spacer
spacer

PDBsum entry 1a4s

Go to PDB code: 
protein Protein-protein interface(s) links
Oxidoreductase PDB id
1a4s
Jmol
Contents
Protein chains
503 a.a. *
Waters ×693
* Residue conservation analysis
PDB id:
1a4s
Name: Oxidoreductase
Title: Betaine aldehyde dehydrogenase from cod liver
Structure: Betaine aldehyde dehydrogenase. Chain: a, b, c, d. Synonym: aldh. Ec: 1.2.1.8
Source: Gadus callarias. Baltic cod. Organism_taxid: 8053. Organ: liver
Biol. unit: Homo-Tetramer (from PDB file)
Resolution:
2.10Å     R-factor:   0.223     R-free:   0.253
Authors: K.Johansson,M.El Ahmad,L.Hjelmqvist,S.Ramaswamy,H.Jornvall, H.Eklund
Key ref:
K.Johansson et al. (1998). Structure of betaine aldehyde dehydrogenase at 2.1 A resolution. Protein Sci, 7, 2106-2117. PubMed id: 9792097 DOI: 10.1002/pro.5560071007
Date:
03-Feb-98     Release date:   08-Apr-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P56533  (BADH_GADMC) -  Betaine aldehyde dehydrogenase
Seq:
Struc:
503 a.a.
503 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 1: E.C.1.2.1.3  - Aldehyde dehydrogenase (NAD(+)).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: An aldehyde + NAD+ + H2O = a carboxylate + NADH
aldehyde
+ NAD(+)
+ H(2)O
= carboxylate
+ NADH
   Enzyme class 2: E.C.1.2.1.8  - Betaine-aldehyde dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Betaine aldehyde + NAD+ + H2O = betaine + NADH
Betaine aldehyde
+ NAD(+)
+ H(2)O
= betaine
+ 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!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   3 terms 
  Biochemical function     oxidoreductase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1002/pro.5560071007 Protein Sci 7:2106-2117 (1998)
PubMed id: 9792097  
 
 
Structure of betaine aldehyde dehydrogenase at 2.1 A resolution.
K.Johansson, M.El-Ahmad, S.Ramaswamy, L.Hjelmqvist, H.Jörnvall, H.Eklund.
 
  ABSTRACT  
 
The three-dimensional structure of betaine aldehyde dehydrogenase, the most abundant aldehyde dehydrogenase (ALDH) of cod liver, has been determined at 2.1 A resolution by the X-ray crystallographic method of molecular replacement. This enzyme represents a novel structure of the highly multiple ALDH, with at least 12 distinct classes in humans. This betaine ALDH of class 9 is different from the two recently determined ALDH structures (classes 2 and 3). Like these, the betaine ALDH structure has three domains, one coenzyme binding domain, one catalytic domain, and one oligomerization domain. Crystals grown in the presence or absence of NAD+ have very similar structures and no significant conformational change occurs upon coenzyme binding. This is probably due to the tight interactions between domains within the subunit and between subunits in the tetramer. The oligomerization domains link the catalytic domains together into two 20-stranded pleated sheet structures. The overall structure is similar to that of the tetrameric bovine class 2 and dimeric rat class 3 ALDH, but the coenzyme binding with the nicotinamide in anti conformation, resembles that of class 2 rather than of class 3.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Domain organization of he ALDH monomer. A: The structure f one subunit of ALDH where he common strands nd helices in the Rossmann type fold of the two domains are colored yellow and blue, respectively. The remaining helices and strands of these domains re colored gray, he oligomerization domain red. The bound NAD' is shown in a red ball andstick andthe active cysteine in green. B: Schematicdrawing f the secondary elements of the three domains colored as in A. Drawings were made by MOLSCRIPT (Kraulis, 991) and rendered using aster3D(Bacon & 1988; Merritt & Murphy, 994).
Figure 2.
Fig. 2. Dimerand tetramer organization of ALDH. A: The ALDH subunits form dimerswhere the oligomerizationdomainpleated sheet is continued into the p sheet of the catalytic domain of the other subunit. The sheet of the coenzyme binding domain is not directly connected to its counterpart inthesecond subunit. B: The tetramerwithheyellow-blue dimer interacting back to backwith red-greendimer.
 
  The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1998, 7, 2106-2117) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20174634 C.G.Langendorf, T.L.Key, G.Fenalti, W.T.Kan, A.M.Buckle, T.Caradoc-Davies, K.L.Tuck, R.H.Law, and J.C.Whisstock (2010).
The X-ray crystal structure of Escherichia coli succinic semialdehyde dehydrogenase; structural insights into NADP+/enzyme interactions.
  PLoS One, 5, e9280.
PDB code: 3jz4
20495892 H.F.Lo, and Y.J.Chen (2010).
gene cloning and biochemical characterization of a NAD(P)+ -dependent aldehyde dehydrogenase from Bacillus licheniformis.
  Mol Biotechnol, 46, 157-167.  
18848533 S.A.Krupenko (2009).
FDH: an aldehyde dehydrogenase fusion enzyme in folate metabolism.
  Chem Biol Interact, 178, 84-93.  
18661182 Z.J.Gu, L.Wang, D.Le Rudulier, B.Zhang, and S.S.Yang (2008).
Characterization of the glycine betaine biosynthetic genes in the moderately halophilic bacterium Halobacillus dabanensis D-8(T).
  Curr Microbiol, 57, 306-311.  
17940016 A.Korostelev, S.Trakhanov, H.Asahara, M.Laurberg, L.Lancaster, and H.F.Noller (2007).
Interactions and dynamics of the Shine Dalgarno helix in the 70S ribosome.
  Proc Natl Acad Sci U S A, 104, 16840-16843.
PDB codes: 1vsp 2qnh
17173928 L.Di Costanzo, G.A.Gomez, and D.W.Christianson (2007).
Crystal structure of lactaldehyde dehydrogenase from Escherichia coli and inferences regarding substrate and cofactor specificity.
  J Mol Biol, 366, 481-493.
PDB codes: 2hg2 2ilu 2imp
17587673 M.Hassan, S.Morimoto, H.Murakami, T.Ichiyanagi, and N.Mori (2007).
Purification and characterization of 4-N-trimethylamino-1-butanol dehydrogenase of Pseudomonas sp. 13CM.
  Biosci Biotechnol Biochem, 71, 1439-1446.  
16731973 J.S.Rodríguez-Zavala, A.Allali-Hassani, and H.Weiner (2006).
Characterization of E. coli tetrameric aldehyde dehydrogenases with atypical properties compared to other aldehyde dehydrogenases.
  Protein Sci, 15, 1387-1396.  
  16511109 E.Inagaki, H.Takahashi, C.Kuroishi, and T.H.Tahirov (2005).
Crystallization and avoiding the problem of hemihedral twinning in crystals of Delta1-pyrroline-5-carboxylate dehydrogenase from Thermus thermophilus.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 609-611.  
15272169 H.Dubourg, C.Stines-Chaumeil, C.Didierjean, F.Talfournier, S.Rahuel-Clermont, G.Branlant, and A.Aubry (2004).
Expression, purification, crystallization and preliminary X-ray diffraction data of methylmalonate-semialdehyde dehydrogenase from Bacillus subtilis.
  Acta Crystallogr D Biol Crystallogr, 60, 1435-1437.  
11842181 J.A.Barbosa, J.Sivaraman, Y.Li, R.Larocque, A.Matte, J.D.Schrag, and M.Cygler (2002).
Mechanism of action and NAD+-binding mode revealed by the crystal structure of L-histidinol dehydrogenase.
  Proc Natl Acad Sci U S A, 99, 1859-1864.
PDB codes: 1k75 1kae 1kah 1kar
12081471 J.S.Rodriguez-Zavala, and H.Weiner (2002).
Structural aspects of aldehyde dehydrogenase that influence dimer-tetramer formation.
  Biochemistry, 41, 8229-8237.  
11306030 H.Weiner, B.Wei, and J.Zhou (2001).
Subunit communication in tetrameric class 2 human liver aldehyde dehydrogenase as the basis for half-of-the-site reactivity and the dominance of the oriental subunit in a heterotetramer.
  Chem Biol Interact, 130, 47-56.  
11168411 J.Hempel, I.Kuo, J.Perozich, B.C.Wang, R.Lindahl, and H.Nicholas (2001).
Aldehyde dehydrogenase. Maintaining critical active site geometry at motif 8 in the class 3 enzyme.
  Eur J Biochem, 268, 722-726.  
11306028 L.Zhang, B.Ahvazi, R.Szittner, A.Vrielink, and E.Meighen (2001).
Differences in nucleotide specificity and catalytic mechanism between Vibrio harveyi aldehyde dehydrogenase and other members of the aldehyde dehydrogenase superfamily.
  Chem Biol Interact, 130, 29-38.  
11306026 T.D.Hurley, S.Perez-Miller, and H.Breen (2001).
Order and disorder in mitochondrial aldehyde dehydrogenase.
  Chem Biol Interact, 130, 3.
PDB code: 1o05
11106411 A.Incharoensakdi, N.Matsuda, T.Hibino, Y.L.Meng, H.Ishikawa, A.Hara, T.Funaguma, T.Takabe, and T.Takabe (2000).
Overproduction of spinach betaine aldehyde dehydrogenase in Escherichia coli. Structural and functional properties of wild-type, mutants and E. coli enzymes.
  Eur J Biochem, 267, 7015-7023.  
11012673 J.Perozich, I.Kuo, B.C.Wang, J.S.Boesch, R.Lindahl, and J.Hempel (2000).
Shifting the NAD/NADP preference in class 3 aldehyde dehydrogenase.
  Eur J Biochem, 267, 6197-6203.  
11087393 L.Zhang, B.Ahvazi, R.Szittner, A.Vrielink, and E.Meighen (2000).
A histidine residue in the catalytic mechanism distinguishes Vibrio harveyi aldehyde dehydrogenase from other members of the aldehyde dehydrogenase superfamily.
  Biochemistry, 39, 14409-14418.  
10801498 S.Suresh, S.Turley, F.R.Opperdoes, P.A.Michels, and W.G.Hol (2000).
A potential target enzyme for trypanocidal drugs revealed by the crystal structure of NAD-dependent glycerol-3-phosphate dehydrogenase from Leishmania mexicana.
  Structure, 8, 541-552.
PDB codes: 1evy 1evz
  10548037 C.J.Mann, and H.Weiner (1999).
Differences in the roles of conserved glutamic acid residues in the active site of human class 3 and class 2 aldehyde dehydrogenases.
  Protein Sci, 8, 1922-1929.  
  10210192 J.Perozich, H.Nicholas, B.C.Wang, R.Lindahl, and J.Hempel (1999).
Relationships within the aldehyde dehydrogenase extended family.
  Protein Sci, 8, 137-146.  
  10543811 J.Toth, A.A.Ismaiel, and J.S.Chen (1999).
The ald gene, encoding a coenzyme A-acylating aldehyde dehydrogenase, distinguishes Clostridium beijerinckii and two other solvent-producing clostridia from Clostridium acetobutylicum.
  Appl Environ Microbiol, 65, 4973-4980.  
  10631996 L.Ni, J.Zhou, T.D.Hurley, and H.Weiner (1999).
Human liver mitochondrial aldehyde dehydrogenase: three-dimensional structure and the restoration of solubility and activity of chimeric forms.
  Protein Sci, 8, 2784-2790.
PDB code: 1cw3
  9973357 R.Velasco-García, C.Mújica-Jiménez, G.Mendoza-Hernández, and R.A.Muñoz-Clares (1999).
Rapid purification and properties of betaine aldehyde dehydrogenase from Pseudomonas aeruginosa.
  J Bacteriol, 181, 1292-1300.  
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.