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PDBsum entry 2ilu

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protein ligands links
Oxidoreductase PDB id
2ilu
Jmol
Contents
Protein chain
477 a.a. *
Ligands
SO4 ×2
NDP
Waters ×32
* Residue conservation analysis
PDB id:
2ilu
Name: Oxidoreductase
Title: Crystal structure of lactaldehyde dehydrogenase from e. Coli binary complex with NADPH
Structure: Aldehyde dehydrogenase a. Chain: a. Synonym: lactaldehyde dehydrogenase, glycolaldehyde dehydro engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: alda. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.70Å     R-factor:   0.212     R-free:   0.253
Authors: L.Di Costanzo,G.Gomez,D.W.Christianson
Key ref:
L.Di Costanzo et al. (2007). Crystal Structure of Lactaldehyde Dehydrogenase from Escherichia coli and Inferences Regarding Substrate and Cofactor Specificity. J Mol Biol, 366, 481-493. PubMed id: 17173928 DOI: 10.1016/j.jmb.2006.11.023
Date:
03-Oct-06     Release date:   08-May-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P25553  (ALDA_ECOLI) -  Lactaldehyde dehydrogenase
Seq:
Struc:
479 a.a.
477 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class 1: E.C.1.2.1.21  - Glycolaldehyde dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Glycolaldehyde + NAD+ + H2O = glycolate + NADH
Glycolaldehyde
+
NAD(+)
Bound ligand (Het Group name = NDP)
matches with 91.67% similarity
+ H(2)O
= glycolate
+ NADH
   Enzyme class 2: E.C.1.2.1.22  - Lactaldehyde dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (S)-lactaldehyde + NAD+ + H2O = (S)-lactate + NADH
(S)-lactaldehyde
+
NAD(+)
Bound ligand (Het Group name = NDP)
matches with 91.67% similarity
+ H(2)O
= (S)-lactate
+ NADH
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   4 terms 
  Biochemical function     oxidoreductase activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2006.11.023 J Mol Biol 366:481-493 (2007)
PubMed id: 17173928  
 
 
Crystal Structure of Lactaldehyde Dehydrogenase from Escherichia coli and Inferences Regarding Substrate and Cofactor Specificity.
L.Di Costanzo, G.A.Gomez, D.W.Christianson.
 
  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 (</=5%) side-product subsequent to its unexpected crystallization. Accordingly, we now report the serendipitous crystal structure determination of unliganded lactaldehyde dehydrogenase from E. coli determined by the technique of multiple isomorphous replacement using anomalous scattering at 2.2 A resolution. Additionally, we report the crystal structure of the ternary enzyme complex with products lactate and NADH at 2.1 A resolution, and the crystal structure of the enzyme complex with NADPH at 2.7 A resolution. The structure of the ternary complex reveals that the nicotinamide ring of the cofactor is disordered between two conformations: one with the ring positioned in the active site in the so-called hydrolysis conformation, and another with the ring extended out of the active site into the solvent region, designated the out conformation. This represents the first crystal structure of an aldehyde dehydrogenase-product complex. The active site pocket in which lactate binds is more constricted than that of medium-chain dehydrogenases such as the YdcW gene product of E. coli. The structure of the binary complex with NADPH reveals the first view of the structural basis of specificity for NADH: the negatively charged carboxylate group of E179 destabilizes the binding of the 2'-phosphate group of NADPH sterically and electrostatically, thereby accounting for the lack of enzyme activity with this cofactor.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Pathways of l-fucose and l-rhamnose metabolism in E. coli. Lactaldehyde dehydrogenase generates l-lactate, which is converted to pyruvate for entry into the central metabolic processes of the cell. Figure 1. Pathways of l-fucose and l-rhamnose metabolism in E. coli. Lactaldehyde dehydrogenase generates l-lactate, which is converted to pyruvate for entry into the central metabolic processes of the cell.
Figure 2.
Figure 2. The NAD^+-dependent oxidation of lactaldehyde to lactate catalyzed by lactaldehyde dehydrogenase. Figure 2. The NAD^+-dependent oxidation of lactaldehyde to lactate catalyzed by lactaldehyde dehydrogenase.
 
  The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2007, 366, 481-493) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20543070 C.Lee, I.Kim, J.Lee, K.L.Lee, B.Min, and C.Park (2010).
Transcriptional activation of the aldehyde reductase YqhD by YqhC and its implication in glyoxal metabolism of Escherichia coli K-12.
  J Bacteriol, 192, 4205-4214.  
20634950 S.O.Kotchoni, J.C.Jimenez-Lopez, D.Gao, V.Edwards, E.W.Gachomo, V.M.Margam, and M.J.Seufferheld (2010).
Modeling-dependent protein characterization of the rice aldehyde dehydrogenase (ALDH) superfamily reveals distinct functional and structural features.
  PLoS One, 5, e11516.  
19155215 J.Crawford, O.Grujic, E.Bruic, M.Czjzek, M.E.Grigg, and M.J.Boulanger (2009).
Structural characterization of the bradyzoite surface antigen (BSR4) from toxoplasma gondii, a unique addition to the surface antigen glycoprotein 1-related superfamily.
  J Biol Chem, 284, 9192-9198.
PDB code: 2jks
19300440 Y.G.Kim, S.Lee, O.S.Kwon, S.Y.Park, S.J.Lee, B.J.Park, and K.J.Kim (2009).
Redox-switch modulation of human SSADH by dynamic catalytic loop.
  EMBO J, 28, 959-968.
PDB codes: 2w8n 2w8o 2w8p 2w8q 2w8r
18312637 G.N.Parkinson, D.Vines, P.C.Driscoll, and S.Djordjevic (2008).
Crystal structures of PI3K-C2alpha PX domain indicate conformational change associated with ligand binding.
  BMC Struct Biol, 8, 13.
PDB codes: 2rea 2red
18218709 J.S.Rodríguez-Zavala (2008).
Enhancement of coenzyme binding by a single point mutation at the coenzyme binding domain of E. coli lactaldehyde dehydrogenase.
  Protein Sci, 17, 563-570.  
18793327 S.Watanabe, S.Piyanart, and K.Makino (2008).
Metabolic fate of L-lactaldehyde derived from an alternative L-rhamnose pathway.
  FEBS J, 275, 5139-5149.  
17890343 K.R.Hristova, R.Schmidt, A.Y.Chakicherla, T.C.Legler, J.Wu, P.S.Chain, K.M.Scow, and S.R.Kane (2007).
Comparative transcriptome analysis of Methylibium petroleiphilum PM1 exposed to the fuel oxygenates methyl tert-butyl ether and ethanol.
  Appl Environ Microbiol, 73, 7347-7357.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.