PDBsum entry: 1b57

Lyase

PDB id: 1b57

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

Protein chains

P0AB71  (ALF_ECOLI) -  Fructose-bisphosphate aldolase class 2

Seq: 359 a.a.

Struc: 346 a.a.

Enzyme reactions

• Enzyme class: E.C.4.1.2.13 - Fructose-bisphosphate aldolase.
• 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: Zinc

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (2 terms)
• Biochemical function: catalytic activity (6 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.