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Lyase(aldehyde) PDB id
1fba
Jmol
Contents
Protein chains
361 a.a. *
Waters ×1816
* Residue conservation analysis
PDB id:
1fba
Name: Lyase(aldehyde)
Title: The crystal structure of fructose-1,6-bisphosphate aldolase from drosophila melanogaster at 2.5 angstroms resolution
Structure: Fructose 1,6-bisphosphate aldolase. Chain: a, b, c, d. Engineered: yes
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227
Biol. unit: Tetramer (from PQS)
Resolution:
1.90Å     R-factor:   0.179    
Authors: K.Piontek,G.Hester,O.Brenner-Holzach
Key ref:
G.Hester et al. (1991). The crystal structure of fructose-1,6-bisphosphate aldolase from Drosophila melanogaster at 2.5 A resolution. FEBS Lett, 292, 237-242. PubMed id: 1959612 DOI: 10.1016/0014-5793(91)80875-4
Date:
08-Jun-92     Release date:   31-Oct-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P07764  (ALF_DROME) -  Fructose-bisphosphate aldolase
Seq:
Struc: 		361 a.a.
360 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.1.2.13  - Fructose-bisphosphate aldolase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate
D-fructose 1,6-bisphosphate
 = glycerone phosphate
 + D-glyceraldehyde 3-phosphate
      Cofactor: Zinc
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1016/0014-5793(91)80875-4 FEBS Lett 292:237-242 (1991)
PubMed id: 1959612  
 
 
The crystal structure of fructose-1,6-bisphosphate aldolase from Drosophila melanogaster at 2.5 A resolution.
G.Hester, O.Brenner-Holzach, F.A.Rossi, M.Struck-Donatz, K.H.Winterhalter, J.D.Smit, K.Piontek.
 
  ABSTRACT  
 
The structure of fructose-1,6-bisphosphate aldolase from Drosophila melanogaster has been determined by X-ray diffraction at 2.5 A resolution. The insect enzyme crystallizes in space group P2(1)2(1)2(1) with lattice replacement with rabbit muscle aldolase as a search model has been employed to solve the structure. To improve the initial phases real space averaging, including phase extension from 4.0 to 2.5 A, has been applied. Refinement of the atomic positions by molecular dynamics resulted in a crystallographic R-factor of 0.214. The tertiary structure resembles in most parts that of the vertebrate aldolase from rabbit muscle. Significant differences were found in surface loops and the N- and C-terminal regions of the protein. Here we present the first aldolase structure where the functionally important C-terminal arm is described completely.
 
  Selected figure(s)  
 
Figure 1.
ig. 1. Residues Val-343 to Ala-348 of DALD (thick lines) and the equivalent residues of MALD (thin lines). This part forms the beginning of the C-terminal arm. (A) Electron density map in this region before real space averaging. (B) Electron density map after eal space averaging. Both maps are contoured t 1.5 tr. 		Figure 4.
Fig. 4. C= stereo-plot of one subunit of DALD (thick lines) uperimposed with one subunit of RMALD (thin lines).
 
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (1991, 292, 237-242) copyright 1991.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20934451 D.W.Song, J.G.Lee, H.S.Youn, S.H.Eom, and d.o. .H.Kim (2011).
Ryanodine receptor assembly: A novel systems biology approach to 3D mapping.
  Prog Biophys Mol Biol, 105, 145-161.  
17154157 C.A.Buscaglia, W.G.Hol, V.Nussenzweig, and T.Cardozo (2007).
Modeling the interaction between aldolase and the thrombospondin-related anonymous protein, a key connection of the malaria parasite invasion machinery.
  Proteins, 66, 528-537.  
14993682 B.Liotard, and J.Sygusch (2004).
Purification, crystallization and preliminary X-ray analysis of native and selenomethionine class I tagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes.
  Acta Crystallogr D Biol Crystallogr, 60, 528-530.  
14699122 T.Izard, and J.Sygusch (2004).
Induced fit movements and metal cofactor selectivity of class II aldolases: structure of Thermus aquaticus fructose-1,6-bisphosphate aldolase.
  J Biol Chem, 279, 11825-11833.
PDB codes: 1rv8 1rvg
12829507 C.Sukow, and D.J.DeRosier (2003).
Order, disorder, and perturbations in actin-aldolase rafts.
  Biophys J, 85, 525-536.  
11779856 A.Maurady, A.Zdanov, D.de Moissac, D.Beaudry, and J.Sygusch (2002).
A conserved glutamate residue exhibits multifunctional catalytic roles in D-fructose-1,6-bisphosphate aldolases.
  J Biol Chem, 277, 9474-9483.
PDB codes: 1ewd 1ewe 1ewg 1ex5 3b8d
11679716 A.R.Dalby, D.R.Tolan, and J.A.Littlechild (2001).
The structure of human liver fructose-1,6-bisphosphate aldolase.
  Acta Crystallogr D Biol Crystallogr, 57, 1526-1533.
PDB code: 1qo5
  10048322 A.Dalby, Z.Dauter, and J.A.Littlechild (1999).
Crystal structure of human muscle aldolase complexed with fructose 1,6-bisphosphate: mechanistic implications.
  Protein Sci, 8, 291-297.
PDB codes: 2ald 4ald
9521758 H.Kim, U.Certa, H.Döbeli, P.Jakob, and W.G.Hol (1998).
Crystal structure of fructose-1,6-bisphosphate aldolase from the human malaria parasite Plasmodium falciparum.
  Biochemistry, 37, 4388-4396.
PDB code: 1a5c
9405338 C.F.Barbas, A.Heine, G.Zhong, T.Hoffmann, S.Gramatikova, R.Björnestedt, B.List, J.Anderson, E.A.Stura, I.A.Wilson, and R.A.Lerner (1997).
Immune versus natural selection: antibody aldolases with enzymic rates but broader scope.
  Science, 278, 2085-2092.
PDB code: 1axt
  9007983 J.Jia, U.Schörken, Y.Lindqvist, G.A.Sprenger, and G.Schneider (1997).
Crystal structure of the reduced Schiff-base intermediate complex of transaldolase B from Escherichia coli: mechanistic implications for class I aldolases.
  Protein Sci, 6, 119-124.
PDB code: 1ucw
9063881 J.P.Shaw, G.A.Petsko, and D.Ringe (1997).
Determination of the structure of alanine racemase from Bacillus stearothermophilus at 1.9-A resolution.
  Biochemistry, 36, 1329-1342.
PDB code: 1sft
8989320 N.Blom, and J.Sygusch (1997).
Product binding and role of the C-terminal region in class I D-fructose 1,6-bisphosphate aldolase.
  Nat Struct Biol, 4, 36-39.
PDB code: 1ado
8994627 O.Byron (1997).
Construction of hydrodynamic bead models from high-resolution X-ray crystallographic or nuclear magnetic resonance data.
  Biophys J, 72, 408-415.  
9406553 P.T.Erskine, N.Senior, S.Awan, R.Lambert, G.Lewis, I.J.Tickle, M.Sarwar, P.Spencer, P.Thomas, M.J.Warren, P.M.Shoolingin-Jordan, S.P.Wood, and J.B.Cooper (1997).
X-ray structure of 5-aminolaevulinate dehydratase, a hybrid aldolase.
  Nat Struct Biol, 4, 1025-1031.
PDB code: 1aw5
  9300484 S.Raychaudhuri, F.Younas, P.A.Karplus, C.H.Faerman, and D.R.Ripoll (1997).
Backbone makes a significant contribution to the electrostatics of alpha/beta-barrel proteins.
  Protein Sci, 6, 1849-1857.  
  8935175 A.Dalby, and J.A.Littlechild (1996).
Studies with type I aldolase to understand fructose intolerance and combat parasitic disease.
  J Pharm Pharmacol, 48, 214-217.  
  8805555 J.Jia, W.Huang, U.Schörken, H.Sahm, G.A.Sprenger, Y.Lindqvist, and G.Schneider (1996).
Crystal structure of transaldolase B from Escherichia coli suggests a circular permutation of the alpha/beta barrel within the class I aldolase family.
  Structure, 4, 715-724.
PDB code: 1onr
8718854 J.Sakon, W.S.Adney, M.E.Himmel, S.R.Thomas, and P.A.Karplus (1996).
Crystal structure of thermostable family 5 endocellulase E1 from Acidothermus cellulolyticus in complex with cellotetraose.
  Biochemistry, 35, 10648-10660.
PDB code: 1ece
8836102 N.S.Blom, S.Tétreault, R.Coulombe, and J.Sygusch (1996).
Novel active site in Escherichia coli fructose 1,6-bisphosphate aldolase.
  Nat Struct Biol, 3, 856-862.
PDB code: 1dos
  8939754 S.J.Cooper, G.A.Leonard, S.M.McSweeney, A.W.Thompson, J.H.Naismith, S.Qamar, A.Plater, A.Berry, and W.N.Hunter (1996).
The crystal structure of a class II fructose-1,6-bisphosphate aldolase shows a novel binuclear metal-binding active site embedded in a familiar fold.
  Structure, 4, 1303-1315.
PDB code: 1zen
  8771208 S.Qamar, K.Marsh, and A.Berry (1996).
Identification of arginine 331 as an important active site residue in the class II fructose-1,6-bisphosphate aldolase of Escherichia coli.
  Protein Sci, 5, 154-161.  
8710874 Z.Y.Zhu, and S.Karlin (1996).
Clusters of charged residues in protein three-dimensional structures.
  Proc Natl Acad Sci U S A, 93, 8350-8355.  
7592564 E.K.Jaffe (1995).
Porphobilinogen synthase, the first source of heme's asymmetry.
  J Bioenerg Biomembr, 27, 169-179.  
7851430 L.C.Packman, and A.Berry (1995).
A reactive, surface cysteine residue of the class-II fructose-1,6-bisphosphate aldolase of Escherichia coli revealed by electrospray ionisation mass spectrometry.
  Eur J Biochem, 227, 510-515.  
  8081752 T.Izard, M.C.Lawrence, R.L.Malby, G.G.Lilley, and P.M.Colman (1994).
The three-dimensional structure of N-acetylneuraminate lyase from Escherichia coli.
  Structure, 2, 361-369.
PDB code: 1nal
8488556 J.A.Littlechild, and H.C.Watson (1993).
A data-based reaction mechanism for type I fructose bisphosphate aldolase.
  Trends Biochem Sci, 18, 36-39.  
8513801 S.Gupta, R.Hollenstein, S.Kochhar, and P.Christen (1993).
Paracatalytic self-inactivation of fructose-1,6-bisphosphate aldolase. Structure of the crosslink formed at the active site.
  Eur J Biochem, 214, 515-519.  
8141995 S.Janecek, and S.Baláz (1993).
Evolution of parallel beta/alpha-barrel enzyme family lightened by structural data on starch-processing enzymes.
  J Protein Chem, 12, 509-514.  
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 codes are shown on the right.