5G4K | pdb_00005g4k

Phloroglucinol reductase from Clostridium sp. apo-form

• PDB DOI: https://doi.org/10.2210/pdb5G4K/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Clostridium sp.
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-05-13 Released: 2016-12-07 
• Deposition Author(s): Conradt, D., Hermann, B., Gerhardt, S., Einsle, O., Mueller, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 
  0.182 (Depositor) 
• R-Value Work: 
  0.157 (Depositor) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Biocatalytic Properties and Structural Analysis of Phloroglucinol Reductases.

Conradt, D., Hermann, B., Gerhardt, S., Einsle, O., Mueller, M.

(2016) Angew Chem Int Ed Engl 55: 15531

• PubMed: 27874239 
• DOI: https://doi.org/10.1002/anie.201607494
• Primary Citation Related Structures: 
  5G4K, 5G4L


• PubMed Abstract: 
  

  Phloroglucinol reductases (PGRs) are involved in anaerobic degradation in bacteria, in which they catalyze the dearomatization of phloroglucinol into dihydrophloroglucinol. We identified three PGRs, from different bacterial species, that are members of the family of NAD(P)H-dependent short-chain dehydrogenases/reductases (SDRs). In addition to catalyzing the reduction of the physiological substrate, the three enzymes exhibit activity towards 2,4,6-trihydroxybenzaldehyde, 2,4,6-trihydroxyacetophenone, and methyl 2,4,6-trihydroxybenzoate. Structural elucidation of PGRcl and comparison to known SDRs revealed a high degree of conservation. Several amino acid positions were identified as being conserved within the PGR subfamily and might be involved in substrate differentiation. The results enable the enzymatic dearomatization of monoaromatic phenol derivatives and provide insight into the functional diversity that may be found in families of enzymes displaying a high degree of structural homology.

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Organizational Affiliation: 
• Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany.
Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 62.27 kDa 
• Atom Count: 4,356 
• Modeled Residue Count: 528 
• Deposited Residue Count: 572 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OXIDOREDUCTASE, SHORT CHAIN DEHYDROGENASE/REDUCTASE FAMILY PROTEIN	A	286	Clostridium sp.	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
OXIDOREDUCTASE, SHORT CHAIN DEHYDROGENASE/REDUCTASE FAMILY PROTEIN	B	286	Clostridium sp.	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free:  0.182 (Depositor) 
• R-Value Work:  0.157 (Depositor) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.756	α = 90
b = 125.391	β = 90
c = 55.468	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-07 
Deposition Author(s): Conradt, D., Hermann, B., Gerhardt, S., Einsle, O., Mueller, M.

Revision History  

• Version 1.0: 2016-12-07
  Type: Initial release
  
• Version 1.1: 2016-12-14
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Other, Refinement description