The Enzyme Database

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EC 1.14.13.247     
Accepted name: stachydrine N-demethylase
Reaction: L-proline betaine + NAD(P)H + H+ + O2 = N-methyl-L-proline + formaldehyde + NAD(P)+ + H2O
Other name(s): L-proline betaine N-demethylase; stc2 (gene name)
Systematic name: L-proline betaine,NAD(P)H:oxygen oxidoreductase (formaldehyde-forming)
Comments: The enzyme, characterized from the bacterium Sinorhizobium meliloti 1021, consists of three different types of subunits. The catalytic unit contains a Rieske [2Fe-2S] iron-sulfur cluster, and catalyses the monooxygenation of a methyl group. The resulting N-methoxyl group is unstable and decomposes spontaneously to form formaldehyde. The other subunits are involved in the transfer of electrons from NAD(P)H to the catalytic subunit.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Daughtry, K.D., Xiao, Y., Stoner-Ma, D., Cho, E., Orville, A.M., Liu, P. and Allen, K.N. Quaternary ammonium oxidative demethylation: X-ray crystallographic, resonance Raman, and UV-visible spectroscopic analysis of a Rieske-type demethylase. J. Am. Chem. Soc. 134 (2012) 2823–2834. [PMID: 22224443]
2.  Kumar, R., Zhao, S., Vetting, M.W., Wood, B.M., Sakai, A., Cho, K., Solbiati, J., Almo, S.C., Sweedler, J.V., Jacobson, M.P., Gerlt, J.A. and Cronan, J.E. Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine. MBio 5 (2014) e00933. [DOI] [PMID: 24520058]
[EC 1.14.13.247 created 2017]
 
 
EC 2.1.1.388     
Accepted name: proline betaine—corrinoid protein Co-methyltransferase
Reaction: L-proline betaine + a [Co(I) quaternary-amine-specific corrinoid protein] = a [methyl-Co(III) quaternary-amine-specific corrinoid protein] + N-methyl-L-proline
Glossary: L-proline betaine = (2S)-1,1-dimethylpyrrolidinium-2-carboxylate
Other name(s): mtpB (gene name)
Systematic name: L-proline betaine:[Co(I) quaternary-amine-specific corrinoid protein] Co-methyltransferase
Comments: The enzyme, characterized from the bacterium Eubacterium limosum, is a component of a system that transfers a methyl group from L-proline betaine to tetrahydrofolate, as part of an L-proline betaine degradation pathway. The resulting 5-methyltetrahydrofolate is processed to acetyl-CoA via the Wood—Ljungdahl pathway.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Picking, J.W., Behrman, E.J., Zhang, L. and Krzycki, J.A. MtpB, a member of the MttB superfamily from the human intestinal acetogen Eubacterium limosum, catalyzes proline betaine demethylation. J. Biol. Chem. 294 (2019) 13697–13707. [DOI] [PMID: 31341018]
[EC 2.1.1.388 created 2023]
 
 
EC 2.1.1.389     
Accepted name: [methyl-Co(III) quaternary-amine-specific corrinoid protein]—tetrahydrofolate methyltransferase
Reaction: a [methyl-Co(III) quaternary-amine-specific corrinoid protein] + tetrahydrofolate = N5-methyltetrahydrofolate + a [Co(I) quaternary-amine-specific corrinoid protein]
Other name(s): mtqA (gene name) (ambiguous); [methyl-Co(III) MtqC corrinoid protein]—tetrahydrofolate methyltransferase
Systematic name: [methyl-Co(III) quaternary-amine-specific corrinoid protein]:tetrahydrofolate methyltransferase
Comments: The enzyme, characterized from the acetogenic gut bacterium Eubacterium limosum, participates in a pathway for the degradation of some quaternary amine compounds (L-proline betaine and L-carnitine). The enzyme catalyses the transfer of a methyl group bound to the cobalt cofactor of a dedicated corrinoid protein (bacterial MtqC) to tetrahydrofolate. The resulting 5-methyltetrahydrofolate is processed to acetyl-CoA via the Wood—Ljungdahl pathway.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Picking, J.W., Behrman, E.J., Zhang, L. and Krzycki, J.A. MtpB, a member of the MttB superfamily from the human intestinal acetogen Eubacterium limosum, catalyzes proline betaine demethylation. J. Biol. Chem. 294 (2019) 13697–13707. [DOI] [PMID: 31341018]
2.  Kountz, D.J., Behrman, E.J., Zhang, L. and Krzycki, J.A. MtcB, a member of the MttB superfamily from the human gut acetogen Eubacterium limosum, is a cobalamin-dependent carnitine demethylase. J. Biol. Chem. 295 (2020) 11971–11981. [DOI] [PMID: 32571881]
[EC 2.1.1.389 created 2023]
 
 
EC 5.1.1.22     
Accepted name: 4-hydroxyproline betaine 2-epimerase
Reaction: (1) trans-4-hydroxy-L-proline betaine = cis-4-hydroxy-D-proline betaine
(2) L-proline betaine = D-proline betaine
Glossary: trans-4-hydroxy-L-proline betaine = (2S,4R)-4-hydroxy-1,1-dimethylpyrrolidinium-2-carboxylate
cis-4-hydroxy-D-proline betaine = (2R,4R)-4-hydroxy-1,1-dimethylpyrrolidinium-2-carboxylate
L-proline betaine = (2S)-1,1-dimethylpyrrolidinium-2-carboxylate
D-proline betaine = (2R)-1,1-dimethylpyrrolidinium-2-carboxylate
Other name(s): hpbD (gene name); Hyp-B 2-epimerase; (4R)-4-hydroxyproline betaine 2-epimerase
Systematic name: 4-hydroxyproline betaine 2-epimerase
Comments: The enzyme, characterized from the bacteria Pelagibaca bermudensis and Paracoccus denitrificans, specifically catalyses racemization of trans-4-hydroxy-L-proline betaine and L-proline betaine at the C-2 position.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Zhao, S., Kumar, R., Sakai, A., Vetting, M.W., Wood, B.M., Brown, S., Bonanno, J.B., Hillerich, B.S., Seidel, R.D., Babbitt, P.C., Almo, S.C., Sweedler, J.V., Gerlt, J.A., Cronan, J.E. and Jacobson, M.P. Discovery of new enzymes and metabolic pathways by using structure and genome context. Nature 502 (2013) 698–702. [DOI] [PMID: 24056934]
2.  Kumar, R., Zhao, S., Vetting, M.W., Wood, B.M., Sakai, A., Cho, K., Solbiati, J., Almo, S.C., Sweedler, J.V., Jacobson, M.P., Gerlt, J.A. and Cronan, J.E. Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine. MBio 5 (2014) e00933. [DOI] [PMID: 24520058]
[EC 5.1.1.22 created 2017]
 
 


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