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Protein

Delta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase

Gene

dpkA

Organism
Pseudomonas syringae pv. tomato
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the reduction of both Delta(1)-pyrroline-2-carboxylate (Pyr2C) and Delta(1)-piperideine-2-carboxylate (Pip2C) to L-proline and L-pipecolate, respectively, using NADPH as the electron donor. Can catalyze the reverse oxidation reactions, albeit at a much lower rate. Is also able to catalyze in vitro the NADPH-dependent formation of N-methylalanine from pyruvate and N-methylamine; can act on other alpha-keto acids and specifically uses methylamine and not ammonia for these reductive amination reactions. Can use NADH instead of NADPH, although with much less efficiency.1 Publication

Catalytic activityi

L-pipecolate + NADP+ = 1-piperideine-2-carboxylate + NADPH.1 Publication
L-proline + NADP+ = 1-pyrroline-2-carboxylate + NADPH.1 Publication
N-methyl-L-alanine + H2O + NADP+ = pyruvate + methylamine + NADPH.1 Publication

Enzyme regulationi

Is inhibited by the substrate analog pyrrole-2-carboxylate, and by 2-picolinate.1 Publication

Temperature dependencei

Optimum temperature is 30-45 degrees Celsius. Is stable between 0 and 35 degrees Celsius after incubation of 30 minutes.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei53Charge relay system1 Publication1
Active sitei54Proton donor1 Publication1
Binding sitei58Substrate1 Publication1
Binding sitei166Substrate1 Publication1
Active sitei194Charge relay system1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi126 – 130NADPCombined sources1 Publication5
Nucleotide bindingi184 – 186NADPCombined sources1 Publication3
Nucleotide bindingi236 – 237NADP; shared with dimeric partnerCombined sources1 Publication2
Nucleotide bindingi309 – 315NADPCombined sources1 Publication7

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

NADP, Nucleotide-binding

Enzyme and pathway databases

BRENDAi1.5.1.1. 5193.
1.5.1.21. 5193.

Names & Taxonomyi

Protein namesi
Recommended name:
Delta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase1 Publication (EC:1.5.1.211 Publication)
Short name:
Pyr2C/Pip2C reductase1 Publication
Alternative name(s):
N-methyl-L-amino acid dehydrogenase1 Publication (EC:1.4.1.171 Publication)
Gene namesi
Name:dpkA1 Publication
ORF Names:NB04_21545Imported
OrganismiPseudomonas syringae pv. tomato
Taxonomic identifieri323 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004322891 – 343Delta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductaseAdd BLAST343

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi223283.PSPTO_2359.

Structurei

Secondary structure

1343
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi11 – 13Combined sources3
Helixi15 – 28Combined sources14
Helixi33 – 48Combined sources16
Helixi52 – 54Combined sources3
Helixi56 – 58Combined sources3
Helixi59 – 67Combined sources9
Beta strandi78 – 83Combined sources6
Beta strandi86 – 90Combined sources5
Helixi96 – 114Combined sources19
Beta strandi115 – 125Combined sources11
Helixi131 – 139Combined sources9
Beta strandi143 – 147Combined sources5
Beta strandi169 – 175Combined sources7
Beta strandi178 – 185Combined sources8
Beta strandi187 – 190Combined sources4
Helixi192 – 200Combined sources9
Beta strandi209 – 211Combined sources3
Helixi221 – 225Combined sources5
Turni233 – 235Combined sources3
Helixi236 – 249Combined sources14
Turni250 – 253Combined sources4
Beta strandi273 – 281Combined sources9
Turni283 – 286Combined sources4
Helixi291 – 304Combined sources14
Helixi313 – 325Combined sources13
Beta strandi327 – 329Combined sources3
Helixi331 – 340Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1WTJX-ray1.55A/B1-343[»]
2CWFX-ray1.80A/B1-343[»]
2CWHX-ray1.70A/B1-343[»]
ProteinModelPortaliQ4U331.
SMRiQ4U331.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ4U331.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni192 – 193Substrate binding1 Publication2

Sequence similaritiesi

Belongs to the LDH2/MDH2 oxidoreductase family.Curated

Phylogenomic databases

eggNOGiENOG4105DG4. Bacteria.
COG2055. LUCA.

Family and domain databases

InterProiIPR003767. Malate/L-lactate_DH.
[Graphical view]
PANTHERiPTHR11091. PTHR11091. 1 hit.
PfamiPF02615. Ldh_2. 1 hit.
[Graphical view]
SUPFAMiSSF89733. SSF89733. 1 hit.

Sequencei

Sequence statusi: Complete.

Q4U331-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSASHADQPT QTVSYPQLID LLRRIFVVHG TSPEVADVLA ENCASAQRDG
60 70 80 90 100
SHSHGIFRIP GYLSSLASGW VDGKAVPVVE DVGAAFVRVD ACNGFAQPAL
110 120 130 140 150
AAARSLLIDK ARSAGVAILA IRGSHHFAAL WPDVEPFAEQ GLVALSMVNS
160 170 180 190 200
MTCVVPHGAR QPLFGTNPIA FGAPRAGGEP IVFDLATSAI AHGDVQIAAR
210 220 230 240 250
EGRLLPAGMG VDRDGLPTQE PRAILDGGAL LPFGGHKGSA LSMMVELLAA
260 270 280 290 300
GLTGGNFSFE FDWSKHPGAQ TPWTGQLLIV IDPDKGAGQH FAQRSEELVR
310 320 330 340
QLHGVGQERL PGDRRYLERA RSMAHGIVIA QADLERLQEL AGH
Length:343
Mass (Da):36,249
Last modified:July 5, 2005 - v1
Checksum:i7CC78CEDB2151A54
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ017704 Genomic DNA. Translation: AAY43734.1.
JRRA01000024 Genomic DNA. Translation: KGK93380.1.
RefSeqiWP_007246364.1. NZ_LNKZ01000118.1.

Genome annotation databases

EnsemblBacteriaiKGK93380; KGK93380; NB04_21545.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ017704 Genomic DNA. Translation: AAY43734.1.
JRRA01000024 Genomic DNA. Translation: KGK93380.1.
RefSeqiWP_007246364.1. NZ_LNKZ01000118.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1WTJX-ray1.55A/B1-343[»]
2CWFX-ray1.80A/B1-343[»]
2CWHX-ray1.70A/B1-343[»]
ProteinModelPortaliQ4U331.
SMRiQ4U331.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi223283.PSPTO_2359.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiKGK93380; KGK93380; NB04_21545.

Phylogenomic databases

eggNOGiENOG4105DG4. Bacteria.
COG2055. LUCA.

Enzyme and pathway databases

BRENDAi1.5.1.1. 5193.
1.5.1.21. 5193.

Miscellaneous databases

EvolutionaryTraceiQ4U331.

Family and domain databases

InterProiIPR003767. Malate/L-lactate_DH.
[Graphical view]
PANTHERiPTHR11091. PTHR11091. 1 hit.
PfamiPF02615. Ldh_2. 1 hit.
[Graphical view]
SUPFAMiSSF89733. SSF89733. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiPY2CR_PSEUB
AccessioniPrimary (citable) accession number: Q4U331
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 4, 2015
Last sequence update: July 5, 2005
Last modified: November 2, 2016
This is version 50 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.