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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)DescriptionActionsGraphical viewLength
    Binding sitei43NADCombined sources1 Publication1
    Binding sitei67SubstrateCombined sources1 Publication1
    Active sitei79Proton donor/acceptor1 Publication1
    Binding sitei119NADCombined sources1 Publication1
    Binding sitei150NADCombined sources1 Publication1
    Binding sitei154NADCombined sources1 Publication1
    Binding sitei211NADCombined sources1 Publication1
    Binding sitei263SubstrateCombined sources1 Publication1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi183 – 189NADCombined sourcesCurated1 Publication7
    Nucleotide bindingi206 – 207NADCombined sources1 Publication2
    Nucleotide bindingi240 – 241NADCombined sources1 Publication2
    Nucleotide bindingi261 – 263NADCombined sources1 Publication3

    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)DescriptionActionsGraphical viewLength
    Initiator methionineiRemoved1 Publication
    ChainiPRO_00004346082 – 356Phenylalanine dehydrogenaseAdd BLAST355

    Interactioni

    Subunit structurei

    Homotetramer, dimer of dimers.1 Publication1 Publication

    Structurei

    Secondary structure

    1356
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi3 – 7Combined sources5
    Beta strandi11 – 19Combined sources9
    Turni20 – 23Combined sources4
    Beta strandi24 – 32Combined sources9
    Beta strandi34 – 45Combined sources12
    Helixi50 – 70Combined sources21
    Beta strandi76 – 83Combined sources8
    Helixi88 – 90Combined sources3
    Helixi93 – 109Combined sources17
    Turni110 – 112Combined sources3
    Beta strandi113 – 118Combined sources6
    Helixi124 – 133Combined sources10
    Helixi142 – 144Combined sources3
    Helixi151 – 168Combined sources18
    Beta strandi178 – 182Combined sources5
    Helixi186 – 197Combined sources12
    Beta strandi201 – 205Combined sources5
    Helixi209 – 217Combined sources9
    Helixi225 – 230Combined sources6
    Beta strandi234 – 238Combined sources5
    Helixi247 – 252Combined sources6
    Beta strandi256 – 258Combined sources3
    Beta strandi266 – 268Combined sources3
    Helixi269 – 277Combined sources9
    Helixi285 – 288Combined sources4
    Helixi291 – 300Combined sources10
    Helixi306 – 314Combined sources9
    Helixi316 – 330Combined sources15
    Helixi334 – 348Combined sources15

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ59771.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni118 – 119Substrate bindingCombined sources1 Publication2

    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
    PDB 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.
    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...

    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: November 2, 2016
    This is version 84 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.