PDBsum entry: 1w8r

Lyase

PDB id: 1w8r

Contents

Protein chains

(+ 4 more) 250 a.a. *

Ligands

F2P ×10

Waters ×1511

* Residue conservation analysis

Superseded by:

2yce

PDB id:

1w8r

Name:

Lyase

Title:

The mechanism of the schiff base forming fructose-1,6-bisphosphate aldolase: structural analysis of reaction intermediates

Structure:

Fructose-bisphosphate aldolase class i. Chain: a, b, c, d, e, f, g, h, i, j. Synonym: fbp aldolase. Engineered: yes. Mutation: yes. Other_details: k177 covalently bound to fbp

Source:

Thermoproteus tenax. Organism_taxid: 2271. Expressed in: escherichia coli. Expression_system_taxid: 511693. Expression_system_variant: de3.

Biol. unit:

Pentamer (from PDB file)

Resolution:

1.93Å R-factor: 0.149 R-free: 0.187

Authors:

E.Lorentzen,R.Hensel,B.Siebers,E.Pohl

Key ref:

E.Lorentzen et al. (2005). Mechanism of the Schiff base forming fructose-1,6-bisphosphate aldolase: structural analysis of reaction intermediates. Biochemistry, 44, 4222-4229. PubMed id: 15766250 DOI: 10.1021/bi048192o

Date:

27-Sep-04 Release date: 23-Mar-05

Protein chains

P58315  (ALF1_THETE) -  Fructose-bisphosphate aldolase class 1

Seq: 263 a.a.

Struc: 250 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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 (Bound ligand (Het Group name = F2P) corresponds exactly) = glycerone phosphate + D-glyceraldehyde 3-phosphate

• Cofactor: Zinc

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: metabolic process (2 terms)
• Biochemical function: catalytic activity (3 terms)

reference

DOI no: 10.1021/bi048192o

Biochemistry 44:4222-4229 (2005)

PubMed id: 15766250

Mechanism of the Schiff base forming fructose-1,6-bisphosphate aldolase: structural analysis of reaction intermediates.

E.Lorentzen, B.Siebers, R.Hensel, E.Pohl.

ABSTRACT

The glycolytic enzyme fructose-1,6-bisphosphate aldolase (FBPA) catalyzes the reversible cleavage of fructose 1,6-bisphosphate to glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. Catalysis of Schiff base forming class I FBPA relies on a number of intermediates covalently bound to the catalytic lysine. Using active site mutants of FBPA I from Thermoproteus tenax, we have solved the crystal structures of the enzyme covalently bound to the carbinolamine of the substrate fructose 1,6-bisphosphate and noncovalently bound to the cyclic form of the substrate. The structures, determined at a resolution of 1.9 A and refined to crystallographic R factors of 0.148 and 0.149, respectively, represent the first view of any FBPA I in these two stages of the reaction pathway and allow detailed analysis of the roles of active site residues in catalysis. The active site geometry of the Tyr146Phe FBPA variant with the carbinolamine intermediate supports the notion that in the archaeal FBPA I Tyr146 is the proton donor catalyzing the conversion between the carbinolamine and Schiff base. Our structural analysis furthermore indicates that Glu187 is the proton donor in the eukaryotic FBPA I, whereas an aspartic acid, conserved in all FBPA I enzymes, is in a perfect position to be the general base facilitating carbon-carbon cleavage. The crystal structure of the Trp144Glu, Tyr146Phe double-mutant substrate complex represents the first example where the cyclic form of beta-fructose 1,6-bisphosphate is noncovalently bound to FBPA I. The structure thus allows for the first time the catalytic mechanism of ring opening to be unraveled.