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Protein

Phenylalanine dehydrogenase

Gene

pdh

Organism
Rhodococcus sp.
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the reversible, NAD-dependent deamination of L-phenylalanine to phenyl pyruvate, ammonia and NADH.2 Publications

Catalytic activityi

L-phenylalanine + H2O + NAD+ = phenylpyruvate + NH3 + NADH.2 Publications

Enzyme regulationi

Subject to competitive inhibition by 3-phenylpropionate for the conversion of L-phenylalanine to phenylpyruvate. Subject to competitive inhibition by D-phenylalanine for the conversion of phenylpyruvate to L-phenylalanine.1 Publication

Kineticsi

  1. KM=1.4 mM for NAD in the forward reaction
  2. KM=0.03 mM for NADH in the reverse reaction
  3. KM=0.12 mM for phenylpyruvate in the reverse reaction
  4. KM=5.5 mM for L-phenylalanine in the forward reaction

    Pathwayi: L-phenylalanine biosynthesis

    This protein is involved in step 1 of the subpathway that synthesizes L-phenylalanine from phenylpyruvate (PDH route).1 Publication
    Proteins known to be involved in this subpathway in this organism are:
    1. Phenylalanine dehydrogenase (pdh)
    This subpathway is part of the pathway L-phenylalanine biosynthesis, which is itself part of Amino-acid biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-phenylalanine from phenylpyruvate (PDH route), the pathway L-phenylalanine biosynthesis and in Amino-acid biosynthesis.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei43 – 431NADCombined sources1 Publication
    Binding sitei67 – 671SubstrateCombined sources1 Publication
    Active sitei79 – 791Proton donor/acceptor1 Publication
    Binding sitei119 – 1191NADCombined sources1 Publication
    Binding sitei150 – 1501NADCombined sources1 Publication
    Binding sitei154 – 1541NADCombined sources1 Publication
    Binding sitei211 – 2111NADCombined sources1 Publication
    Binding sitei263 – 2631SubstrateCombined sources1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi183 – 1897NADCombined sourcesCurated1 Publication
    Nucleotide bindingi206 – 2072NADCombined sources1 Publication
    Nucleotide bindingi240 – 2412NADCombined sources1 Publication
    Nucleotide bindingi261 – 2633NADCombined sources1 Publication

    GO - Molecular functioni

    • nucleotide binding Source: UniProtKB-KW
    • phenylalanine dehydrogenase activity Source: UniProtKB

    GO - Biological processi

    • L-phenylalanine biosynthetic process Source: UniProtKB-UniPathway
    • L-phenylalanine catabolic process Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    NAD, Nucleotide-binding

    Enzyme and pathway databases

    UniPathwayiUPA00121; UER00346.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Phenylalanine dehydrogenase2 Publications (EC:1.4.1.202 Publications)
    Short name:
    PheDH
    Gene namesi
    Name:pdh1 PublicationImported
    OrganismiRhodococcus sp.Imported
    Taxonomic identifieri1831 [NCBI]
    Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesNocardiaceaeRhodococcus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methionineiRemoved1 Publication
    Chaini2 – 356355Phenylalanine dehydrogenasePRO_0000434608Add
    BLAST

    Interactioni

    Subunit structurei

    Homotetramer, dimer of dimers.1 Publication1 Publication

    Structurei

    Secondary structure

    1
    356
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi3 – 75Combined sources
    Beta strandi11 – 199Combined sources
    Turni20 – 234Combined sources
    Beta strandi24 – 329Combined sources
    Beta strandi34 – 4512Combined sources
    Helixi50 – 7021Combined sources
    Beta strandi76 – 838Combined sources
    Helixi88 – 903Combined sources
    Helixi93 – 10917Combined sources
    Turni110 – 1123Combined sources
    Beta strandi113 – 1186Combined sources
    Helixi124 – 13310Combined sources
    Helixi142 – 1443Combined sources
    Helixi151 – 16818Combined sources
    Beta strandi178 – 1825Combined sources
    Helixi186 – 19712Combined sources
    Beta strandi201 – 2055Combined sources
    Helixi209 – 2179Combined sources
    Helixi225 – 2306Combined sources
    Beta strandi234 – 2385Combined sources
    Helixi247 – 2526Combined sources
    Beta strandi256 – 2583Combined sources
    Beta strandi266 – 2683Combined sources
    Helixi269 – 2779Combined sources
    Helixi285 – 2884Combined sources
    Helixi291 – 30010Combined sources
    Helixi306 – 3149Combined sources
    Helixi316 – 33015Combined sources
    Helixi334 – 34815Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1BW9X-ray1.50A/B1-356[»]
    1BXGX-ray2.30A/B1-356[»]
    1C1DX-ray1.25A/B2-356[»]
    1C1XX-ray1.40A/B2-356[»]
    ProteinModelPortaliQ59771.
    SMRiQ59771. Positions 2-348.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ59771.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni118 – 1192Substrate bindingCombined sources1 Publication

    Sequence similaritiesi

    Belongs to the Glu/Leu/Phe/Val dehydrogenases family.UniRule annotation

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    InterProiIPR006095. Glu/Leu/Phe/Val_DH.
    IPR006096. Glu/Leu/Phe/Val_DH_C.
    IPR006097. Glu/Leu/Phe/Val_DH_dimer_dom.
    IPR016211. Glu/Phe/Leu/Val_DH_bac/arc.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PANTHERiPTHR11606:SF3. PTHR11606:SF3. 1 hit.
    PfamiPF00208. ELFV_dehydrog. 1 hit.
    PF02812. ELFV_dehydrog_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000188. Phe_leu_dh. 1 hit.
    PRINTSiPR00082. GLFDHDRGNASE.
    SMARTiSM00839. ELFV_dehydrog. 1 hit.
    [Graphical view]
    SUPFAMiSSF51735. SSF51735. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    Q59771-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSIDSALNWD GEMTVTRFDR ETGAHFVIRL DSTQLGPAAG GTRAAQYSQL
    60 70 80 90 100
    ADALTDAGKL AGAMTLKMAV SNLPMGGGKS VIALPAPRHS IDPSTWARIL
    110 120 130 140 150
    RIHAENIDKL SGNYWTGPDV NTNSADMDTL NDTTEFVFGR SLERGGAGSS
    160 170 180 190 200
    AFTTAVGVFE AMKATVAHRG LGSLDGLTVL VQGLGAVGGS LASLAAEAGA
    210 220 230 240 250
    QLLVADTDTE RVAHAVALGH TAVALEDVLS TPCDVFAPCA MGGVITTEVA
    260 270 280 290 300
    RTLDCSVVAG AANNVIADEA ASDILHARGI LYAPDFVANA GGAIHLVGRE
    310 320 330 340 350
    VLGWSESVVH ERAVAIGDTL NQVFEISDND GVTPDEAART LAGRRAREAS

    TTTATA
    Length:356
    Mass (Da):36,609
    Last modified:December 1, 2001 - v2
    Checksum:iA969C29E9466935E
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U08381 Genomic DNA. Translation: AAA21461.1.
    PIRiA54038.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U08381 Genomic DNA. Translation: AAA21461.1.
    PIRiA54038.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1BW9X-ray1.50A/B1-356[»]
    1BXGX-ray2.30A/B1-356[»]
    1C1DX-ray1.25A/B2-356[»]
    1C1XX-ray1.40A/B2-356[»]
    ProteinModelPortaliQ59771.
    SMRiQ59771. Positions 2-348.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Enzyme and pathway databases

    UniPathwayiUPA00121; UER00346.

    Miscellaneous databases

    EvolutionaryTraceiQ59771.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    InterProiIPR006095. Glu/Leu/Phe/Val_DH.
    IPR006096. Glu/Leu/Phe/Val_DH_C.
    IPR006097. Glu/Leu/Phe/Val_DH_dimer_dom.
    IPR016211. Glu/Phe/Leu/Val_DH_bac/arc.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PANTHERiPTHR11606:SF3. PTHR11606:SF3. 1 hit.
    PfamiPF00208. ELFV_dehydrog. 1 hit.
    PF02812. ELFV_dehydrog_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000188. Phe_leu_dh. 1 hit.
    PRINTSiPR00082. GLFDHDRGNASE.
    SMARTiSM00839. ELFV_dehydrog. 1 hit.
    [Graphical view]
    SUPFAMiSSF51735. SSF51735. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    1. "Cloning, sequencing, and expression of Rhodococcus L-phenylalanine dehydrogenase. Sequence comparisons to amino-acid dehydrogenases."
      Brunhuber N.M., Banerjee A., Jacobs W.R. Jr., Blanchard J.S.
      J. Biol. Chem. 269:16203-16211(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-38; 90-95; 97-114 AND 300-312, FUNCTION, CATALYTIC ACTIVITY.
      Strain: M4Imported.
    2. "Phenylalanine dehydrogenase from Rhodococcus sp. M4: high-resolution X-ray analyses of inhibitory ternary complexes reveal key features in the oxidative deamination mechanism."
      Vanhooke J.L., Thoden J.B., Brunhuber N.M., Blanchard J.S., Holden H.M.
      Biochemistry 38:2326-2339(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) IN COMPLEXES WITH NAD; PHENYLPROPIONATE AND KETO-PHENYLPYRUVATE, SUBUNIT.
    3. "Rhodococcus L-phenylalanine dehydrogenase: kinetics, mechanism, and structural basis for catalytic specificity."
      Brunhuber N.M., Thoden J.B., Blanchard J.S., Vanhooke J.L.
      Biochemistry 39:9174-9187(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.25 ANGSTROMS) OF 2-356 IN COMPLEX WITH NAD AND SUBSTRATE, FUNCTION, PATHWAY, CATALYTIC ACTIVITY, ENZYME REGULATION, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVE SITE.

    Entry informationi

    Entry nameiDHPH_RHOSO
    AccessioniPrimary (citable) accession number: Q59771
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 11, 2015
    Last sequence update: December 1, 2001
    Last modified: January 20, 2016
    This is version 82 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. 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.