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CSA entry for 1iyd
Original Entry
Title:
Transferase
Compound:
Branched-chain amino acid aminotransferase
Mutant:
No
UniProt/Swiss-Prot:
P00510-ILVE_ECOLI
EC Class:
2.6.1.42
Other CSA Entries:
Overview of all sites for 1iyd
Homologues of 1iyd
Entries for UniProt/Swiss-Prot: P00510
Entries for EC: 2.6.1.42
Other Databases:
PDB entry: 1iyd
PDBsum entry: 1iyd
UniProt/Swiss-Prot: P00510
IntEnz entry: 2.6.1.42
Literature Report:
Introduction:
Branched-chain amino acid aminotransferase is involved in the biosynthesis of hydrophobic amino acids ie leucine, isoleucine, valine. The enzyme reversibly catalyses the transfer of the amino group of a hydrophobic amino acide to 2-oxoglutarate to form a 2-oxo acid and a glutamate. This enzyme is a pyridoxal 5'-phosphate-dependent enzyme.
Mechanism:
The mechanism of branched-chain amino acid aminotransferase has a double substrate recognition component for the reversibility of this enzyme. The substrate approaches, and the C4' of PLP, activated by protonation of the Schiff base, is nucleophilically attacked by the substrate alpha-amino group and through the tetrahedral intermediate a new Schiff base is formed, with release of Lys 159 by protonation with the substrate. Lys 159 makes a hydrogen bond to the O3' of PLP to lower the free energy of the transition states. This Lys also facilitates proton transfer to the C-alpha atom of the substrate and the C4' of the cofactor. The deprotonated Lys 159 abstracts a proton from the substrate to yield the quinonoid intermediate. After this alpha-proton elimination, Lys 159 adds a proton to the C4' atom of the quinonoid intermediate to yield the ketimine intermediate. The ketimine intermediate is hydrolysed using Lys 159 to activate the water as a general base catalyst to yield 2-oxoglutarate and PMP.
Sites:

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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
LYSA 159 160Sidechain
Acid/baseWater
Acid/baseSubstrate
ModifiedModified
Involved in proton transfer and general acid/base catalysis.
Evidence from paper Evidence concerns Evidence type
PubMed ID 12667063 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
PLPA 413 0
ModifiedModified
ElectrophileSubstrate
ElectrostaticSubstrate
Acts as a cofactor to bind the substrate covalently through a Schiff base.
Evidence from paper Evidence concerns Evidence type
PubMed ID 12667063 Current protein Residue is covalently bound to intermediate, based on structural data
PubMed ID 12667063 Current protein Residue is positioned appropriately (ligand position known)
References:
1
Crystal structures of branched-chain amino acid aminotransferase complexed with glutamate and glutarate: true reaction intermediate and double substrate recognition of the enzyme.
M. Goto and I. Miyahara and H. Hayashi and H. Kagamiyama and K. Hirotsu
Biochemistry 42, (13) 3725-33, (2003).
12667063
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