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PDBsum entry 1b57

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
1b57
Jmol
Contents
Protein chains
346 a.a. *
Ligands
PGH ×2
Metals
_ZN ×7
_NA ×2
_CL
Waters ×225
* Residue conservation analysis
PDB id:
1b57
Name: Lyase
Title: Class ii fructose-1,6-bisphosphate aldolase in complex with phosphoglycolohydroxamate
Structure: Protein (fructose-bisphosphate aldolase ii). Chain: a, b. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Strain: k12 cs520. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.192     R-free:   0.230
Authors: D.R.Hall,W.N.Hunter
Key ref:
D.R.Hall et al. (1999). The crystal structure of Escherichia coli class II fructose-1, 6-bisphosphate aldolase in complex with phosphoglycolohydroxamate reveals details of mechanism and specificity. J Mol Biol, 287, 383-394. PubMed id: 10080900 DOI: 10.1006/jmbi.1999.2609
Date:
12-Jan-99     Release date:   07-Jan-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0AB71  (ALF_ECOLI) -  Fructose-bisphosphate aldolase class 2
Seq:
Struc:
359 a.a.
346 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.1.2.13  - Fructose-bisphosphate aldolase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate
D-fructose 1,6-bisphosphate
=
glycerone phosphate
Bound ligand (Het Group name = PGH)
matches with 66.00% similarity
+ D-glyceraldehyde 3-phosphate
      Cofactor: Zn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   2 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1999.2609 J Mol Biol 287:383-394 (1999)
PubMed id: 10080900  
 
 
The crystal structure of Escherichia coli class II fructose-1, 6-bisphosphate aldolase in complex with phosphoglycolohydroxamate reveals details of mechanism and specificity.
D.R.Hall, G.A.Leonard, C.D.Reed, C.I.Watt, A.Berry, W.N.Hunter.
 
  ABSTRACT  
 
The structure of a class II fructose-1,6-bisphosphate aldolase in complex with the substrate analogue and inhibitor phosphoglycolohydroxamate (PGH) has been determined using X-ray diffraction terms to a resolution of 2.0 A (1 A=0.1 nm). The crystals are trigonal, space group P3121 with a=b=78.24 A, c=289.69 A. The asymmetric unit is a homodimer of (alpha/beta)8 barrels and the model has refined to give R-work 19.2 %, R-free (based on 5 % of the data) 23.0 %. PGH resembles the ene-diolate transition state of the physiological substrate dihydroxyacetone phosphate. It is well ordered and bound in a deep polar cavity at the C-terminal end of the (alpha/beta)8 barrel, where it chelates the catalytic zinc ion using hydroxyl and enolate oxygen atoms. Trigonal bipyramidal coordination of the zinc ion is completed by three histidine residues. The complex network of hydrogen bonds at the catalytic centre is required to organise the position of key functional groups and metal ion ligands. A well-defined monovalent cation-binding site is observed following significant re-organisation of loop structures. This assists the formation of a phosphate-binding site on one side of the barrel that tethers PGH in the catalytic site. The positions of functional groups of substrate and putative interactions with key amino acid residues are identified. Knowledge of the complex structure complements the results of spectroscopic and site-directed mutagenesis studies, and contributes to our understanding of the mechanism and substrate specificity of this family of enzymes. A reaction mechanism distinct from that proposed for other class II aldolases is discussed. The results suggest that the class II aldolases should be sub-divided into two groups on the basis of both distinct folds and mechanism.
 
  Selected figure(s)  
 
Figure 4.
Figure 6.
Figure 6. The proposed mechanism of the E. coli class II FBP-aldolase. Each of the five steps is discussed in the text.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 287, 383-394) copyright 1999.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference Google scholar

  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.  
19236002 A.Galkin, Z.Li, L.Li, L.Kulakova, L.R.Pal, D.Dunaway-Mariano, and O.Herzberg (2009).
Structural insights into the substrate binding and stereoselectivity of giardia fructose-1,6-bisphosphate aldolase.
  Biochemistry, 48, 3186-3196.
PDB codes: 3gak 3gay 3gb6
19690370 J.Praaenikar, P.V.Afonine, G.Guncar, P.D.Adams, and D.Turk (2009).
Averaged kick maps: less noise, more signal... and probably less bias.
  Acta Crystallogr D Biol Crystallogr, 65, 921-931.  
19167403 S.D.Pegan, K.Rukseree, S.G.Franzblau, and A.D.Mesecar (2009).
Structural basis for catalysis of a tetrameric class IIa fructose 1,6-bisphosphate aldolase from Mycobacterium tuberculosis.
  J Mol Biol, 386, 1038-1053.
PDB codes: 3ekl 3ekz 3elf
18453687 T.C.Terwilliger, R.W.Grosse-Kunstleve, P.V.Afonine, N.W.Moriarty, P.D.Adams, R.J.Read, P.H.Zwart, and L.W.Hung (2008).
Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias.
  Acta Crystallogr D Biol Crystallogr, 64, 515-524.  
17166851 A.Galkin, L.Kulakova, E.Melamud, L.Li, C.Wu, P.Mariano, D.Dunaway-Mariano, T.E.Nash, and O.Herzberg (2007).
Characterization, kinetics, and crystal structures of fructose-1,6-bisphosphate aldolase from the human parasite, Giardia lamblia.
  J Biol Chem, 282, 4859-4867.
PDB codes: 2isv 2isw
17326786 L.E.Chávez de Paz, G.Bergenholtz, G.Dahlén, and G.Svensäter (2007).
Response to alkaline stress by root canal bacteria in biofilms.
  Int Endod J, 40, 344-355.  
16267046 E.Di Cera (2006).
A structural perspective on enzymes activated by monovalent cations.
  J Biol Chem, 281, 1305-1308.  
16326908 V.F.Waingeh, C.D.Gustafson, E.I.Kozliak, S.L.Lowe, H.R.Knull, and K.A.Thomasson (2006).
Glycolytic enzyme interactions with yeast and skeletal muscle F-actin.
  Biophys J, 90, 1371-1384.  
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.  
14699122 T.Izard, and J.Sygusch (2004).
Induced fit movements and metal cofactor selectivity of class II aldolases: structure of Thermus aquaticus fructose-1,6-bisphosphate aldolase.
  J Biol Chem, 279, 11825-11833.
PDB codes: 1rv8 1rvg
12595741 D.R.Hall, L.E.Kemp, G.A.Leonard, K.Marshall, A.Berry, and W.N.Hunter (2003).
The organization of divalent cations in the active site of cadmium Escherichia coli fructose-1,6-bisphosphate aldolase.
  Acta Crystallogr D Biol Crystallogr, 59, 611-614.
PDB code: 1gyn
14567674 E.L.Wise, W.S.Yew, J.A.Gerlt, and I.Rayment (2003).
Structural evidence for a 1,2-enediolate intermediate in the reaction catalyzed by 3-keto-L-gulonate 6-phosphate decarboxylase, a member of the orotidine 5'-monophosphate decarboxylase suprafamily.
  Biochemistry, 42, 12133-12142.
PDB codes: 1q6l 1q6o 1q6q 1q6r
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.  
12626743 G.J.Williams, S.Domann, A.Nelson, and A.Berry (2003).
Modifying the stereochemistry of an enzyme-catalyzed reaction by directed evolution.
  Proc Natl Acad Sci U S A, 100, 3143-3148.  
11940603 D.R.Hall, C.S.Bond, G.A.Leonard, C.I.Watt, A.Berry, and W.N.Hunter (2002).
Structure of tagatose-1,6-bisphosphate aldolase. Insight into chiral discrimination, mechanism, and specificity of class II aldolases.
  J Biol Chem, 277, 22018-22024.
PDB code: 1gvf
  11525240 S.Kedzierska, G.Jezierski, and A.Taylor (2001).
DnaK/DnaJ chaperone system reactivates endogenous E. coli thermostable FBP aldolase in vivo and in vitro; the effect is enhanced by GroE heat shock proteins.
  Cell Stress Chaperones, 6, 29-37.  
11173490 V.Sauvé, and J.Sygusch (2001).
Crystallization and preliminary X-ray analysis of native and selenomethionine fructose-1,6-bisphosphate aldolase from Thermus aquaticus.
  Acta Crystallogr D Biol Crystallogr, 57, 310-313.  
11114510 H.Erlandsen, E.E.Abola, and R.C.Stevens (2000).
Combining structural genomics and enzymology: completing the picture in metabolic pathways and enzyme active sites.
  Curr Opin Struct Biol, 10, 719-730.  
10675594 M.Y.Galperin, L.Aravind, and E.V.Koonin (2000).
Aldolases of the DhnA family: a possible solution to the problem of pentose and hexose biosynthesis in archaea.
  FEMS Microbiol Lett, 183, 259-264.  
10712619 S.M.Zgiby, G.J.Thomson, S.Qamar, and A.Berry (2000).
Exploring substrate binding and discrimination in fructose1, 6-bisphosphate and tagatose 1,6-bisphosphate aldolases.
  Eur J Biochem, 267, 1858-1868.  
10531504 L.V.Buchanan, N.Mehta, L.Pocivavsek, S.Niranjanakumari, E.J.Toone, and J.H.Naismith (1999).
Initiating a structural study of 2-keto-3-deoxy-6-phosphogluconate aldolase from Escherichia coli.
  Acta Crystallogr D Biol Crystallogr, 55, 1946-1948.  
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.