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PDBsum entry 4fua

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protein ligands metals links
Lyase (aldehyde) PDB id
4fua
Jmol PyMol
Contents
Protein chain
206 a.a. *
Ligands
SO4
BME
PGH
Metals
_ZN
Waters ×66
* Residue conservation analysis
PDB id:
4fua
Name: Lyase (aldehyde)
Title: L-fuculose-1-phosphate aldolase complex with pgh
Structure: L-fuculose-1-phosphate aldolase. Chain: a. Engineered: yes. Other_details: pgh is a transition state analogue inhibitor
Source: Escherichia coli. Organism_taxid: 562. Strain: k12 ecl116. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PDB file)
Resolution:
2.43Å     R-factor:   0.185    
Authors: M.K.Dreyer,G.E.Schulz
Key ref:
M.K.Dreyer and G.E.Schulz (1996). Catalytic mechanism of the metal-dependent fuculose aldolase from Escherichia coli as derived from the structure. J Mol Biol, 259, 458-466. PubMed id: 8676381 DOI: 10.1006/jmbi.1996.0332
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.
206 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
Bound ligand (Het Group name = PGH)
matches with 66.67% similarity
+
(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!
  Cellular component     cytosol   1 term 
  Biological process     carbohydrate metabolic process   5 terms 
  Biochemical function     lyase activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1996.0332 J Mol Biol 259:458-466 (1996)
PubMed id: 8676381  
 
 
Catalytic mechanism of the metal-dependent fuculose aldolase from Escherichia coli as derived from the structure.
M.K.Dreyer, G.E.Schulz.
 
  ABSTRACT  
 
The structure of L-fuculose-1-phosphate aldolase in a cubic crystal form has been determined with and without the inhibitor phosphoglycolohydroxamate at 2.4 and 2.7 angstrom (1 angstrom = 0.1 nm) resolution, respectively. This inhibitor mimics the enediolate transition state of the substrate moiety dihydroxyacetone phosphate. The structures showed that dihydroxyacetone phosphate ligates the zinc ion of this metal-dependent class II aldolase with its hydroxyl and keto oxygen atoms, shifting Glu73 away from the zinc coordination sphere to a non-polar environment. At this position Glu73 accepts a proton in the initial reaction step, producing the enediolate which is then stabilized by the zinc ion. The other substrate moiety L-lactaldehyde was modeled, because no binding structure is yet available.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Stereo view of the active center of FucA with positive (green) and negative (red) difference density at 23.5s levels after soaking with PGH. Phases were taken from the unligated structure without sulfate, chloride and water. The depicted residues are 21 to 31, 40 to 46 and 70 to 162 (black). Residues of the neighboring subunit are 109' to 123', 159' to 174' and 198' to 206' (blue). The fitted PGH model is given in gold. The side-chains of Ala27, Asn29, Thr43, Ser71, Ser72, Glu73 (still in the Zn 2+ coordination sphere), Phe131, Tyr113' and Phe206' are introduced.
Figure 5.
Figure 5. B-factor distribution of FucA in crystal form K (continuous line). The dotted line depicts the B-factor distribution of the complex FucA:PGH.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 259, 458-466) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18604568 C.Andreini, I.Bertini, G.Cavallaro, G.L.Holliday, and J.M.Thornton (2008).
Metal ions in biological catalysis: from enzyme databases to general principles.
  J Biol Inorg Chem, 13, 1205-1218.  
17957392 S.A.Gabel, and R.E.London (2008).
Ternary borate-nucleoside complex stabilization by ribonuclease A demonstrates phosphate mimicry.
  J Biol Inorg Chem, 13, 207-217.  
17973403 T.Mukherjee, K.M.McCulloch, S.E.Ealick, and T.P.Begley (2007).
Gene identification and structural characterization of the pyridoxal 5'-phosphate degradative protein 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase from mesorhizobium loti MAFF303099.
  Biochemistry, 46, 13606-13615.
PDB code: 2z7b
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.  
16491487 M.S.Taylor, and E.N.Jacobsen (2006).
Asymmetric catalysis by chiral hydrogen-bond donors.
  Angew Chem Int Ed Engl, 45, 1520-1543.  
15981250 A.Berchanski, D.Segal, and M.Eisenstein (2005).
Modeling oligomers with Cn or Dn symmetry: application to CAPRI target 10.
  Proteins, 60, 202-206.  
15889167 J.Kofoed, J.L.Reymond, and T.Darbre (2005).
Prebiotic carbohydrate synthesis: zinc-proline catalyzes direct aqueous aldol reactions of alpha-hydroxy aldehydes and ketones.
  Org Biomol Chem, 3, 1850-1855.  
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.  
15625671 Z.Zhong, B.J.Postnikova, R.E.Hanes, V.M.Lynch, and E.V.Anslyn (2005).
Large pKa shifts of alpha-carbon acids induced by copper(II) complexes.
  Chemistry, 11, 2385-2394.  
12764229 B.A.Manjasetty, J.Powlowski, and A.Vrielink (2003).
Crystal structure of a bifunctional aldolase-dehydrogenase: sequestering a reactive and volatile intermediate.
  Proc Natl Acad Sci U S A, 100, 6992-6997.
PDB code: 1nvm
12777382 F.Pojer, R.Kahlich, B.Kammerer, S.M.Li, and L.Heide (2003).
CloR, a bifunctional non-heme iron oxygenase involved in clorobiocin biosynthesis.
  J Biol Chem, 278, 30661-30668.  
12837791 F.Schmitzberger, A.G.Smith, C.Abell, and T.L.Blundell (2003).
Comparative analysis of the Escherichia coli ketopantoate hydroxymethyltransferase crystal structure confirms that it is a member of the (betaalpha)8 phosphoenolpyruvate/pyruvate superfamily.
  J Bacteriol, 185, 4163-4171.  
12874287 R.L.Tuinstra, and H.M.Miziorko (2003).
Investigation of conserved acidic residues in 3-hydroxy-3-methylglutaryl-CoA lyase: implications for human disease and for functional roles in a family of related proteins.
  J Biol Chem, 278, 37092-37098.  
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
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.  
10769138 L.V.Lee, M.V.Vu, and W.W.Cleland (2000).
13C and deuterium isotope effects suggest an aldol cleavage mechanism for L-ribulose-5-phosphate 4-epimerase.
  Biochemistry, 39, 4808-4820.  
10769139 L.V.Lee, R.R.Poyner, M.V.Vu, and W.W.Cleland (2000).
Role of metal ions in the reaction catalyzed by L-ribulose-5-phosphate 4-epimerase.
  Biochemistry, 39, 4821-4830.  
10099128 P.J.O'Brien, and D.Herschlag (1999).
Catalytic promiscuity and the evolution of new enzymatic activities.
  Chem Biol, 6, R91.  
9548961 A.E.Johnson, and M.E.Tanner (1998).
Epimerization via carbon-carbon bond cleavage. L-ribulose-5-phosphate 4-epimerase as a masked class II aldolase.
  Biochemistry, 37, 5746-5754.  
9667911 W.D.Fessner (1998).
Enzyme mediated C-C bond formation.
  Curr Opin Chem Biol, 2, 85-97.  
9343352 S.Takayama, G.J.McGarvey, and C.H.Wong (1997).
Microbial aldolases and transketolases: new biocatalytic approaches to simple and complex sugars.
  Annu Rev Microbiol, 51, 285-310.  
8939754 S.J.Cooper, G.A.Leonard, S.M.McSweeney, A.W.Thompson, J.H.Naismith, S.Qamar, A.Plater, A.Berry, and W.N.Hunter (1996).
The crystal structure of a class II fructose-1,6-bisphosphate aldolase shows a novel binuclear metal-binding active site embedded in a familiar fold.
  Structure, 4, 1303-1315.
PDB code: 1zen
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.

 

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