDD will utilize both (S)-1,2-propanediol and (R)-1,2-propanediol as a substrate, with an observed preference for the S enantiomer. Based on the new structural information we developed and successfully tested a hypothesis that explains the functional differences we observe.

---

Organizational Affiliation: 
• From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602 and.
BRASKEM S.A., Rua Lemos Moonteiro, 120 Edifício Odebrecht São Paulo, Butantã 05501-050-São Paulo, SP Brasil.
From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602 and [e-mail].

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)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 188.88 kDa 
• Atom Count: 14,399 
• Modeled Residue Count: 1,673 
• Deposited Residue Count: 1,686 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diol-dehydratase	A, B	843	Roseburia inulinivorans	Mutation(s): 0
UniProt
Find proteins for Q1A666 (Roseburia inulinivorans) Explore Q1A666  Go to UniProtKB:  Q1A666

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	C [auth A], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.183 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.206	α = 90
b = 183.225	β = 90
c = 228.339	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-01 
Deposition Author(s): LaMattina, J.W., Reitzer, P., Kapoor, S., Galzerani, F., Koch, D.J., Gouvea, I.E., Lanzilotta, W.N.

Revision History  

• Version 1.0: 2016-06-01
  Type: Initial release
  
• Version 1.1: 2016-06-15
  Changes: Database references, Structure summary
• Version 1.2: 2016-08-10
  Changes: Database references
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references, Derived calculations