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Catalytic Site Atlas

CSA LITERATURE entry for 1mt1

E.C. namearginine decarboxylase
SpeciesMethanococcus jannaschii ()
E.C. Number (IntEnz) 4.1.1.19
CSA Homologues of 1mt1
CSA Entries With UniProtID Q57764
CSA Entries With EC Number 4.1.1.19
PDBe Entry 1mt1
PDBSum Entry 1mt1
MACiE Entry 1mt1

Literature Report

IntroductionThree classes of arginine decarboxylase exist, of which two use the cofactor pyridoxal 5'-phosphate and a third uses a pyruvoyl group. Methanococcus jannaschii uses pyruvoyl-dependent arginine decarboxylase (PvlArgDC) to convert L-arginine into agmatine, which can be converted to putrescine by agmatine ureohydrolase. Putrescine can be used to biosynthesize polyamines. These are essential for cell growth and proliferation and are found in all organisms.
Some pathogenic microorganisms, such as Chlamydia spp., are thought to import L-Arg from the host, decarboxylate it, and export the agmatine product, depleting the host's L-Arg supply and increasing the extracellular pH. Agmatine is also an inhibitor of nitric-oxide synthase and a suppressor of apoptosis.
PvlArgDC is translated as a proenzyme (pi-chain), which cleaves itself between Ser52 and Ser53 by autocatalytic serinolysis to form two polypeptide (alpha and beta) chains. The alpha chain begins with the newly created pyruvoyl group, which is the cofactor in the decarboxylation reaction, and the smaller beta fragment terminates with a new carboxyl group at Ser52.
MechansimThe mechanism of action for the decarboxylation is similar to that of pyridoxal 5'-phosphate-dependent enzymes. However, unlike PLP-dependent enzymes, where PLP forms an internal aldimine with the epsilon-amino group of a specific lysyl residue in the resting enzyme, the carbonyl group of the pyruvoyl enzymes is free.
The amino acid substrate (L-Arg) reacts with the pyruvoyl carbonyl to form an iminium ion. The protonated Schiff base promotes decarboxylation by stabilising the alpha-carbanion intermediate through a resonance network. After release of CO2, the alpha-carbon is reprotonated at the re face.
Reaction

Catalytic Sites for 1mt1

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GluB109109macie:sideChainIn decarboxylation, Glu109 has been suggested to act as the acid protonating the decarboxylated reaction intermediate. Although important in decarboxylation, other factors are involved.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GluD109109macie:sideChainIn decarboxylation, Glu109 has been suggested to act as the acid protonating the decarboxylated reaction intermediate. Although important in decarboxylation, other factors are involved.

Annotated By Reference To The Literature - Site 3 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GluF109109macie:sideChainIn decarboxylation, Glu109 has been suggested to act as the acid protonating the decarboxylated reaction intermediate. Although important in decarboxylation, other factors are involved.

Annotated By Reference To The Literature - Site 4 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GluH109109macie:sideChainIn decarboxylation, Glu109 has been suggested to act as the acid protonating the decarboxylated reaction intermediate. Although important in decarboxylation, other factors are involved.

Annotated By Reference To The Literature - Site 5 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GluJ109109macie:sideChainIn decarboxylation, Glu109 has been suggested to act as the acid protonating the decarboxylated reaction intermediate. Although important in decarboxylation, other factors are involved.

Annotated By Reference To The Literature - Site 6 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GluL109109macie:sideChainIn decarboxylation, Glu109 has been suggested to act as the acid protonating the decarboxylated reaction intermediate. Although important in decarboxylation, other factors are involved.

Literature References

Notes:As the PDB file had the pyruvoyl group in it, the mechanism for its formation from the proenzyme was excluded.
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