1NBW

Glycerol dehydratase reactivase

• PDB DOI: https://doi.org/10.2210/pdb1NBW/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-12-04 Released: 2003-01-14 
• Deposition Author(s): Liao, D.-I., Reiss, L., Turner Jr., I., Dotson, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.271 
• R-Value Work: 0.232 

Literature

Structure of glycerol dehydratase reactivase: A new type of molecular chaperone

Liao, D.-I., Reiss, L., Turner Jr., I., Dotson, G.

(2003) Structure 11: 109-119

• PubMed: 12517345 
• DOI: https://doi.org/10.1016/s0969-2126(02)00935-8
• Primary Citation of Related Structures:  
  1NBW


• PubMed Abstract: 
  

  The function of glycerol dehydratase (GDH) reactivase is to remove damaged coenzyme B(12) from GDH that has suffered mechanism-based inactivation. The structure of GDH reactivase from Klebsiella pneumoniae was determined at 2.4 A resolution by the single isomorphous replacement with anomalous signal (SIR/AS) method. Each tetramer contains two elongated 63 kDa alpha subunits and two globular 14 kDa beta subunits. The alpha subunit contains structural features resembling both GroEL and Hsp70 groups of chaperones, and it appears chaperone like in its interactions with ATP. The fold of the beta subunit resembles that of the beta subunit of glycerol dehydratase, except that it lacks some coenzyme B(12) binding elements. A hypothesis for the reactivation mechanism of reactivase is proposed based on these structural features.

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Organizational Affiliation: 

DuPont Central Research and Development, Experimental Station, Wilmington, DE 19880, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 151.39 kDa 
• Atom Count: 11,079 
• Modelled Residue Count: 1,436 
• Deposited Residue Count: 1,448 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCEROL DEHYDRATASE REACTIVASE ALPHA SUBUNIT	A, C	607	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: dhaB4 EC: 4.2.1.30
UniProt
Find proteins for Q59474 (Klebsiella pneumoniae) Explore Q59474  Go to UniProtKB:  Q59474

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCEROL DEHYDRATASE REACTIVASE BETA SUBUNIT	B, D	117	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: orf2b
UniProt
Find proteins for Q48423 (Klebsiella pneumoniae) Explore Q48423  Go to UniProtKB:  Q48423

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A], F [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.271 
• R-Value Work: 0.232 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110	α = 90
b = 110	β = 90
c = 332.2	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASES	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-01-14 
Deposition Author(s): Liao, D.-I., Reiss, L., Turner Jr., I., Dotson, G.

Revision History  

• Version 1.0: 2003-01-14
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary