2.0 2012-05-31 10:22:27 -0600 2015-09-13 12:56:06 -0600 ECMDB00162 M2MDB000064 L-Proline L-Proline is one of the twenty amino acids used in living organisms as the building blocks of proteins. Proline is sometimes called an imino acid, although the IUPAC definition of an imine requires a carbon-nitrogen double bond. Proline is a non-essential amino acid that is synthesized from glutamic acid. It is an essential component of collagen and is important for proper functioning of joints and tendons. (-)-(S)-Proline (-)-2-Pyrrolidinecarboxylate (-)-2-Pyrrolidinecarboxylic acid (-)-Proline (S)-(-)-Proline (S)-(-)-Pyrrolidine-2-carboxylate (S)-(-)-Pyrrolidine-2-carboxylic acid (S)-2-Carboxypyrrolidine (S)-2-Pyrralidinecarboxylate (S)-2-Pyrralidinecarboxylic acid (S)-2-Pyrrolidinecarboxylate (S)-2-Pyrrolidinecarboxylic acid (S)-Proline 2-Pyrrolidinecarboxylate 2-Pyrrolidinecarboxylic acid P Pro Prol Proline C5H9NO2 115.1305 115.063328537 (2S)-pyrrolidine-2-carboxylic acid L-proline 147-85-3 OC(=O)[C@@H]1CCCN1 InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1 ONIBWKKTOPOVIA-BYPYZUCNSA-N Solid Cytosol Extra-organism Periplasm logp -2.71 ALOGPS logs 0.50 ALOGPS solubility 3.65e+02 g/l ALOGPS melting_point 221 oC logp -2.6 ChemAxon pka_strongest_acidic 1.94 ChemAxon pka_strongest_basic 11.33 ChemAxon iupac (2S)-pyrrolidine-2-carboxylic acid ChemAxon average_mass 115.1305 ChemAxon mono_mass 115.063328537 ChemAxon smiles OC(=O)[C@@H]1CCCN1 ChemAxon formula C5H9NO2 ChemAxon inchi InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1 ChemAxon inchikey ONIBWKKTOPOVIA-BYPYZUCNSA-N ChemAxon polar_surface_area 49.33 ChemAxon refractivity 28.06 ChemAxon polarizability 11.5 ChemAxon rotatable_bond_count 1 ChemAxon acceptor_count 3 ChemAxon donor_count 2 ChemAxon physiological_charge 0 ChemAxon formal_charge 0 ChemAxon Alanine, aspartate and glutamate metabolism ec00250 Arginine and proline metabolism ec00330 Novobiocin biosynthesis ec00401 Aminoacyl-tRNA biosynthesis ec00970 ABC transporters ec02010 Metabolic pathways eco01100 proline metabolism The biosynthesis of L-proline in E. coli involves L-glutamic acid being phosphorylated through an ATP driven glutamate 5-kinase resulting in a L-glutamic acid 5-phosphate. This compound is then reduced through a NADPH driven gamma glutamyl phosphate reductase resulting in the release of a phosphate, a NADP and a L-glutamic gamma-semialdehyde. L-glutamic gamma-semialdehyde is dehydrated spontaneously, resulting in a release of water,hydrogen ion and 1-Pyrroline-5-carboxylic acid. The latter compound is reduced by an NADPH driven pyrroline-5-carboxylate reductase which is subsequently reduced to L-proline. L-proline works as a repressor of the pyrroline-5-carboxylate reductase enzyme and glutamate 5-kinase. In E. coli, the biosynthesis of L-proline from L-glutamate is governed by three genetic loci namely proB, proA and proC. The first reaction in the pathway is catalyzed by γ-glutamyl kinase, encoded by proB . The second reaction, NADPH-dependent reduction of γ-glutamyl phosphate to glutamate-5-semialdehyde, in the pathway is catalyzed by glutamate-5-semialdehyde dehydrogenase, encoded by proA . These two enzymes aggregate into a multimeric bi-functional enzyme complex known as γ-glutamyl kinase-GP-reductase multienzyme complex. It is believed that the complex formation serves to protect the highly labile glutamyl phosphate from the hostile nucleophilic and aqueous environment found in the cell . The final step in the pathway, the reduction of pyrroline 5-carboxylate to L-proline, is catalyzed by an NADPH-dependent pyrroline-5-carboxylate reductase encoded by proC . Proline is metabolized by being converted back to L-glutamate, which is further degraded to α-ketoglutarate, an intermediate of the TCA cycle. Curiously, L-glutamate, the obligate intermediate of the proline degradation pathway, cannot itself serve as a total source of carbon and energy for E. coli, because glutamate transport supplies exogenous glutamate at an inadequate rate. The proces by which proline is turned into L-glutamate starts with L-proline interacting with ubiquinone through a bifunctional protein putA resulting in an ubiquinol, a hydrogen ion and a 1-pyrroline-5-carboxylic acid. The latter compound is then hydrated spontaneously resulting in a L-glutamic gamma-semialdehyde. This compound is then processed by interacting with water through an NAD driven bifunctional protein putA resulting in a hydrogen ion, NADH and L-glutamic acid. PW000794 Metabolic tRNA Charging 2 This pathway groups together all E. coli tRNA charging reactions. PW000803 Metabolic tRNA charging This pathway groups together all E. coli tRNA charging reactions. PW000799 Metabolic tRNA charging TRNA-CHARGING-PWY proline degradation PROUT-PWY proline biosynthesis I PROSYN-PWY Specdb::CMs 395 Specdb::CMs 396 Specdb::CMs 397 Specdb::CMs 398 Specdb::CMs 949 Specdb::CMs 1027 Specdb::CMs 1046 Specdb::CMs 2426 Specdb::CMs 29555 Specdb::CMs 30077 Specdb::CMs 30380 Specdb::CMs 30381 Specdb::CMs 30608 Specdb::CMs 30729 Specdb::CMs 30799 Specdb::CMs 31035 Specdb::CMs 31036 Specdb::CMs 31037 Specdb::CMs 37331 Specdb::CMs 156130 Specdb::CMs 1051764 Specdb::CMs 1051766 Specdb::CMs 1051768 Specdb::NmrOneD 1122 Specdb::NmrOneD 1179 Specdb::NmrOneD 4872 Specdb::NmrOneD 142630 Specdb::NmrOneD 142631 Specdb::NmrOneD 142632 Specdb::NmrOneD 142633 Specdb::NmrOneD 142634 Specdb::NmrOneD 142635 Specdb::NmrOneD 142636 Specdb::NmrOneD 142637 Specdb::NmrOneD 142638 Specdb::NmrOneD 142639 Specdb::NmrOneD 142640 Specdb::NmrOneD 142641 Specdb::NmrOneD 142642 Specdb::NmrOneD 142643 Specdb::NmrOneD 142644 Specdb::NmrOneD 142645 Specdb::NmrOneD 142646 Specdb::NmrOneD 142647 Specdb::NmrOneD 142648 Specdb::NmrOneD 142649 Specdb::NmrOneD 166490 Specdb::MsMs 254 Specdb::MsMs 255 Specdb::MsMs 256 Specdb::MsMs 3233 Specdb::MsMs 3234 Specdb::MsMs 3235 Specdb::MsMs 3236 Specdb::MsMs 3237 Specdb::MsMs 3238 Specdb::MsMs 3239 Specdb::MsMs 3240 Specdb::MsMs 3241 Specdb::MsMs 3242 Specdb::MsMs 3243 Specdb::MsMs 3244 Specdb::MsMs 3245 Specdb::MsMs 3246 Specdb::MsMs 3247 Specdb::MsMs 3248 Specdb::MsMs 3249 Specdb::MsMs 3254 Specdb::MsMs 3255 Specdb::MsMs 3256 Specdb::MsMs 3257 Specdb::MsMs 178125 Specdb::NmrTwoD 977 Specdb::NmrTwoD 1179 HMDB00162 145742 128566 C00148 17203 PRO PRO_LFZW L-Proline Keseler, I. 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Bulletin of the Chemical Society of Japan (1963), 36(1), 25-9 http://hmdb.ca/system/metabolites/msds/000/000/113/original/HMDB00162.pdf?1358894688 Aminopeptidase N P04825 AMPN_ECOLI pepN http://ecmdb.ca/proteins/P04825.xml Bifunctional protein putA P09546 PUTA_ECOLI putA http://ecmdb.ca/proteins/P09546.xml Pyrroline-5-carboxylate reductase P0A9L8 P5CR_ECOLI proC http://ecmdb.ca/proteins/P0A9L8.xml Glycine betaine/L-proline transport ATP-binding protein proV P14175 PROV_ECOLI proV http://ecmdb.ca/proteins/P14175.xml Aminoacyl-histidine dipeptidase P15288 PEPD_ECOLI pepD http://ecmdb.ca/proteins/P15288.xml Prolyl-tRNA synthetase P16659 SYP_ECOLI proS http://ecmdb.ca/proteins/P16659.xml Xaa-Pro dipeptidase P21165 PEPQ_ECOLI pepQ http://ecmdb.ca/proteins/P21165.xml Peptidase B P37095 PEPB_ECOLI pepB http://ecmdb.ca/proteins/P37095.xml Cytosol aminopeptidase P68767 AMPA_ECOLI pepA http://ecmdb.ca/proteins/P68767.xml Glycine betaine/L-proline transport system permease protein proW P14176 PROW_ECOLI proW http://ecmdb.ca/proteins/P14176.xml Glycine betaine-binding periplasmic protein P0AFM2 PROX_ECOLI proX http://ecmdb.ca/proteins/P0AFM2.xml Aminopeptidase N P04825 AMPN_ECOLI pepN http://ecmdb.ca/proteins/P04825.xml Sodium/proline symporter P07117 PUTP_ECOLI putP http://ecmdb.ca/proteins/P07117.xml Uncharacterized amino-acid ABC transporter ATP-binding protein yecC P37774 YECC_ECOLI yecC http://ecmdb.ca/proteins/P37774.xml Inner membrane amino-acid ABC transporter permease protein yecS P0AFT2 YECS_ECOLI yecS http://ecmdb.ca/proteins/P0AFT2.xml Proline-specific permease proY P0AAE2 PROY_ECOLI proY http://ecmdb.ca/proteins/P0AAE2.xml Proline/betaine transporter P0C0L7 PROP_ECOLI proP http://ecmdb.ca/proteins/P0C0L7.xml Glycine betaine/L-proline transport system permease protein proW P14176 PROW_ECOLI proW http://ecmdb.ca/proteins/P14176.xml Outer membrane protein N P77747 OMPN_ECOLI ompN http://ecmdb.ca/proteins/P77747.xml Outer membrane pore protein E P02932 PHOE_ECOLI phoE http://ecmdb.ca/proteins/P02932.xml Outer membrane protein F P02931 OMPF_ECOLI ompF http://ecmdb.ca/proteins/P02931.xml Outer membrane protein C P06996 OMPC_ECOLI ompC http://ecmdb.ca/proteins/P06996.xml Adenosine triphosphate + Water + L-Proline > ADP + Hydrogen ion + Phosphate + L-Proline ABC-26-RXN Adenosine triphosphate + Water + L-Proline > ADP + Hydrogen ion + Phosphate + L-Proline ABC-26-RXN Water + L-Prolinylglycine > Glycine + L-Proline Adenosine triphosphate + L-Proline + tRNA(Pro) + tRNA(Pro) <> Adenosine monophosphate + Pyrophosphate + L-Prolyl-tRNA(Pro) + L-Prolyl-tRNA(Pro) R03661 L-D-1-Pyrroline-5-carboxylic acid + 2 Hydrogen ion + NADPH > NADP + L-Proline R01251 FAD + L-Proline > L-D-1-Pyrroline-5-carboxylic acid + FADH2 + Hydrogen ion L-Proline + NAD <> L-D-1-Pyrroline-5-carboxylic acid + NADH + Hydrogen ion R01248 L-Proline + NADP <> L-D-1-Pyrroline-5-carboxylic acid + NADPH + Hydrogen ion R01251 L-Proline + Acceptor + Quinone <> L-D-1-Pyrroline-5-carboxylic acid + Reduced acceptor + (S)-1-pyrroline-5-carboxylate + Hydroquinone R01253 Adenosine triphosphate + L-Proline + tRNA(Pro) <> Adenosine monophosphate + Pyrophosphate + L-Prolyl-tRNA(Pro) R03661 a dipeptide with proline at carboxy terminal + Water L-Proline + a standard &alpha; amino acid 3.4.13.9-RXN Adenosine triphosphate + L-Proline + Water > ADP + Phosphate + L-Proline + Hydrogen ion ABC-26-RXN Adenosine triphosphate + L-Proline + Water > ADP + Phosphate + L-Proline + Hydrogen ion ABC-26-RXN NAD(P)⁺ + L-Proline < NAD(P)H + L-D-1-Pyrroline-5-carboxylic acid + Hydrogen ion PYRROLINECARBREDUCT-RXN L-Proline + an oxidized electron acceptor > L-D-1-Pyrroline-5-carboxylic acid + a reduced electron acceptor + Hydrogen ion RXN-821 glycylproline + Water > Glycine + L-Proline RXN0-6988 L-Proline + NAD(P)(+) > L-D-1-Pyrroline-5-carboxylic acid + NAD(P)H L-Proline + acceptor > (S)-1-pyrroline-5-carboxylate + reduced acceptor Adenosine triphosphate + L-Proline + tRNA(Pro) > Adenosine monophosphate + Pyrophosphate + L-prolyl-tRNA(Pro) L-Proline + NAD + NADP <> (S)-1-pyrroline-5-carboxylate + NADH + NADPH + Hydrogen ion R01248 R01251 1-Pyrroline-5-carboxylic acid + Hydrogen ion + NADPH + L-D-1-Pyrroline-5-carboxylic acid + NADPH > NADP + L-Proline + L-Proline PW_R002719 L-Proline + Ubiquinone-1 + L-Proline > Hydrogen ion + Ubiquinol-1 + 1-Pyrroline-5-carboxylic acid + L-D-1-Pyrroline-5-carboxylic acid PW_R002720 L-Proline + Adenosine triphosphate + Hydrogen ion + tRNA(Pro) + L-Proline > Adenosine monophosphate + Pyrophosphate + L-prolyl-tRNA(Pro) PW_R002842 L-Proline + Adenosine triphosphate + Water + L-Proline > L-Proline + Adenosine diphosphate + Phosphate + Hydrogen ion + ADP PW_RCT000112 L-D-1-Pyrroline-5-carboxylic acid + 2 Hydrogen ion + NADPH > NADP + L-Proline Adenosine triphosphate + L-Proline + tRNA(Pro) <> Adenosine monophosphate + Pyrophosphate + L-Prolyl-tRNA(Pro) Adenosine triphosphate + L-Proline + tRNA(Pro) <> Adenosine monophosphate + Pyrophosphate + L-Prolyl-tRNA(Pro) Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L glucose Shake flask and filter culture 385.0 uM 0.0 37 oC K12 NCM3722 Mid-Log Phase 1540000 0 Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. 19561621 Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L glycerol Shake flask and filter culture 451.0 uM 0.0 37 oC K12 NCM3722 Mid-Log Phase 1804000 0 Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. 19561621 Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L acetate Shake flask and filter culture 361.0 uM 0.0 37 oC K12 NCM3722 Mid-Log Phase 1444000 0 Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. 19561621 48 mM Na2HPO4, 22 mM KH2PO4, 10 mM NaCl, 45 mM (NH4)2SO4, supplemented with 1 mM MgSO4, 1 mg/l thiamine·HCl, 5.6 mg/l CaCl2, 8 mg/l FeCl3, 1 mg/l MnCl2·4H2O, 1.7 mg/l ZnCl2, 0.43 mg/l CuCl2·2H2O, 0.6 mg/l CoCl2·2H2O and 0.6 mg/l Na2MoO4·2H2O. 4 g/L Gluco Bioreactor, pH controlled, O2 and CO2 controlled, dilution rate: 0.2/h 143.0 uM 0.0 37 oC BW25113 Stationary Phase, glucose limited 572000 0 Ishii, N., Nakahigashi, K., Baba, T., Robert, M., Soga, T., Kanai, A., Hirasawa, T., Naba, M., Hirai, K., Hoque, A., Ho, P. Y., Kakazu, Y., Sugawara, K., Igarashi, S., Harada, S., Masuda, T., Sugiyama, N., Togashi, T., Hasegawa, M., Takai, Y., Yugi, K., Arakawa, K., Iwata, N., Toya, Y., Nakayama, Y., Nishioka, T., Shimizu, K., Mori, H., Tomita, M. (2007). "Multiple high-throughput analyses monitor the response of E. coli to perturbations." Science 316:593-597. 17379776 Luria-Bertani (LB) media Shake flask 550.0 uM true 45.0 37 oC BL21 DE3 Stationary phase cultures (overnight culture) 2201600 180000 Lin, Z., Johnson, L. C., Weissbach, H., Brot, N., Lively, M. O., Lowther, W. T. (2007). "Free methionine-(R)-sulfoxide reductase from Escherichia coli reveals a new GAF domain function." Proc Natl Acad Sci U S A 104:9597-9602. 17535911 Luria-Bertani (LB) media Shake flask 531.67 uM true 11.37 37 oC BL21 DE3 Stationary phase cultures (overnight culture) 2126667 45490 Lin, Z., Johnson, L. C., Weissbach, H., Brot, N., Lively, M. O., Lowther, W. T. (2007). "Free methionine-(R)-sulfoxide reductase from Escherichia coli reveals a new GAF domain function." Proc Natl Acad Sci U S A 104:9597-9602. 17535911