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Catalytic Site Atlas Version 2.2.12
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CSA entry for 1fc4
Original Entry
Title:
Transferase
Compound:
2-amino-3-ketobutyrate conenzyme a ligase
Mutant:
No
UniProt/Swiss-Prot:
P07912-KBL_ECOLI
EC Class:
2.3.1.29
Other CSA Entries:
Overview of all sites for 1fc4
Homologues of 1fc4
Entries for UniProt/Swiss-Prot: P07912
Entries for EC: 2.3.1.29
Other Databases:
PDB entry: 1fc4
PDBsum entry: 1fc4
UniProt/Swiss-Prot: P07912
IntEnz entry: 2.3.1.29
Literature Report:
Introduction:
Threonine is degraded into glycine and the acetyl group in a pathway common to prokaryotic and eukaryotic cells. The pathway is two steps long; the first step is the oxidation of the hydroxy group of threonine to create 2-amino-3-ketobutyrate. The second step is catalysed by 2-amino-3-ketobutyrate CoA ligase (KBL); this is a PLP-dependent acetyltransferase, transferring the newly formed acetyl group of the substrate to Coenzyme A to give glycine and acetyl-CoA.

The two enzymes needed for the pathway form a complex; this is because the aminoketobutyrate intermediate (substrate for KBL) spontaneously decarboxylates in aqueous solution.

Mechanism:
1) Lys 244 has a Schiff base linkage with the PLP cofactor. It is displaced by the amino acid substrate, in the usual fashion to give an external aldimine (PLP and threonine with a Schiff base linkage). In these steps His 213 acts as a general acid to the phenolic oxygen of PLP (with the phenolic proton being transferred to Lys 244), and a general base to the amino group of the joining threonine.

2) The thiol of CoA is nucleophilic and attacks the carbon of the carbonyl group of the aldimine. This gives a tetrahedral intermediate where the oxyanion is stabilised by hydrogen bonding to Ser 185. Lys 244 deprotonates the sulphur atom.

3) The tetrahedral intermediate collapses to release acetyl-CoA. The glycine moiety and PLP are held in a quinoid intermediate.

4) Lys 244 protonates the nitrogen of the glycine moiety, regenerating the substrate-PLP Schiff base link.

5) Lys 244 displaces the group bound to PLP in the usual fashion (His 213 again acting as a general acid/base) to release glycine and regenerate the original active PLP-enzyme adduct.

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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
1201 0
ElectrophileSubstrate
ModifiedResidue
The PLP cofactor is covalently bound to the resting enzyme via a Schiff base linkage to Lys 244. During the catalytic reaction it becomes bound to the amino acid substrate, allowing the reaction to occur. After this the product is released from PLP.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11318637 Current protein Residue is covalently bound to intermediate, based on structural data
PubMed ID 11318637 Current protein Structural similarity to homologue of known mechanism

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
HISA 213 213Sidechain
Acid/baseCofactor
Acid/baseSubstrate
His 213 acts as a general acid and base during the steps where the PLP Schiff base linkage is transferred from Lys 244 to the amino acid, and vice versa.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11318637 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
LYSA 244 244Sidechain
Acid/baseSubstrate
ModifiedCofactor
Lys 244 is Schiff base-linked to the PLP cofactor in the resting state, and displaces the glycine product in the last step of the reaction. Lys 244 deprotonates the thiol after the formation of the tetrahedral intermediate. The proton is transferred to the nitrogen atom of the glycine moiety of the quinoid intermediate to regenerate the imine linkage.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11318637 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 11318637 Current protein Conservation of residue
PubMed ID 11318637 Current protein Chemical modification of residue
Notes:
Although the active site runs between the monomers, the catalytic residues only come from one of the monomers.

References:
1
Three-dimensional structure of 2-amino-3-ketobutyrate CoA ligase from Escherichia coli complexed with a PLP-substrate intermediate: inferred reaction mechanism.
A. Schmidt and J. Sivaraman and Y. Li and R. Larocque and J. A. Barbosa and C. Smith and A. Matte and J. D. Schrag and M. Cygler
Biochemistry 40, (17) 5151-60, (2001).
11318637
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