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Protein

Aklavinone 12-hydroxylase RdmE

Gene

rdmE

Organism
Streptomyces purpurascens
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the biosynthesis of the anthracyclines carminomycin, rhodomycin and daunorubicin (daunomycin) which are aromatic polyketide antibiotics that exhibit high cytotoxicity and are widely applied in the chemotherapy of a variety of cancers. Catalyzes the incorporation of a hydroxyl group at position C-11 of aklavinone, resulting in epsilon-rhodomycinone. It can not accept substrates glycosylated at position C-7 and is specific for the C-9R configuration of anthracyclines. It can use both NAD or NADP but it is slowly inactivated in the presence of NADH.2 Publications

Catalytic activityi

Aklavinone + NADPH + O2 = epsilon-rhodomycinone + NADP+ + H2O.1 Publication

Cofactori

FAD1 Publication

Enzyme regulationi

Inhibited by phenylglyoxal and 2,3-butanedione. NADP provides a partial protection against inhibition by phenylglyoxal. Increasing the methanol concentration in the assay causes inhibition of the enzyme.1 Publication

Kineticsi

  1. KM=2 µM for NAD (at pH 7.5)1 Publication
  2. KM=10 µM for aklavinone (at pH 7.5)1 Publication
  3. KM=2 mM for NADP (at pH 7.5)1 Publication

    pH dependencei

    Optimum pH is near 7.4.1 Publication

    Temperature dependencei

    Optimum temperature is 37 degrees Celsius.1 Publication

    Pathwayi: daunorubicin biosynthesis

    This protein is involved in the pathway daunorubicin biosynthesis, which is part of Antibiotic biosynthesis.
    View all proteins of this organism that are known to be involved in the pathway daunorubicin biosynthesis and in Antibiotic biosynthesis.

    Pathwayi: carminomycin biosynthesis

    This protein is involved in the pathway carminomycin biosynthesis, which is part of Antibiotic biosynthesis.
    View all proteins of this organism that are known to be involved in the pathway carminomycin biosynthesis and in Antibiotic biosynthesis.

    Pathwayi: rhodomycin biosynthesis

    This protein is involved in the pathway rhodomycin biosynthesis, which is part of Antibiotic biosynthesis.
    View all proteins of this organism that are known to be involved in the pathway rhodomycin biosynthesis and in Antibiotic biosynthesis.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei35 – 351FAD1 Publication
    Binding sitei119 – 1191FAD1 Publication
    Binding sitei143 – 1431FAD; via amide nitrogen1 Publication
    Active sitei224 – 2241Proton acceptor1 Publication
    Binding sitei308 – 3081FAD1 Publication
    Binding sitei317 – 3171Aklavinone; via amide nitrogen1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi15 – 162FAD1 Publication

    GO - Molecular functioni

    GO - Biological processi

    • daunorubicin biosynthetic process Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Antibiotic biosynthesis

    Keywords - Ligandi

    FAD, Flavoprotein, NAD, NADP, Nucleotide-binding

    Enzyme and pathway databases

    BRENDAi1.14.13.180. 6079.
    UniPathwayiUPA00054.
    UPA01040.
    UPA01042.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Aklavinone 12-hydroxylase RdmE (EC:1.14.13.180)
    Alternative name(s):
    Aklavinone 11-hydroxylase
    Gene namesi
    Name:rdmE
    OrganismiStreptomyces purpurascens
    Taxonomic identifieri1924 [NCBI]
    Taxonomic lineageiBacteriaActinobacteriaStreptomycetalesStreptomycetaceaeStreptomyces

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi224 – 2241Y → F: Loss of hydroxylase activity. 1 Publication
    Mutagenesisi373 – 3731R → A: Hydroxylase activity similar as the wild-type enzyme. 1 Publication
    Mutagenesisi373 – 3731R → M: Hydroxylase activity similar as the wild-type enzyme. 1 Publication
    Mutagenesisi373 – 3731R → Q: Hydroxylase activity similar as the wild-type enzyme. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methionineiRemoved1 Publication
    Chaini2 – 535534Aklavinone 12-hydroxylase RdmEPRO_0000425675Add
    BLAST

    Interactioni

    Subunit structurei

    Monomer.2 Publications

    Structurei

    Secondary structure

    1
    535
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi5 – 117Combined sources
    Helixi15 – 2511Combined sources
    Turni26 – 283Combined sources
    Beta strandi31 – 344Combined sources
    Beta strandi36 – 394Combined sources
    Helixi51 – 599Combined sources
    Helixi63 – 686Combined sources
    Beta strandi80 – 8910Combined sources
    Beta strandi91 – 977Combined sources
    Helixi99 – 1046Combined sources
    Helixi107 – 1093Combined sources
    Helixi119 – 13214Combined sources
    Beta strandi136 – 1405Combined sources
    Beta strandi142 – 1498Combined sources
    Helixi151 – 1533Combined sources
    Beta strandi155 – 1639Combined sources
    Beta strandi166 – 17712Combined sources
    Helixi184 – 1885Combined sources
    Beta strandi193 – 20816Combined sources
    Helixi211 – 2133Combined sources
    Beta strandi221 – 2266Combined sources
    Beta strandi231 – 2366Combined sources
    Beta strandi242 – 2498Combined sources
    Turni251 – 2544Combined sources
    Helixi257 – 2593Combined sources
    Helixi262 – 27312Combined sources
    Beta strandi281 – 29616Combined sources
    Beta strandi298 – 3003Combined sources
    Beta strandi303 – 3053Combined sources
    Turni307 – 3104Combined sources
    Helixi320 – 33920Combined sources
    Helixi347 – 37327Combined sources
    Helixi376 – 3783Combined sources
    Turni379 – 3813Combined sources
    Helixi388 – 3925Combined sources
    Beta strandi430 – 4334Combined sources
    Beta strandi436 – 4394Combined sources
    Helixi440 – 4434Combined sources
    Beta strandi445 – 4528Combined sources
    Helixi457 – 47014Combined sources
    Beta strandi474 – 4796Combined sources
    Turni480 – 4823Combined sources
    Helixi490 – 4934Combined sources
    Turni497 – 4993Combined sources
    Beta strandi501 – 5044Combined sources
    Beta strandi508 – 5169Combined sources
    Helixi521 – 53212Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3IHGX-ray2.49A/B/C1-535[»]
    ProteinModelPortaliQ54530.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ54530.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the PheA/TfdB FAD monooxygenase family.Curated

    Phylogenomic databases

    KOiK15950.

    Family and domain databases

    Gene3Di3.50.50.60. 3 hits.
    InterProiIPR002938. FAD-bd.
    IPR023753. FAD/NAD-binding_dom.
    [Graphical view]
    PfamiPF01494. FAD_binding_3. 1 hit.
    [Graphical view]
    SUPFAMiSSF51905. SSF51905. 2 hits.

    Sequencei

    Sequence statusi: Complete.

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

    Q54530-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MNDHEVDVLV VGAGLGGLST AMFLARQGVR VLVVERRPGL SPYPRAAGQN
    60 70 80 90 100
    PRTMELLRIG GVADEVVRAD DIRGTQGDFV IRLAESVRGE ILRTVSESFD
    110 120 130 140 150
    DMVAATEPCT PAGWAMLSQD KLEPILLAQA RKHGGAIRFG TRLLSFRQHD
    160 170 180 190 200
    DDAGAGVTAR LAGPDGEYDL RAGYLVGADG NRSLVRESLG IGRYGHGTLT
    210 220 230 240 250
    HMVGVIFDAD LSGIMEPGTT GWYYLHHPEF KGTFGPTDRP DRHTLFVEYD
    260 270 280 290 300
    PDEGERPEDF TPQRCVELIG LALDAPEVKP ELVDIQGWEM AARIAERWRE
    310 320 330 340 350
    GRVFLAGDAA KVTPPTGGMS GNAAVADGFD LAWKLAAVLQ GQAGAGLLDT
    360 370 380 390 400
    YEDERKVAAE LVVAEALAIY AQRMAPHMAE VWDKSVGYPE TLLGFRYRSS
    410 420 430 440 450
    AVLATDDDPA RVENPLTPSG RPGFRGPHVL VSRHGERLST VDLFGDGWTL
    460 470 480 490 500
    LAGELGADWV AAAEAVSAEL GVPVRAYRVG AGLTDPESAV SERYGIGKAG
    510 520 530
    ASLVRPDGIV AWRTDEAAAD AAQTLEGVLR RVLDR
    Length:535
    Mass (Da):57,437
    Last modified:November 1, 1996 - v1
    Checksum:i969CAAB6FEB6AD4F
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U10405 Genomic DNA. Translation: AAA83424.1.

    Genome annotation databases

    KEGGiag:AAA83424.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U10405 Genomic DNA. Translation: AAA83424.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3IHGX-ray2.49A/B/C1-535[»]
    ProteinModelPortaliQ54530.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    KEGGiag:AAA83424.

    Phylogenomic databases

    KOiK15950.

    Enzyme and pathway databases

    UniPathwayiUPA00054.
    UPA01040.
    UPA01042.
    BRENDAi1.14.13.180. 6079.

    Miscellaneous databases

    EvolutionaryTraceiQ54530.

    Family and domain databases

    Gene3Di3.50.50.60. 3 hits.
    InterProiIPR002938. FAD-bd.
    IPR023753. FAD/NAD-binding_dom.
    [Graphical view]
    PfamiPF01494. FAD_binding_3. 1 hit.
    [Graphical view]
    SUPFAMiSSF51905. SSF51905. 2 hits.
    ProtoNetiSearch...

    Publicationsi

    1. "Hybrid anthracycline antibiotics: production of new anthracyclines by cloned genes from Streptomyces purpurascens in Streptomyces galilaeus."
      Niemi J., Ylihonko K., Hakala J., Parssinen R., Kopio A., Mantsala P.
      Microbiology 140:1351-1358(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 25489 / DSM 40310 / JCM 4509 / NBRC 13077 / Maria 515.
    2. "Characterization of the gene cluster involved in rhodomycin biosynthesis."
      Halo L., Wang Y., Mantsala P., Hakala J., Ylihonko K.
      Submitted (AUG-1994) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 25489 / DSM 40310 / JCM 4509 / NBRC 13077 / Maria 515.
    3. "Nucleotide sequences and expression of genes from Streptomyces purpurascens that cause the production of new anthracyclines in Streptomyces galilaeus."
      Niemi J., Mantsala P.
      J. Bacteriol. 177:2942-2945(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 25489 / DSM 40310 / JCM 4509 / NBRC 13077 / Maria 515.
    4. Halo L., Wang Y., Mantsala P., Hakala J., Ylihonko K.
      Submitted (OCT-2001) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 25489 / DSM 40310 / JCM 4509 / NBRC 13077 / Maria 515.
    5. "Characterization of aklavinone-11-hydroxylase from Streptomyces purpurascens."
      Niemi J., Wang Y., Airas K., Ylihonko K., Hakala J., Mantsala P.
      Biochim. Biophys. Acta 1430:57-64(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-13, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, ENZYME REGULATION, SUBUNIT.
    6. "Structural basis for substrate recognition and specificity in aklavinone-11-hydroxylase from rhodomycin biosynthesis."
      Lindqvist Y., Koskiniemi H., Jansson A., Sandalova T., Schnell R., Liu Z., Mantsala P., Niemi J., Schneider G.
      J. Mol. Biol. 393:966-977(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.49 ANGSTROMS) IN COMPLEX WITH FAD AND AKLAVINONE, FUNCTION, ACTIVE SITE, MUTAGENESIS OF TYR-224 AND ARG-373, SUBSTRATE SPECIFICITY, REACTION MECHANISM, COFACTOR, SUBUNIT.

    Entry informationi

    Entry nameiDNRF_STREF
    AccessioniPrimary (citable) accession number: Q54530
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 19, 2014
    Last sequence update: November 1, 1996
    Last modified: November 11, 2015
    This is version 76 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, 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.