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Protein

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

Gene

lhpD

Organism
Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
Status
Reviewed-Annotation score: Annotation score: 4 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. Cannot use NADH instead of NADPH. Is likely involved in a degradation pathway that converts trans-3-hydroxy-L-proline (t3LHyp) to L-proline, which would allow P.aeruginosa to grow on t3LHyp as a sole carbon source. Can also catalyze the reverse oxidation reactions, albeit at a much lower rate. Is also able to use Delta(1)-pyrroline-(4S)-hydroxy-2-carboxylate (Pyr4SH2C) and cis-4-hydroxy-L-proline (c4LHyp) as substrates, and might be involved in the metabolism of c4LHyp, a compound which is generated by the hydroxylation of free L-proline in bacteria.2 Publications

Catalytic activityi

L-pipecolate + NADP+ = 1-piperideine-2-carboxylate + NADPH.1 Publication
L-proline + NADP+ = 1-pyrroline-2-carboxylate + NADPH.2 Publications
cis-4-hydroxy-L-proline + NADP+ = Delta(1)-pyrroline-(4S)-hydroxy-2-carboxylate + NADPH.1 Publication

Kineticsi

kcat is 2500 min(-1) for Pyr2C reduction. kcat is 2120 min(-1) for Pip2C reduction. kcat is 868 min(-1) for Pyr4SH2C reduction. kcat is 205 min(-1) for L-proline oxidation. kcat is 135 min(-1) for L-pipecolate oxidation. kcat is 272 min(-1) for t3LHyp oxidation.1 Publication

  1. KM=0.447 mM for Delta(1)-pyrroline-2-carboxylate (at pH 7.0)1 Publication
  2. KM=1.57 mM for Delta(1)-piperideine-2-carboxylate (at pH 7.0)1 Publication
  3. KM=0.835 mM for Delta(1)-pyrroline-(4S)-hydroxy-2-carboxylate (at pH 7.0)1 Publication
  4. KM=18.5 mM for L-proline (at pH 10.0)1 Publication
  5. KM=34.8 mM for L-pipecolate (at pH 10.0)1 Publication
  6. KM=132 mM for trans-3-hydroxy-L-proline (at pH 10.0)1 Publication
  7. KM=0.41 mM for NADPH1 Publication

    pH dependencei

    Optimum pH is 7.0 for Pyr2C reduction and 10.0 for L-proline oxidation.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei44 – 441Charge relay systemBy similarity
    Active sitei45 – 451Proton donorBy similarity
    Binding sitei49 – 491SubstrateBy similarity
    Binding sitei157 – 1571SubstrateBy similarity
    Active sitei185 – 1851Charge relay systemBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi117 – 1215NADPBy similarity
    Nucleotide bindingi175 – 1773NADPBy similarity
    Nucleotide bindingi226 – 2272NADP; shared with dimeric partnerBy similarity
    Nucleotide bindingi301 – 3077NADPBy similarity

    GO - Molecular functioni

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    NADP

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Delta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase1 Publication (EC:1.5.1.212 Publications)
    Short name:
    Pyr2C/Pip2C reductase1 Publication
    Alternative name(s):
    Delta(1)-pyrroline-(4S)-hydroxy-2-carboxylate reductase1 Publication (EC:1.5.1.-1 Publication)
    Short name:
    Pyr4SH2C reductase1 Publication
    Proline ketimine reductase1 Publication
    Gene namesi
    Name:lhpD1 Publication
    Ordered Locus Names:PA1252
    OrganismiPseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
    Taxonomic identifieri208964 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
    Proteomesi
    • UP000002438 Componenti: Chromosome

    Organism-specific databases

    PseudoCAPiPA1252.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 334334Delta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductasePRO_0000083843Add
    BLAST

    Proteomic databases

    PaxDbiQ9I492.
    PRIDEiQ9I492.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    STRINGi208964.PA1252.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9I492.
    SMRiQ9I492. Positions 11-324.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni183 – 1842Substrate bindingBy similarity

    Sequence similaritiesi

    Belongs to the LDH2/MDH2 oxidoreductase family.Curated

    Phylogenomic databases

    eggNOGiENOG4105DG4. Bacteria.
    COG2055. LUCA.
    HOGENOMiHOG000173270.
    InParanoidiQ9I492.
    OMAiERDGCAS.
    OrthoDBiEOG64N9XZ.
    PhylomeDBiQ9I492.

    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.

    Q9I492-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MIRMTLDEVR ELAVRILRRH AFSEAHVQAV ADTLVAGERD ECASHGIWRL
    60 70 80 90 100
    LGCIATLKAG KVSADAEPEL HDIAPGLLRV DAHGGFSQCA FRLGLPHLLE
    110 120 130 140 150
    KARSQGIAAM AVNRCVHFSA LWVEVEALTE AGLVALATTP SHAWVAPAGG
    160 170 180 190 200
    RKPIFGTNPI AFGWPRPDGP PFVFDFATSA VARGEIQLHE RAGKPIPLGW
    210 220 230 240 250
    GVDEQGEPTT DASAALRGAM LTFGGHKGSA LAAMVELLAG PLIGDLTSAE
    260 270 280 290 300
    SLAYDEGSRS SPYGGELLIA IDPRRMLGAS AEEHLARAET LFEGIVEQGA
    310 320 330
    RLPSQRRFEA RERSARDGVT IPEALHRELL ALLE
    Length:334
    Mass (Da):35,684
    Last modified:March 1, 2001 - v1
    Checksum:iEF9A6AB407515A7E
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE004091 Genomic DNA. Translation: AAG04641.1.
    PIRiB83488.
    RefSeqiNP_249943.1. NC_002516.2.
    WP_003082545.1. NZ_ASJY01000173.1.

    Genome annotation databases

    EnsemblBacteriaiAAG04641; AAG04641; PA1252.
    GeneIDi881290.
    KEGGipae:PA1252.
    PATRICi19836828. VBIPseAer58763_1300.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE004091 Genomic DNA. Translation: AAG04641.1.
    PIRiB83488.
    RefSeqiNP_249943.1. NC_002516.2.
    WP_003082545.1. NZ_ASJY01000173.1.

    3D structure databases

    ProteinModelPortaliQ9I492.
    SMRiQ9I492. Positions 11-324.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi208964.PA1252.

    Proteomic databases

    PaxDbiQ9I492.
    PRIDEiQ9I492.

    Protocols and materials databases

    DNASUi881290.
    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAG04641; AAG04641; PA1252.
    GeneIDi881290.
    KEGGipae:PA1252.
    PATRICi19836828. VBIPseAer58763_1300.

    Organism-specific databases

    PseudoCAPiPA1252.

    Phylogenomic databases

    eggNOGiENOG4105DG4. Bacteria.
    COG2055. LUCA.
    HOGENOMiHOG000173270.
    InParanoidiQ9I492.
    OMAiERDGCAS.
    OrthoDBiEOG64N9XZ.
    PhylomeDBiQ9I492.

    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...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228.
    2. "Identification and characterization of trans-3-hydroxy-L-proline dehydratase and Delta(1)-pyrroline-2-carboxylate reductase involved in trans-3-hydroxy-L-proline metabolism of bacteria."
      Watanabe S., Tanimoto Y., Yamauchi S., Tozawa Y., Sawayama S., Watanabe Y.
      FEBS Open Bio 4:240-250(2014) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES.
      Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228.
    3. "Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks."
      Zhao S., Sakai A., Zhang X., Vetting M.W., Kumar R., Hillerich B., San Francisco B., Solbiati J., Steves A., Brown S., Akiva E., Barber A., Seidel R.D., Babbitt P.C., Almo S.C., Gerlt J.A., Jacobson M.P.
      Elife 3:0-0(2014) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES.
      Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228.

    Entry informationi

    Entry nameiPY2CR_PSEAE
    AccessioniPrimary (citable) accession number: Q9I492
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 16, 2001
    Last sequence update: March 1, 2001
    Last modified: November 11, 2015
    This is version 77 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

    Complete proteome, Reference proteome

    Documents

    1. 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.