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PDBsum entry 2fua

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protein ligands metals links
Lyase (aldehyde) PDB id
2fua
Jmol
Contents
Protein chain
210 a.a. *
Ligands
SO4 ×2
BME
Metals
_CO
Waters ×108
* Residue conservation analysis
PDB id:
2fua
Name: Lyase (aldehyde)
Title: L-fuculose 1-phosphate aldolase crystal form t with cobalt
Structure: L-fuculose-1-phosphate aldolase. Chain: a. Engineered: yes. Other_details: cobalt in this structure replaces the natura occurring zinc ion
Source: Escherichia coli. Organism_taxid: 562. Strain: k12 ecl116. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PDB file)
Resolution:
2.00Å     R-factor:   0.180    
Authors: M.K.Dreyer,G.E.Schulz
Key ref:
M.K.Dreyer and G.E.Schulz (1996). Refined high-resolution structure of the metal-ion dependent L-fuculose-1-phosphate aldolase (class II) from Escherichia coli. Acta Crystallogr D Biol Crystallogr, 52, 1082-1091. PubMed id: 15299567 DOI: 10.1107/S0907444996009146
Date:
14-Feb-96     Release date:   14-Oct-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0AB87  (FUCA_ECOLI) -  L-fuculose phosphate aldolase
Seq:
Struc:
215 a.a.
210 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 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: 10.1107/S0907444996009146 Acta Crystallogr D Biol Crystallogr 52:1082-1091 (1996)
PubMed id: 15299567  
 
 
Refined high-resolution structure of the metal-ion dependent L-fuculose-1-phosphate aldolase (class II) from Escherichia coli.
M.K.Dreyer, G.E.Schulz.
 
  ABSTRACT  
 
The structure of the class II zinc-ion dependent L-fuculose-1-phosphate aldolase from Escherichia coli in its tetragonal crystal form has been established at 1.92 A resolution. The homotetrameric enzyme has a molecular mass of 4 x 24 kDa and follows C(4) symmetry. The structure model is exactly symmetrical, which contradicts an observed birefringence anomaly of the crystals. The four catalytic centers are located in deep clefts at the interfaces of adjacent subunits. The zinc ion is coordinated by three histidines and one glutamate in an almost tetrahedral arrangement. In contrast to numerous other catalytically competent zinc ions, there is no water molecule in the ligand sphere. Replacement of zinc by a cobalt ion caused only small structural changes. A search through the Protein Data Bank indicated that the chain fold is novel. Sequence homology searches revealed a significant similarity to the bacterial L-ribulose-5-phosphate 4-epimerase.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Th tetragonal crystal form T in a plastic dish vewed exactly along the fourfold axis under the polarzing microscope where no birefringence should be expected. Still, the two pairs of opposite triangles change colors differently upon rotation. Under glss, the whole crystal is uniformly dark at 0 and 90 ° rotation and uniformly bright at 45 ° . At angles between these positions, the pirs of opposite triangles show different brightnesses (different colors under plastic). All faces of the crystals are optically flat, i.e. there is no pyramidal growth.
Figure 5.
Fig. 5. Stereo ribbn dagram of th FucA tetramer, view- ing approximately down the molecular fourfold axis. Black dots indicate the zinc ions at the ubunit interfaces. Some residue positions are labeled.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1996, 52, 1082-1091) copyright 1996.  
  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.  
18322711 A.Jiménez, P.Clapés, and R.Crehuet (2008).
A dynamic view of enzyme catalysis.
  J Mol Model, 14, 735-746.  
16585745 L.L.Grochowski, H.Xu, and R.H.White (2006).
Identification of lactaldehyde dehydrogenase in Methanocaldococcus jannaschii and its involvement in production of lactate for F420 biosynthesis.
  J Bacteriol, 188, 2836-2844.  
  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
10099128 P.J.O'Brien, and D.Herschlag (1999).
Catalytic promiscuity and the evolution of new enzymatic activities.
  Chem Biol, 6, R91.  
10545376 U.Ryde (1999).
Carboxylate binding modes in zinc proteins: A theoretical study
  Biophys J, 77, 2777-2787.  
  10082367 I.L.Alberts, K.Nadassy, and S.J.Wodak (1998).
Analysis of zinc binding sites in protein crystal structures.
  Protein Sci, 7, 1700-1716.  
9667911 W.D.Fessner (1998).
Enzyme mediated C-C bond formation.
  Curr Opin Chem Biol, 2, 85-97.  
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