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Catalytic Site Atlas Search Results
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Catalytic Site Atlas

CSA LITERATURE entry for 1xrs

E.C. namebeta-lysine 5,6-aminomutase
SpeciesClostridium sticklandii ()
E.C. Number (IntEnz) 5.4.3.3
CSA Homologues of 1xrsThere are 27 Homologs
CSA Entries With UniProtID
CSA Entries With EC Number 5.4.3.3
PDBe Entry 1xrs
PDBSum Entry 1xrs
MACiE Entry 1xrs

Literature Report

IntroductionLysine 5,6-aminomutase (5,6-LAM) is sourced from Clostridium sticklandii. It catalyses the reversible transformations of D-lysine into 2,5-diaminohexanoate and of L-beta-lysine into 3,5-diaminohexanoate. The activity of 5,6-LAM is dependent on pyridoxal-5'-phosphate (PLP) and adenosylcobalamin.
Mechansim1. The substrate Lys displaces Lys 144 from PLP with a standard transaldimination reaction. 2. Adenosylcobalamin (AdoCbl) homolytically cleaves to form Ado-CH2 radical. 3. Ado-CH2 radical accepts a proton and an electron from the substrate Lys delta carbon. 4. A three membered ring is formed between the delta and epsilon carbons and the nitrogen of the substrate Lys, breaking the double bond, leaving just a single bond between the substrate N and PLP C atoms, and a radical PLP. 5. The double bond between the nitrogen of the substrate Lys and the carbon of PLP is reformed, homolytically cleaving the N-C-epsilon bond of the substrate Lys. 6. Ado-CH3 then donates a proton and an electron back to the product, reforming the Ado-CH2 radical. 7. Lys 144 then nucleophilically attacks PLP, to displace the product with a standard transaldimination reaction.
Reaction

Catalytic Sites for 1xrs

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysB144144macie:sideChainLys 144 is covalently attached to PLP. As Lys substrate binds to PLP, Lys 144 accepts a pair of electrons from PLP, breaking the Lys 144 - PLP bond. When the product is formed, Lys 144 acts as a nucleophile and attacks PLP forcing the product to leave.

Literature References

Notes:This mechanism is hypothetical. It is also suspected that the backbone carboxyl group of Ser 238 chain A stabilises PLP. This is based on the fact that most PLP mechanisms have a stabilising residue, and that in this case, Ser 238 is in the right place.
Tang KH
Kinetic and biochemical analysis of the mechanism of action of lysine 5,6-aminomutase.
Arch Biochem Biophys 2003 418 49-54
PubMed: 13679082
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