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PDBsum entry 1ok4

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protein ligands Protein-protein interface(s) links
Lyase PDB id
1ok4
Jmol
Contents
Protein chains
(+ 4 more) 251 a.a. *
Ligands
13P ×10
Waters ×641
* Residue conservation analysis
PDB id:
1ok4
Name: Lyase
Title: Archaeal fructose 1,6-bisphosphate aldolase covalently bound to the substrate dihydroxyacetone phosphate
Structure: Fructose-bisphosphate aldolase class i. Chain: a, b, c, d, e, f, g, h, i, j. Synonym: fbp aldolase. Engineered: yes. Other_details: lys177 schiff-base with dhap
Source: Thermoproteus tenax. Organism_taxid: 2271. Expressed in: escherichia coli. Expression_system_taxid: 511693. Expression_system_variant: de3.
Biol. unit: Pentamer (from PDB file)
Resolution:
2.1Å     R-factor:   0.164     R-free:   0.185
Authors: E.Lorentzen,P.Zwart,A.Stark,R.Hensel,B.Siebers,E.Pohl
Key ref:
E.Lorentzen et al. (2003). Crystal structure of an archaeal class I aldolase and the evolution of (betaalpha)8 barrel proteins. J Biol Chem, 278, 47253-47260. PubMed id: 12941964 DOI: 10.1074/jbc.M305922200
Date:
17-Jul-03     Release date:   04-Sep-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P58315  (ALF1_THETK) -  Fructose-bisphosphate aldolase class 1
Seq:
Struc:
263 a.a.
251 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
Bound ligand (Het Group name = 13P)
matches with 90.00% similarity
+ D-glyceraldehyde 3-phosphate
      Cofactor: Zn(2+)
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     glycolysis   1 term 
  Biochemical function     catalytic activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M305922200 J Biol Chem 278:47253-47260 (2003)
PubMed id: 12941964  
 
 
Crystal structure of an archaeal class I aldolase and the evolution of (betaalpha)8 barrel proteins.
E.Lorentzen, E.Pohl, P.Zwart, A.Stark, R.B.Russell, T.Knura, R.Hensel, B.Siebers.
 
  ABSTRACT  
 
Fructose-1,6-bisphosphate aldolase (FBPA) catalyzes the reversible cleavage of fructose 1,6-bisphosphate to glyceraldehyde 3-phosphate and dihydroxyacetone phosphate in the glycolytic pathway. FBPAs from archaeal organisms have recently been identified and characterized as a divergent family of proteins. Here, we report the first crystal structure of an archaeal FBPA at 1.9-A resolution. The structure of this 280-kDa protein complex was determined using single wavelength anomalous dispersion followed by 10-fold non-crystallographic symmetry averaging and refined to an R-factor of 14.9% (Rfree 17.9%). The protein forms a dimer of pentamers, consisting of subunits adopting the ubiquitous (betaalpha)8 barrel fold. Additionally, a crystal structure of the archaeal FBPA covalently bound to dihydroxyacetone phosphate was solved at 2.1-A resolution. Comparison of the active site residues with those of classical FBPAs, which share no significant sequence identity but display the same overall fold, reveals a common ancestry between these two families of FBPAs. Structural comparisons, furthermore, establish an evolutionary link to the triosephosphate isomerases, a superfamily hitherto considered independent from the superfamily of aldolases.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. A, ribbon diagram of the crystal structure of the Tt-FBPA decamer. Two pentamers face each other with the N-terminal side of the TIM barrels to form the decamer. Each monomer in the pentamers is shown in different colors and the two pentamers in different shadings. The active sites are located at the C termini of the TIM barrels and point away from the pentamer-pentamer interface. B, one pentamer is shown in a view perpendicular to that of A, using the same color coding.
Figure 3.
FIG. 3. Close-up of the central hole of the pentamer in the same orientation and color coding as Fig. 1B. The residues Phe-119, Trp-121, and Lys-122 from each monomer, shown in ball-and-stick representation, point into the central hole of the pentamer and perform a continuous stacking.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 47253-47260) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21983965 J.Du, R.F.Say, W.Lü, G.Fuchs, and O.Einsle (2011).
Active-site remodelling in the bifunctional fructose-1,6-bisphosphate aldolase/phosphatase.
  Nature, 478, 534-537.
PDB codes: 3t2b 3t2c 3t2d 3t2e 3t2f 3t2g
19714241 Z.Diaz, K.B.Xavier, and S.T.Miller (2009).
The crystal structure of the Escherichia coli autoinducer-2 processing protein LsrF.
  PLoS One, 4, e6820.
PDB codes: 3gkf 3glc 3gnd
18318840 A.K.Samland, M.Wang, and G.A.Sprenger (2008).
MJ0400 from Methanocaldococcus jannaschii exhibits fructose-1,6-bisphosphate aldolase activity.
  FEMS Microbiol Lett, 281, 36-41.  
18186475 A.Pauluhn, H.Ahmed, E.Lorentzen, S.Buchinger, D.Schomburg, B.Siebers, and E.Pohl (2008).
Crystal structure and stereochemical studies of KD(P)G aldolase from Thermoproteus tenax.
  Proteins, 72, 35-43.
PDB codes: 2r91 2r94
18491075 M.Zaparty, B.Tjaden, R.Hensel, and B.Siebers (2008).
The central carbohydrate metabolism of the hyperthermophilic crenarchaeote Thermoproteus tenax: pathways and insights into their regulation.
  Arch Microbiol, 190, 231-245.  
  18931429 N.N.Smith, and D.T.Gallagher (2008).
Structure and lability of archaeal dehydroquinase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 886-892.
PDB code: 2ox1
16614860 A.K.Samland, and G.A.Sprenger (2006).
Microbial aldolases as C-C bonding enzymes--unknown treasures and new developments.
  Appl Microbiol Biotechnol, 71, 253-264.  
16326908 V.F.Waingeh, C.D.Gustafson, E.I.Kozliak, S.L.Lowe, H.R.Knull, and K.A.Thomasson (2006).
Glycolytic enzyme interactions with yeast and skeletal muscle F-actin.
  Biophys J, 90, 1371-1384.  
16256419 B.Siebers, and P.Schönheit (2005).
Unusual pathways and enzymes of central carbohydrate metabolism in Archaea.
  Curr Opin Microbiol, 8, 695-705.  
16204887 J.Aishima, D.S.Russel, L.J.Guibas, P.D.Adams, and A.T.Brunger (2005).
Automated crystallographic ligand building using the medial axis transform of an electron-density isosurface.
  Acta Crystallogr D Biol Crystallogr, 61, 1354-1363.  
15296734 A.Stark, A.Shkumatov, and R.B.Russell (2004).
Finding functional sites in structural genomics proteins.
  Structure, 12, 1405-1412.  
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.  
15028704 B.Siebers, B.Tjaden, K.Michalke, C.Dörr, H.Ahmed, M.Zaparty, P.Gordon, C.W.Sensen, A.Zibat, H.P.Klenk, S.C.Schuster, and R.Hensel (2004).
Reconstruction of the central carbohydrate metabolism of Thermoproteus tenax by use of genomic and biochemical data.
  J Bacteriol, 186, 2179-2194.  
15572776 P.H.Zwart, G.G.Langer, and V.S.Lamzin (2004).
Modelling bound ligands in protein crystal structures.
  Acta Crystallogr D Biol Crystallogr, 60, 2230-2239.  
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.