PDBsum entry 1fq0

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Lyase PDB id
Protein chains
213 a.a. *
CIT ×3
Waters ×508
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Kdpg aldolase from escherichia coli
Structure: Kdpg aldolase. Chain: a, b, c. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PQS)
2.10Å     R-factor:   0.195     R-free:   0.251
Authors: J.H.Naismith
Key ref:
N.Wymer et al. (2001). Directed evolution of a new catalytic site in 2-keto-3-deoxy-6-phosphogluconate aldolase from Escherichia coli. Structure, 9, 1-9. PubMed id: 11342129 DOI: 10.1016/S0969-2126(00)00555-4
01-Sep-00     Release date:   04-Oct-00    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P0A955  (ALKH_ECOLI) -  KHG/KDPG aldolase
213 a.a.
213 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: E.C.  - 2-dehydro-3-deoxy-phosphogluconate aldolase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2-dehydro-3-deoxy-6-phosphate-D-gluconate = pyruvate + D-glyceraldehyde 3-phosphate
Bound ligand (Het Group name = CIT)
matches with 46.00% similarity
+ D-glyceraldehyde 3-phosphate
   Enzyme class 3: E.C.  - 4-hydroxy-2-oxoglutarate aldolase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 4-hydroxy-2-oxoglutarate = pyruvate + glyoxylate
Bound ligand (Het Group name = CIT)
matches with 60.00% similarity
= pyruvate
+ glyoxylate
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   3 terms 
  Biological process     metabolic process   1 term 
  Biochemical function     catalytic activity     5 terms  


DOI no: 10.1016/S0969-2126(00)00555-4 Structure 9:1-9 (2001)
PubMed id: 11342129  
Directed evolution of a new catalytic site in 2-keto-3-deoxy-6-phosphogluconate aldolase from Escherichia coli.
N.Wymer, L.V.Buchanan, D.Henderson, N.Mehta, C.H.Botting, L.Pocivavsek, C.A.Fierke, E.J.Toone, J.H.Naismith.
BACKGROUND: Aldolases are carbon bond-forming enzymes that have long been identified as useful tools for the organic chemist. However, their utility is limited in part by their narrow substrate utilization. Site-directed mutagenesis of various enzymes to alter their specificity has been performed for many years, typically without the desired effect. More recently directed evolution has been employed to engineer new activities onto existing scaffoldings. This approach allows random mutation of the gene and then selects for fitness to purpose those proteins with the desired activity. To date such approaches have furnished novel activities through multiple mutations of residues involved in recognition; in no instance has a key catalytic residue been altered while activity is retained. RESULTS: We report a double mutant of E. coli 2-keto-3-deoxy-6-phosphogluconate aldolase with reduced but measurable enzyme activity and a synthetically useful substrate profile. The mutant was identified from directed-evolution experiments. Modification of substrate specificity is achieved by altering the position of the active site lysine from one beta strand to a neighboring strand rather than by modification of the substrate recognition site. The new enzyme is different to all other existing aldolases with respect to the location of its active site to secondary structure. The new enzyme still displays enantiofacial discrimination during aldol addition. We have determined the crystal structure of the wild-type enzyme (by multiple wavelength methods) to 2.17 A and the double mutant enzyme to 2.7 A resolution. CONCLUSIONS: These results suggest that the scope of directed evolution is substantially larger than previously envisioned in that it is possible to perturb the active site residues themselves as well as surrounding loops to alter specificity. The structure of the double mutant shows how catalytic competency is maintained despite spatial reorganization of the active site with respect to substrate.
  Selected figure(s)  
Figure 1.
Figure 1. The Reaction Catalyzed by KDPG Aldolase

  The above figure is reprinted by permission from Cell Press: Structure (2001, 9, 1-9) copyright 2001.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  19923724 I.Campeotto, S.B.Carr, C.H.Trinh, A.S.Nelson, A.Berry, S.E.Phillips, and A.R.Pearson (2009).
Structure of an Escherichia coli N-acetyl-D-neuraminic acid lyase mutant, E192N, in complex with pyruvate at 1.45 angstrom resolution.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 1088-1090.
PDB code: 2wkj
19701186 M.Pavlova, M.Klvana, Z.Prokop, R.Chaloupkova, P.Banas, M.Otyepka, R.C.Wade, M.Tsuda, Y.Nagata, and J.Damborsky (2009).
Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate.
  Nat Chem Biol, 5, 727-733.  
17962400 M.Cheriyan, E.J.Toone, and C.A.Fierke (2007).
Mutagenesis of the phosphate-binding pocket of KDPG aldolase enhances selectivity for hydrophobic substrates.
  Protein Sci, 16, 2368-2377.  
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.  
17001724 F.P.Seebeck, A.Guainazzi, C.Amoreira, K.K.Baldridge, and D.Hilvert (2006).
Stereoselectivity and expanded substrate scope of an engineered PLP-dependent aldolase.
  Angew Chem Int Ed Engl, 45, 6824-6826.  
16923533 J.Kaur, and R.Sharma (2006).
Directed evolution: an approach to engineer enzymes.
  Crit Rev Biotechnol, 26, 165-199.  
15857781 B.Höcker (2005).
Directed evolution of (betaalpha)(8)-barrel enzymes.
  Biomol Eng, 22, 31-38.  
15340924 K.B.Murray, W.R.Taylor, and J.M.Thornton (2004).
Toward the detection and validation of repeats in protein structure.
  Proteins, 57, 365-380.  
15310956 R.Fischetti, S.Stepanov, G.Rosenbaum, R.Barrea, E.Black, D.Gore, R.Heurich, E.Kondrashkina, A.J.Kropf, S.Wang, K.Zhang, T.C.Irving, and G.B.Bunker (2004).
The BioCAT undulator beamline 18ID: a facility for biological non-crystalline diffraction and X-ray absorption spectroscopy at the Advanced Photon Source.
  J Synchrotron Radiat, 11, 399-405.  
15159565 R.H.Lilien, C.Bailey-Kellogg, A.C.Anderson, and B.R.Donald (2004).
A subgroup algorithm to identify cross-rotation peaks consistent with non-crystallographic symmetry.
  Acta Crystallogr D Biol Crystallogr, 60, 1057-1067.  
12876349 B.J.Bell, L.Watanabe, J.L.Rios-Steiner, A.Tulinsky, L.Lebioda, and R.K.Arni (2003).
Structure of 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase from Pseudomonas putida.
  Acta Crystallogr D Biol Crystallogr, 59, 1454-1458.
PDB code: 1mxs
12943851 Vries, and D.B.Janssen (2003).
Biocatalytic conversion of epoxides.
  Curr Opin Biotechnol, 14, 414-420.  
12151227 A.E.Todd, C.A.Orengo, and J.M.Thornton (2002).
Plasticity of enzyme active sites.
  Trends Biochem Sci, 27, 419-426.  
12080133 D.J.Brockwell, G.S.Beddard, J.Clarkson, R.C.Zinober, A.W.Blake, J.Trinick, P.D.Olmsted, D.A.Smith, and S.E.Radford (2002).
The effect of core destabilization on the mechanical resistance of I27.
  Biophys J, 83, 458-472.  
11950559 H.Zhao, K.Chockalingam, and Z.Chen (2002).
Directed evolution of enzymes and pathways for industrial biocatalysis.
  Curr Opin Biotechnol, 13, 104-110.  
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
11598300 A.Heine, G.DeSantis, J.G.Luz, M.Mitchell, C.H.Wong, and I.A.Wilson (2001).
Observation of covalent intermediates in an enzyme mechanism at atomic resolution.
  Science, 294, 369-374.
PDB codes: 1jcj 1jcl
11849936 E.T.Farinas, T.Bulter, and F.H.Arnold (2001).
Directed enzyme evolution.
  Curr Opin Biotechnol, 12, 545-551.  
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 code is shown on the right.