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PDBsum entry 1e4b

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protein ligands metals links
Aldolase (class ii) PDB id
1e4b
Jmol
Contents
Protein chain
206 a.a. *
Ligands
SO4 ×2
BME
Metals
_ZN
Waters ×112
* Residue conservation analysis
PDB id:
1e4b
Name: Aldolase (class ii)
Title: L-fuculose 1-phosphate aldolase from escherichia coli mutant n29q
Structure: L-fuculose 1-phosphate aldolase. Chain: p. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: n29q substitution performed with phosphorothioate method using m13mp19
Biol. unit: Homo-Tetramer (from PDB file)
Resolution:
1.84Å     R-factor:   0.165     R-free:   0.204
Authors: A.C.Joerger,G.E.Schulz
Key ref:
A.C.Joerger et al. (2000). Structures of l-fuculose-1-phosphate aldolase mutants outlining motions during catalysis. J Mol Biol, 303, 531-543. PubMed id: 11054289 DOI: 10.1006/jmbi.2000.4153
Date:
30-Jun-00     Release date:   06-Nov-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0AB87  (FUCA_ECOLI) -  L-fuculose phosphate aldolase
Seq:
Struc:
215 a.a.
206 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.4.1.2.17  - L-fuculose-phosphate aldolase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-fuculose 1-phosphate = glycerone phosphate + (S)-lactaldehyde
L-fuculose 1-phosphate
= glycerone phosphate
+
(S)-lactaldehyde
Bound ligand (Het Group name = BME)
matches with 50.00% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   5 terms 
  Biochemical function     lyase activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.2000.4153 J Mol Biol 303:531-543 (2000)
PubMed id: 11054289  
 
 
Structures of l-fuculose-1-phosphate aldolase mutants outlining motions during catalysis.
A.C.Joerger, C.Mueller-Dieckmann, G.E.Schulz.
 
  ABSTRACT  
 
The crystal structures of l-fuculose-1-phosphate aldolase (FucA) with and without a ligated analogue of dihydroxyacetone phosphate (DHAP) and of a number of active center mutants have resulted in a model of the catalytic mechanism. This model has now been confirmed by structural analyses of further mutations at the zinc coordination sphere and at the phosphate site. In addition, these mutants have revealed new aspects of the catalysis: the hydroxyl group of Tyr113' (from a neighboring subunit), which sits just outside the zinc coordination sphere, steers DHAP towards a productive binding mode at the zinc ion; Glu73 contacts zinc in between the two ligand positions intended for the DHAP oxygen atoms and thus avoids blocking of these positions by a tetrahedrally coordinated hydroxy ion; the FucA polypeptide does not assume its minimum energy state but oscillates between two states of elevated energy as demonstrated by a mutant in a minimum energy state. The back and forth motion involves a mobile loop connecting the phosphate site with intersubunit motions and thus with the Brownian motion of the solvent. The phosphate group is bound strongly at a given distance to the zinc ion, which prevents the formation of too tight a DHAP:zinc complex. This observation explains our failure to find mutants that accept phosphate-free substitutes for DHAP. The FucA zinc coordination sphere is compared with that of carbonic anhydrase.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Stereo views of the active center of FucA: (a) the complex FucA:Sulf with a sulfate ion from the crystallization buffer bound at the phosphate site [Dreyer and Schulz 1993 and Dreyer and Schulz 1996a] containing the mobile loop (23-27) (orange); (b) the complex FucA:PGH with the transition state analogue phosphoglycolohydroxamate [Dreyer and Schulz 1996b] showing the solidified loop (23-27) and including a model (orange) of bound Image -lactaldehyde and solidified Tyr209' [Joerger et al 2000].
Figure 7.
Figure 7. The zinc coordination spheres of FucA:Sulf (yellow), FucA:PGH (red), FucA mutants Glu73->Ser (blue), Glu73->Gln (light blue/grey), E73Q/Y113F/Y209F (magenta), Ser71->Gln (green) and of carbonic anhydrase (pink, tetrahedron drawn out) [Hakansson et al 1992]. The structures were superimposed on the contacting histidine nitrogen atoms and the zinc ion. The N epsilon, Greek atoms of histidine 92, 94 and 155 and the zinc ion of FucA are shown in the respective colors. They correspond to His96-N epsilon, Greek , His94-N epsilon, Greek , and His119-Nd and the zinc ion of carbonic anhydrase, respectively.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 303, 531-543) copyright 2000.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20661960 X.Garrabou, L.Gómez, J.Joglar, S.Gil, T.Parella, J.Bujons, and P.Clapés (2010).
Structure-guided minimalist redesign of the L-fuculose-1-phosphate aldolase active site: expedient synthesis of novel polyhydroxylated pyrrolizidines and their inhibitory properties against glycosidases and intestinal disaccharidases.
  Chemistry, 16, 10691-10706.  
18391471 H.Ashida, Y.Saito, C.Kojima, and A.Yokota (2008).
Enzymatic characterization of 5-methylthioribulose-1-phosphate dehydratase of the methionine salvage pathway in Bacillus subtilis.
  Biosci Biotechnol Biochem, 72, 959-967.  
17139092 S.Keller, F.Pojer, L.Heide, and D.M.Lawson (2006).
Molecular replacement in the 'twilight zone': structure determination of the non-haem iron oxygenase NovR from Streptomyces spheroides through repeated density modification of a poor molecular-replacement solution.
  Acta Crystallogr D Biol Crystallogr, 62, 1564-1570.  
15669071 L.Espelt, J.Bujons, T.Parella, J.Calveras, J.Joglar, A.Delgado, and P.Clapés (2005).
Aldol additions of dihydroxyacetone phosphate to N-Cbz-amino aldehydes catalyzed by L-fuculose-1-phosphate aldolase in emulsion systems: inversion of stereoselectivity as a function of the acceptor aldehyde.
  Chemistry, 11, 1392-1401.  
11976494 M.Kroemer, and G.E.Schulz (2002).
The structure of L-rhamnulose-1-phosphate aldolase (class II) solved by low-resolution SIR phasing and 20-fold NCS averaging.
  Acta Crystallogr D Biol Crystallogr, 58, 824-832.
PDB code: 1gt7
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