PY2CR_PSEPU
ID PY2CR_PSEPU Reviewed; 341 AA.
AC Q5FB93;
DT 04-MAR-2015, integrated into UniProtKB/Swiss-Prot.
DT 15-MAR-2005, sequence version 1.
DT 03-AUG-2022, entry version 49.
DE RecName: Full=Delta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase {ECO:0000303|PubMed:15561717};
DE Short=Pyr2C/Pip2C reductase {ECO:0000303|PubMed:15561717};
DE EC=1.5.1.21 {ECO:0000269|PubMed:15561717};
DE AltName: Full=N-methyl-L-amino acid dehydrogenase {ECO:0000303|PubMed:15720386};
DE Short=NMAADH {ECO:0000303|PubMed:15720386};
DE EC=1.4.1.17 {ECO:0000269|PubMed:15561717, ECO:0000269|PubMed:15720386};
GN Name=dpkA {ECO:0000303|PubMed:15561717};
OS Pseudomonas putida (Arthrobacter siderocapsulatus).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=303;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF N-TERMINUS, CLEAVAGE
RP OF INITIATOR METHIONINE, FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE
RP SPECIFICITY, AND SUBUNIT.
RC STRAIN=ATCC 12633 / DSM 291 / JCM 13063 / CCUG 12690 / LMG 2257 / NBRC
RC 14164 / NCIMB 9494 / NCTC 10936 / VKM B-2187 / Stanier 90;
RX PubMed=15720386; DOI=10.1111/j.1742-4658.2004.04541.x;
RA Mihara H., Muramatsu H., Kakutani R., Yasuda M., Ueda M., Kurihara T.,
RA Esaki N.;
RT "N-methyl-L-amino acid dehydrogenase from Pseudomonas putida. A novel
RT member of an unusual NAD(P)-dependent oxidoreductase superfamily.";
RL FEBS J. 272:1117-1123(2005).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, ACTIVITY REGULATION, DISRUPTION PHENOTYPE, AND KINETIC
RP MECHANISM.
RC STRAIN=ATCC 12633 / DSM 291 / JCM 13063 / CCUG 12690 / LMG 2257 / NBRC
RC 14164 / NCIMB 9494 / NCTC 10936 / VKM B-2187 / Stanier 90;
RX PubMed=15561717; DOI=10.1074/jbc.m411918200;
RA Muramatsu H., Mihara H., Kakutani R., Yasuda M., Ueda M., Kurihara T.,
RA Esaki N.;
RT "The putative malate/lactate dehydrogenase from Pseudomonas putida is an
RT NADPH-dependent delta1-piperideine-2-carboxylate/delta1-pyrroline-2-
RT carboxylate reductase involved in the catabolism of D-lysine and D-
RT proline.";
RL J. Biol. Chem. 280:5329-5335(2005).
CC -!- FUNCTION: Catalyzes the reduction of both Delta(1)-pyrroline-2-
CC carboxylate (Pyr2C) and Delta(1)-piperideine-2-carboxylate (Pip2C) to
CC L-proline and L-pipecolate, respectively, using NADPH as the electron
CC donor. Can use NADH instead of NADPH, although with much less
CC efficiency. Plays an essential role in the catabolism of D-proline and
CC D-lysine, which allows P.putida to grow on each of these amino-acids as
CC a sole carbon source; D-lysine appears to be catabolized only through
CC the pipecolate pathway. Can also catalyze the reverse oxidation
CC reactions, albeit at a much lower rate. To a lesser extent, is able to
CC catalyze in vitro the NADPH-dependent formation of N-alkyl-L-amino
CC acids from the corresponding alpha-oxo acids and alkylamines, e.g. the
CC formation of N-methylalanine from pyruvate and N-methylamine; cannot
CC use ammonia as substrate for these reductive amination reactions. Shows
CC neither malate dehydrogenase nor lactate dehydrogenase activity.
CC {ECO:0000269|PubMed:15561717}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-pipecolate + NADP(+) = Delta(1)-piperideine-2-carboxylate +
CC H(+) + NADPH; Xref=Rhea:RHEA:12524, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:57783, ChEBI:CHEBI:58349, ChEBI:CHEBI:61185,
CC ChEBI:CHEBI:77631; EC=1.5.1.21;
CC Evidence={ECO:0000269|PubMed:15561717};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-proline + NADP(+) = 1-pyrroline-2-carboxylate + H(+) +
CC NADPH; Xref=Rhea:RHEA:20317, ChEBI:CHEBI:15378, ChEBI:CHEBI:39785,
CC ChEBI:CHEBI:57783, ChEBI:CHEBI:58349, ChEBI:CHEBI:60039; EC=1.5.1.21;
CC Evidence={ECO:0000269|PubMed:15561717};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N-methyl-L-alanine + NADP(+) = H(+) + methylamine +
CC NADPH + pyruvate; Xref=Rhea:RHEA:21768, ChEBI:CHEBI:15361,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:57783,
CC ChEBI:CHEBI:58175, ChEBI:CHEBI:58349, ChEBI:CHEBI:59338; EC=1.4.1.17;
CC Evidence={ECO:0000269|PubMed:15561717, ECO:0000269|PubMed:15720386};
CC -!- ACTIVITY REGULATION: Is inhibited by the substrate analog pyrrole-2-
CC carboxylate, but not by N-formylphenylalanine.
CC {ECO:0000269|PubMed:15561717}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=43 uM for Delta(1)-pyrroline-2-carboxylate
CC {ECO:0000269|PubMed:15561717};
CC KM=15 uM for Delta(1)-piperideine-2-carboxylate
CC {ECO:0000269|PubMed:15561717};
CC KM=144 mM for L-proline {ECO:0000269|PubMed:15561717};
CC KM=32.4 mM for L-pipecolate {ECO:0000269|PubMed:15561717};
CC KM=34 uM for NADPH (with Pyr2C as cosubstrate)
CC {ECO:0000269|PubMed:15561717};
CC KM=140 uM for NADPH (with Pip2C as cosubstrate)
CC {ECO:0000269|PubMed:15561717};
CC KM=211 uM for NADP(+) (with L-proline as cosubstrate)
CC {ECO:0000269|PubMed:15561717};
CC KM=112 uM for NADP(+) (with L-pipecolate as cosubstrate)
CC {ECO:0000269|PubMed:15561717};
CC Vmax=168 umol/min/mg enzyme for Pyr2C reduction
CC {ECO:0000269|PubMed:15561717};
CC Vmax=220 umol/min/mg enzyme for Pip2C reduction
CC {ECO:0000269|PubMed:15561717};
CC Vmax=0.271 umol/min/mg enzyme for L-proline oxidation
CC {ECO:0000269|PubMed:15561717};
CC Vmax=0.118 umol/min/mg enzyme for L-pipecolate oxidation
CC {ECO:0000269|PubMed:15561717};
CC pH dependence:
CC Optimum pH is 7.0 for Pyr2C reduction, 8.0 for Pip2C reduction, and
CC 10.0 for L-proline and L-pipecolate oxidation.
CC {ECO:0000269|PubMed:15561717};
CC Temperature dependence:
CC Optimum temperature is 35 degrees Celsius. Is inactivated at a rate
CC of about a 30% decrease in 30 minutes at 35 degrees Celsius. The
CC enzyme keeps its full activity, however, at 30 degrees Celsius for at
CC least 30 minutes. {ECO:0000269|PubMed:15561717};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:15720386}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene loss their ability to
CC grow on D-lysine and also on D-proline as a sole carbon source.
CC Moreover, the mutant strain grows only slowly in the medium containing
CC L-lysine as a sole carbon source in contrast to the wild-type strain.
CC No difference is evident between the two strains in other media
CC containing as a sole carbon source L-pipecolate, L-proline, and the
CC following D-amino acids: D-alanine, D-valine, D-leucine, D-isoleucine,
CC D-serine, D-threonine, D-aspartate, D-glutamate, D-glutamine, D-
CC arginine, and D-phenylalanine. {ECO:0000269|PubMed:15561717}.
CC -!- MISCELLANEOUS: The enzyme reaction proceeds through an ordered Bi-Bi
CC mechanism. {ECO:0000269|PubMed:15561717}.
CC -!- SIMILARITY: Belongs to the LDH2/MDH2 oxidoreductase family.
CC {ECO:0000305}.
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DR EMBL; AB190215; BAD89743.1; -; Genomic_DNA.
DR AlphaFoldDB; Q5FB93; -.
DR SMR; Q5FB93; -.
DR KEGG; ag:BAD89743; -.
DR BRENDA; 1.5.1.21; 5092.
DR GO; GO:0047125; F:delta1-piperideine-2-carboxylate reductase activity; IEA:UniProtKB-EC.
DR GO; GO:0050132; F:N-methylalanine dehydrogenase activity; IEA:UniProtKB-EC.
DR Gene3D; 1.10.1530.10; -; 1.
DR Gene3D; 3.30.1370.60; -; 1.
DR InterPro; IPR043144; Mal/L-sulf/L-lact_DH-like_ah.
DR InterPro; IPR043143; Mal/L-sulf/L-lact_DH-like_NADP.
DR InterPro; IPR036111; Mal/L-sulfo/L-lacto_DH-like_sf.
DR InterPro; IPR003767; Malate/L-lactate_DH-like.
DR PANTHER; PTHR11091; PTHR11091; 1.
DR Pfam; PF02615; Ldh_2; 1.
DR SUPFAM; SSF89733; SSF89733; 1.
PE 1: Evidence at protein level;
KW Direct protein sequencing; NADP; Oxidoreductase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:15720386"
FT CHAIN 2..341
FT /note="Delta(1)-pyrroline-2-carboxylate/Delta(1)-
FT piperideine-2-carboxylate reductase"
FT /id="PRO_0000432290"
FT ACT_SITE 52
FT /note="Charge relay system"
FT /evidence="ECO:0000250|UniProtKB:Q4U331"
FT ACT_SITE 53
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:Q4U331"
FT ACT_SITE 193
FT /note="Charge relay system"
FT /evidence="ECO:0000250|UniProtKB:Q4U331"
FT BINDING 57
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q4U331"
FT BINDING 125..129
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:Q4U331"
FT BINDING 165
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q4U331"
FT BINDING 183..185
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:Q4U331"
FT BINDING 191..192
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q4U331"
FT BINDING 235..236
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000250|UniProtKB:Q4U331"
FT BINDING 308..314
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:Q4U331"
SQ SEQUENCE 341 AA; 35973 MW; 1DC92DE2372822C2 CRC64;
MSAPSTSTVV RVPFTELQSL LQAIFQRHGC SEAVARVLAH NCASAQRDGA HSHGVFRMPG
YVSTLASGWV DGQATPQVSD VAAGYVRVDA AGGFAQPALA AARELLVAKA RSAGIAVLAI
HNSHHFAALW PDVEPFAEEG LVALSVVNSM TCVVPHGARK PLFGTNPIAF AAPCAEHDPI
VFDMATSAMA HGDVQIAARA GQQLPEGMGV DADGQPTTDP KAILEGGALL PFGGHKGSAL
SMMVELLAAA LTGGHFSWEF DWSGHPGAKT PWTGQLIIVI NPGKAEGERF AQRSRELVEH
MQAVGLTRMP GERRYREREV AEEEGVAVTE QELQGLKELL G
