2.02012-05-31 10:22:27 -06002015-09-13 12:56:06 -0600ECMDB00162M2MDB000064L-ProlineL-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)-Proline2-Pyrrolidinecarboxylate2-Pyrrolidinecarboxylic acidPProProlProlineC5H9NO2115.1305115.063328537(2S)-pyrrolidine-2-carboxylic acidL-proline147-85-3OC(=O)[C@@H]1CCCN1InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1ONIBWKKTOPOVIA-BYPYZUCNSA-NSolidCytosolExtra-organismPeriplasmlogp-2.71logs0.50solubility3.65e+02 g/lmelting_point221 oClogp-2.6pka_strongest_acidic1.94pka_strongest_basic11.33iupac(2S)-pyrrolidine-2-carboxylic acidaverage_mass115.1305mono_mass115.063328537smilesOC(=O)[C@@H]1CCCN1formulaC5H9NO2inchiInChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1inchikeyONIBWKKTOPOVIA-BYPYZUCNSA-Npolar_surface_area49.33refractivity28.06polarizability11.5rotatable_bond_count1acceptor_count3donor_count2physiological_charge0formal_charge0Alanine, aspartate and glutamate metabolismec00250Arginine and proline metabolismec00330Novobiocin biosynthesisec00401Aminoacyl-tRNA biosynthesisec00970ABC transportersec02010Metabolic pathwayseco01100proline 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.PW000794MetabolictRNA Charging 2This pathway groups together all E. coli tRNA charging reactions.PW000803MetabolictRNA chargingThis pathway groups together all E. coli tRNA charging reactions.PW000799MetabolictRNA chargingTRNA-CHARGING-PWYproline degradationPROUT-PWYproline biosynthesis IPROSYN-PWYSpecdb::CMs395Specdb::CMs396Specdb::CMs397Specdb::CMs398Specdb::CMs949Specdb::CMs1027Specdb::CMs1046Specdb::CMs2426Specdb::CMs29555Specdb::CMs30077Specdb::CMs30380Specdb::CMs30381Specdb::CMs30608Specdb::CMs30729Specdb::CMs30799Specdb::CMs31035Specdb::CMs31036Specdb::CMs31037Specdb::CMs37331Specdb::CMs156130Specdb::CMs1051764Specdb::CMs1051766Specdb::CMs1051768Specdb::NmrOneD1122Specdb::NmrOneD1179Specdb::NmrOneD4872Specdb::NmrOneD142630Specdb::NmrOneD142631Specdb::NmrOneD142632Specdb::NmrOneD142633Specdb::NmrOneD142634Specdb::NmrOneD142635Specdb::NmrOneD142636Specdb::NmrOneD142637Specdb::NmrOneD142638Specdb::NmrOneD142639Specdb::NmrOneD142640Specdb::NmrOneD142641Specdb::NmrOneD142642Specdb::NmrOneD142643Specdb::NmrOneD142644Specdb::NmrOneD142645Specdb::NmrOneD142646Specdb::NmrOneD142647Specdb::NmrOneD142648Specdb::NmrOneD142649Specdb::NmrOneD166490Specdb::MsMs254Specdb::MsMs255Specdb::MsMs256Specdb::MsMs3233Specdb::MsMs3234Specdb::MsMs3235Specdb::MsMs3236Specdb::MsMs3237Specdb::MsMs3238Specdb::MsMs3239Specdb::MsMs3240Specdb::MsMs3241Specdb::MsMs3242Specdb::MsMs3243Specdb::MsMs3244Specdb::MsMs3245Specdb::MsMs3246Specdb::MsMs3247Specdb::MsMs3248Specdb::MsMs3249Specdb::MsMs3254Specdb::MsMs3255Specdb::MsMs3256Specdb::MsMs3257Specdb::MsMs178125Specdb::NmrTwoD977Specdb::NmrTwoD1179HMDB00162145742128566C0014817203PROPRO_LFZWL-ProlineKeseler, I. 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Bulletin of the Chemical Society of Japan (1963), 36(1), 25-9http://hmdb.ca/system/metabolites/msds/000/000/113/original/HMDB00162.pdf?1358894688Aminopeptidase NP04825AMPN_ECOLIpepNhttp://ecmdb.ca/proteins/P04825.xmlBifunctional protein putAP09546PUTA_ECOLIputAhttp://ecmdb.ca/proteins/P09546.xmlPyrroline-5-carboxylate reductaseP0A9L8P5CR_ECOLIproChttp://ecmdb.ca/proteins/P0A9L8.xmlGlycine betaine/L-proline transport ATP-binding protein proVP14175PROV_ECOLIproVhttp://ecmdb.ca/proteins/P14175.xmlAminoacyl-histidine dipeptidaseP15288PEPD_ECOLIpepDhttp://ecmdb.ca/proteins/P15288.xmlProlyl-tRNA synthetaseP16659SYP_ECOLIproShttp://ecmdb.ca/proteins/P16659.xmlXaa-Pro dipeptidaseP21165PEPQ_ECOLIpepQhttp://ecmdb.ca/proteins/P21165.xmlPeptidase BP37095PEPB_ECOLIpepBhttp://ecmdb.ca/proteins/P37095.xmlCytosol aminopeptidaseP68767AMPA_ECOLIpepAhttp://ecmdb.ca/proteins/P68767.xmlGlycine betaine/L-proline transport system permease protein proWP14176PROW_ECOLIproWhttp://ecmdb.ca/proteins/P14176.xmlGlycine betaine-binding periplasmic proteinP0AFM2PROX_ECOLIproXhttp://ecmdb.ca/proteins/P0AFM2.xmlAminopeptidase NP04825AMPN_ECOLIpepNhttp://ecmdb.ca/proteins/P04825.xmlSodium/proline symporterP07117PUTP_ECOLIputPhttp://ecmdb.ca/proteins/P07117.xmlUncharacterized amino-acid ABC transporter ATP-binding protein yecCP37774YECC_ECOLIyecChttp://ecmdb.ca/proteins/P37774.xmlInner membrane amino-acid ABC transporter permease protein yecSP0AFT2YECS_ECOLIyecShttp://ecmdb.ca/proteins/P0AFT2.xmlProline-specific permease proYP0AAE2PROY_ECOLIproYhttp://ecmdb.ca/proteins/P0AAE2.xmlProline/betaine transporterP0C0L7PROP_ECOLIproPhttp://ecmdb.ca/proteins/P0C0L7.xmlGlycine betaine/L-proline transport system permease protein proWP14176PROW_ECOLIproWhttp://ecmdb.ca/proteins/P14176.xmlOuter membrane protein NP77747OMPN_ECOLIompNhttp://ecmdb.ca/proteins/P77747.xmlOuter membrane pore protein EP02932PHOE_ECOLIphoEhttp://ecmdb.ca/proteins/P02932.xmlOuter membrane protein FP02931OMPF_ECOLIompFhttp://ecmdb.ca/proteins/P02931.xmlOuter membrane protein CP06996OMPC_ECOLIompChttp://ecmdb.ca/proteins/P06996.xmlAdenosine triphosphate + Water + L-Proline > ADP + Hydrogen ion + Phosphate + L-ProlineABC-26-RXNAdenosine triphosphate + Water + L-Proline > ADP + Hydrogen ion + Phosphate + L-ProlineABC-26-RXNWater + L-Prolinylglycine > Glycine + L-ProlineAdenosine triphosphate + L-Proline + tRNA(Pro) + tRNA(Pro) <> Adenosine monophosphate + Pyrophosphate + L-Prolyl-tRNA(Pro) + L-Prolyl-tRNA(Pro)R03661L-D-1-Pyrroline-5-carboxylic acid + 2 Hydrogen ion + NADPH > NADP + L-ProlineR01251FAD + L-Proline > L-D-1-Pyrroline-5-carboxylic acid + FADH2 + Hydrogen ionL-Proline + NAD <> L-D-1-Pyrroline-5-carboxylic acid + NADH + Hydrogen ionR01248L-Proline + NADP <> L-D-1-Pyrroline-5-carboxylic acid + NADPH + Hydrogen ionR01251L-Proline + Acceptor + Quinone <> L-D-1-Pyrroline-5-carboxylic acid + Reduced acceptor + (S)-1-pyrroline-5-carboxylate + HydroquinoneR01253Adenosine triphosphate + L-Proline + tRNA(Pro) <> Adenosine monophosphate + Pyrophosphate + L-Prolyl-tRNA(Pro)R03661a dipeptide with proline at carboxy terminal + Water L-Proline + a standard α amino acid3.4.13.9-RXNAdenosine triphosphate + L-Proline + Water > ADP + Phosphate + L-Proline + Hydrogen ionABC-26-RXNAdenosine triphosphate + L-Proline + Water > ADP + Phosphate + L-Proline + Hydrogen ionABC-26-RXNNAD(P)<sup>+</sup> + L-Proline < NAD(P)H + L-D-1-Pyrroline-5-carboxylic acid + Hydrogen ionPYRROLINECARBREDUCT-RXNL-Proline + an oxidized electron acceptor > L-D-1-Pyrroline-5-carboxylic acid + a reduced electron acceptor + Hydrogen ionRXN-821glycylproline + Water > Glycine + L-ProlineRXN0-6988L-Proline + NAD(P)(+) > L-D-1-Pyrroline-5-carboxylic acid + NAD(P)HL-Proline + acceptor > (S)-1-pyrroline-5-carboxylate + reduced acceptorAdenosine triphosphate + L-Proline + tRNA(Pro) > Adenosine monophosphate + Pyrophosphate + L-prolyl-tRNA(Pro)L-Proline + NAD + NADP <> (S)-1-pyrroline-5-carboxylate + NADH + NADPH + Hydrogen ionR01248 R01251 1-Pyrroline-5-carboxylic acid + Hydrogen ion + NADPH + L-D-1-Pyrroline-5-carboxylic acid + NADPH > NADP + L-Proline + L-ProlinePW_R002719L-Proline + Ubiquinone-1 + L-Proline > Hydrogen ion + Ubiquinol-1 + 1-Pyrroline-5-carboxylic acid + L-D-1-Pyrroline-5-carboxylic acidPW_R002720L-Proline + Adenosine triphosphate + Hydrogen ion + tRNA(Pro) + L-Proline > Adenosine monophosphate + Pyrophosphate + L-prolyl-tRNA(Pro)PW_R002842L-Proline + Adenosine triphosphate + Water + L-Proline > L-Proline + Adenosine diphosphate + Phosphate + Hydrogen ion + ADPPW_RCT000112L-D-1-Pyrroline-5-carboxylic acid + 2 Hydrogen ion + NADPH > NADP + L-ProlineAdenosine 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 glucoseShake flask and filter culture385.0uM0.037 oCK12 NCM3722Mid-Log Phase15400000Bennett, 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 5:593-599.19561621Gutnick 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 glycerolShake flask and filter culture451.0uM0.037 oCK12 NCM3722Mid-Log Phase18040000Bennett, 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 5:593-599.19561621Gutnick 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 acetateShake flask and filter culture361.0uM0.037 oCK12 NCM3722Mid-Log Phase14440000Bennett, 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 5:593-599.1956162148 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 GlucoBioreactor, pH controlled, O2 and CO2 controlled, dilution rate: 0.2/h143.0uM0.037 oCBW25113Stationary Phase, glucose limited5720000Ishii, 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 316:593-597.17379776Luria-Bertani (LB) mediaShake flask550.0uMtrue45.037 oCBL21 DE3Stationary phase cultures (overnight culture)2201600180000Lin, 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 104:9597-9602.17535911Luria-Bertani (LB) mediaShake flask531.67uMtrue11.3737 oCBL21 DE3Stationary phase cultures (overnight culture)212666745490Lin, 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