4A2C | pdb_00004a2c

Crystal structure of galactitol-1-phosphate dehydrogenase from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb4A2C/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-09-26 Released: 2012-08-08 
• Deposition Author(s): Alvarez, Y., Esteban-Torres, M., Acebron, I., de las Rivas, B., Munoz, R., Mancheno, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.273 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

The Crystal Structure of Galactitol-1-Phosphate 5-Dehydrogenase from Escherichia Coli K12 Provides Insights Into its Anomalous Behavior on Imac Processes

Esteban-Torres, M., Alvarez, Y., Acebron, I., De Las Rivas, B., Munoz, R., Kohring, G.-W., Roa, A.M., Sobrino, M., Mancheno, J.M.

(2012) FEBS Lett 586: 3127

• PubMed: 22979983 
• DOI: https://doi.org/10.1016/j.febslet.2012.07.073
• Primary Citation Related Structures: 
  4A2C


• PubMed Abstract: 
  

  Endogenous galactitol-1-phosphate 5-dehydrogenase (GPDH) (EC 1.1.1.251) from Escherichia coli spontaneously interacts with Ni(2+)-NTA matrices becoming a potential contaminant for recombinant, target His-tagged proteins. Purified recombinant, untagged GPDH (rGPDH) converted galactitol into tagatose, and d-tagatose-6-phosphate into galactitol-1-phosphate, in a Zn(2+)- and NAD(H)-dependent manner and readily crystallized what has permitted to solve its crystal structure. In contrast, N-terminally His-tagged GPDH was marginally stable and readily aggregated. The structure of rGPDH revealed metal-binding sites characteristic from the medium-chain dehydrogenase/reductase protein superfamily which may explain its ability to interact with immobilized metals. The structure also provides clues on the harmful effects of the N-terminal His-tag.

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Organizational Affiliation: 
• Laboratorio de Biotecnología Bacteriana, Instituto Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), CSIC, Madrid, Spain.

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: 75.17 kDa 
• Atom Count: 5,923 
• Modeled Residue Count: 692 
• Deposited Residue Count: 692 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GALACTITOL-1-PHOSPHATE 5-DEHYDROGENASE	A, B	346	Escherichia coli K-12	Mutation(s): 0  EC: 1.1.1.251
UniProt
Find proteins for P0A9S3 (Escherichia coli (strain K12)) Explore P0A9S3  Go to UniProtKB:  P0A9S3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NI	C [auth A], D [auth A], F [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.273 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.72	α = 90
b = 77.14	β = 95.36
c = 107.51	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-08 
Deposition Author(s): Alvarez, Y., Esteban-Torres, M., Acebron, I., de las Rivas, B., Munoz, R., Mancheno, J.M.

Revision History  

• Version 1.0: 2012-08-08
  Type: Initial release
  
• Version 1.1: 2012-08-22
  Changes: Database references
• Version 1.2: 2012-10-03
  Changes: Database references
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description