spacer
spacer

PDBsum entry 1dzv

Go to PDB code: 
protein ligands metals links
Lyase (aldehyde) PDB id
1dzv
Jmol
Contents
Protein chain
206 a.a. *
Ligands
SO4
BME
Metals
_ZN
Waters ×110
* Residue conservation analysis
PDB id:
1dzv
Name: Lyase (aldehyde)
Title: L-fuculose-1-phosphate aldolase from escherichia coli mutant y113f/y209f
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: y113f and y209f substitutions performed with phosphorothioate method using m13mp19
Biol. unit: Homo-Tetramer (from PDB file)
Resolution:
1.86Å     R-factor:   0.168     R-free:   0.216
Authors: A.C.Joerger,G.E.Schulz
Key ref:
A.C.Joerger et al. (2000). Catalytic action of fuculose 1-phosphate aldolase (class II) as derived from structure-directed mutagenesis. Biochemistry, 39, 6033-6041. PubMed id: 10821675 DOI: 10.1021/bi9927686
Date:
07-Mar-00     Release date:   02-Jun-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: 10.1021/bi9927686 Biochemistry 39:6033-6041 (2000)
PubMed id: 10821675  
 
 
Catalytic action of fuculose 1-phosphate aldolase (class II) as derived from structure-directed mutagenesis.
A.C.Joerger, C.Gosse, W.D.Fessner, G.E.Schulz.
 
  ABSTRACT  
 
Previous analyses established the structures of unligated L-fuculose 1-phosphate aldolase and of the enzyme ligated with an inhibitor mimicking the substrate dihydroxyacetone phosphate. These data allowed us to suggest a catalytic mechanism. On the basis of this proposal, numerous mutations were now introduced at the active center and tested with respect to their catalytic rates and their product distributions. For several mutants, the structures were determined. The results demonstrate the catalytic importance of some particular residues in defined conformations and in the mobile C-terminal chain end. Moreover, they led to a modification of the proposed mechanism. The effect of some mutations on enantioselectivity and on the ratio of diastereomer formation indicates clearly the binding site of the aldehyde moiety in relation to the other substrate dihydroxyacetone phosphate.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21290439 M.Rale, S.Schneider, G.A.Sprenger, A.K.Samland, and W.D.Fessner (2011).
Broadening deoxysugar glycodiversity: natural and engineered transaldolases unlock a complementary substrate space.
  Chemistry, 17, 2623-2632.  
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.  
16491487 M.S.Taylor, and E.N.Jacobsen (2006).
Asymmetric catalysis by chiral hydrogen-bond donors.
  Angew Chem Int Ed Engl, 45, 1520-1543.  
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.  
14635130 B.D.Silverman (2003).
Hydrophobic moments of tertiary protein structures.
  Proteins, 53, 880-888.  
11316870 J.D.Cronk, J.A.Endrizzi, M.R.Cronk, J.W.O'neill, and K.Y.Zhang (2001).
Crystal structure of E. coli beta-carbonic anhydrase, an enzyme with an unusual pH-dependent activity.
  Protein Sci, 10, 911-922.
PDB codes: 1i6o 1i6p
11371533 R.W.Eaton (2001).
Plasmid-encoded phthalate catabolic pathway in Arthrobacter keyseri 12B.
  J Bacteriol, 183, 3689-3703.  
11849940 W.D.Fessner, and V.Helaine (2001).
Biocatalytic synthesis of hydroxylated natural products using aldolases and related enzymes.
  Curr Opin Biotechnol, 12, 574-586.  
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.