2IMP | pdb_00002imp

Crystal structure of lactaldehyde dehydrogenase from E. coli: the ternary complex with lactate (occupancy 0.5) and NADH. Crystals soaked with (L)-Lactate.

• PDB DOI: https://doi.org/10.2210/pdb2IMP/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-10-04 Released: 2007-02-13 
• Deposition Author(s): Di Costanzo, L., Gomez, G.A., Christianson, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.234 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 

Literature

Crystal Structure of Lactaldehyde Dehydrogenase from Escherichia coli and Inferences Regarding Substrate and Cofactor Specificity.

Di Costanzo, L., Gomez, G.A., Christianson, D.W.

(2007) J Mol Biology 366: 481-493

• PubMed: 17173928 
• DOI: https://doi.org/10.1016/j.jmb.2006.11.023
• Primary Citation of Related Structures:  
  2HG2, 2ILU, 2IMP


• PubMed Abstract: 
  

  Aldehyde dehydrogenases catalyze the oxidation of aldehyde substrates to the corresponding carboxylic acids. Lactaldehyde dehydrogenase from Escherichia coli (aldA gene product, P25553) is an NAD(+)-dependent enzyme implicated in the metabolism of l-fucose and l-rhamnose. During the heterologous expression and purification of taxadiene synthase from the Pacific yew, lactaldehyde dehydrogenase from E. coli was identified as a minor (

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Organizational Affiliation: 

Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA.

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,PQS (software)

Macromolecule Content

• Total Structure Weight: 53.32 kDa 
• Atom Count: 3,991 
• Modelled Residue Count: 477 
• Deposited Residue Count: 479 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactaldehyde dehydrogenase	A	479	Escherichia coli	Mutation(s): 1  EC: 1.2.1.21 (PDB Primary Data), 1.2.1.22 (PDB Primary Data)
UniProt
Find proteins for P25553 (Escherichia coli (strain K12)) Explore P25553  Go to UniProtKB:  P25553

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAI	D [auth A]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
LAC	E [auth A]	LACTIC ACID C3 H6 O3 JVTAAEKCZFNVCJ-UWTATZPHSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS	A	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.234 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.034	α = 90
b = 143.034	β = 90
c = 109.364	γ = 120

Software Package:

Software Name	Purpose
DNA	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-13 
Deposition Author(s): Di Costanzo, L., Gomez, G.A., Christianson, D.W.

Revision History  

• Version 1.0: 2007-02-13
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 2.0: 2019-03-27
  Changes: Atomic model, Data collection, Derived calculations, Experimental preparation, Structure summary
• Version 3.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations