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Protein

S-adenosyl-L-methionine-dependent 2-deoxy-scyllo-inosamine dehydrogenase

Gene

btrN

Organism
Bacillus circulans
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the radical S-adenosyl-L-methionine (SAM)-dependent two-electron oxidation of 2-deoxy-scyllo-inosamine (DOIA) to amino-dideoxy-scyllo-inosose (amino-DOI) in the biosynthetic pathway of butirosin.1 Publication

Catalytic activityi

2-deoxy-scyllo-inosamine + S-adenosyl-L-methionine = 3-amino-2,3-dideoxy-scyllo-inosose + 5'-deoxyadenosine + L-methionine.2 Publications

Cofactori

[4Fe-4S] cluster2 PublicationsNote: Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. A second auxiliary cluster is also in contact with the substrate and is proposed to facilitate the loss of the second electron in the oxidation.2 Publications

Kineticsi

Kinetic parameter was determined with saturating SAM. DOIA displays substrate inhibition.

  1. KM=0.022 mM for DOIA1 Publication

    Pathwayi: butirosin biosynthesis

    This protein is involved in the pathway butirosin biosynthesis, which is part of Antibiotic biosynthesis.1 Publication
    View all proteins of this organism that are known to be involved in the pathway butirosin biosynthesis and in Antibiotic biosynthesis.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi16 – 161Iron-sulfur 1 (4Fe-4S-S-AdoMet)Curated
    Metal bindingi20 – 201Iron-sulfur 1 (4Fe-4S-S-AdoMet)Curated
    Metal bindingi23 – 231Iron-sulfur 1 (4Fe-4S-S-AdoMet)Curated
    Metal bindingi169 – 1691Iron-sulfur 2 (4Fe-4S-substrate)Curated
    Metal bindingi187 – 1871Iron-sulfur 2 (4Fe-4S-substrate)Curated
    Metal bindingi223 – 2231Iron-sulfur 2 (4Fe-4S-substrate)Curated

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Antibiotic biosynthesis

    Keywords - Ligandi

    4Fe-4S, Iron, Iron-sulfur, Metal-binding, S-adenosyl-L-methionine

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-17280.
    BRENDAi1.1.99.38. 649.
    UniPathwayiUPA00964.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    S-adenosyl-L-methionine-dependent 2-deoxy-scyllo-inosamine dehydrogenase (EC:1.1.99.38)
    Alternative name(s):
    Butirosin biosynthesis protein N
    Radical S-adenosylmethionine dehydrogenase BtrN
    Short name:
    RS dehydrogenase BtrN
    Short name:
    Radical SAM dehydrogenase BtrN
    Gene namesi
    Name:btrN
    OrganismiBacillus circulans
    Taxonomic identifieri1397 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi16 – 161C → A: Reduced iron-sulfur content by 50%; when associated with A-20 and A-23. 1 Publication
    Mutagenesisi20 – 201C → A: Reduced iron-sulfur content by 50%; when associated with A-16 and A-23. 1 Publication
    Mutagenesisi23 – 231C → A: Reduced iron-sulfur content by 50%; when associated with A-16 and A-20. 1 Publication
    Mutagenesisi68 – 681C → A: Soluble protein. 1 Publication
    Mutagenesisi169 – 1691C → A: Insoluble protein. 1 Publication
    Mutagenesisi187 – 1871C → A: Insoluble protein. 1 Publication
    Mutagenesisi232 – 2321C → A: Insoluble protein. 1 Publication
    Mutagenesisi235 – 2351C → A: Soluble protein; reduces activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 250250S-adenosyl-L-methionine-dependent 2-deoxy-scyllo-inosamine dehydrogenasePRO_0000424206Add
    BLAST

    Structurei

    Secondary structure

    1
    250
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi6 – 105Combined sources
    Helixi24 – 263Combined sources
    Helixi38 – 5013Combined sources
    Beta strandi55 – 584Combined sources
    Beta strandi61 – 633Combined sources
    Helixi65 – 673Combined sources
    Helixi71 – 8111Combined sources
    Beta strandi85 – 917Combined sources
    Helixi98 – 10710Combined sources
    Beta strandi111 – 1166Combined sources
    Beta strandi118 – 1203Combined sources
    Helixi124 – 1307Combined sources
    Helixi133 – 1364Combined sources
    Beta strandi139 – 1435Combined sources
    Helixi144 – 1463Combined sources
    Turni152 – 1554Combined sources
    Helixi163 – 1664Combined sources
    Helixi171 – 1744Combined sources
    Beta strandi175 – 1784Combined sources
    Beta strandi182 – 1865Combined sources
    Turni200 – 2023Combined sources
    Helixi205 – 2095Combined sources
    Helixi212 – 22211Combined sources
    Helixi226 – 2283Combined sources
    Turni230 – 2345Combined sources
    Beta strandi239 – 2413Combined sources
    Helixi243 – 2464Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4M7SX-ray2.02A1-250[»]
    4M7TX-ray1.56A1-250[»]
    ProteinModelPortaliQ8G907.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the radical SAM superfamily.Curated

    Phylogenomic databases

    KOiK13549.

    Family and domain databases

    Gene3Di3.20.20.70. 2 hits.
    InterProiIPR023885. 4Fe4S-binding_SPASM_dom.
    IPR013785. Aldolase_TIM.
    [Graphical view]
    PfamiPF13186. SPASM. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR04085. rSAM_more_4Fe4S. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q8G907-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MDKLFSMIEV EVNSQCNRTC WYCPNSVSKR KETGEMDPAL YKTLMEQLSS
    60 70 80 90 100
    LDFAGRISFH FYGEPLLCKN LDLFVGMTTE YIPRARPIIY TNGDFLTEKR
    110 120 130 140 150
    LQTLTELGIQ KFIVTQHAGA KHKFRGVYDQ LAGADKEKVV YLDHSDLVLS
    160 170 180 190 200
    NRGGILDNIP QASKANMSCM VPSNLAVVTV LGNVLPCFED FNQKMVMGNI
    210 220 230 240 250
    GEQHISDIWH NDKFTSFRKM LKEGHRGKSD LCKNCNNVSV QTEEQYDYVL
    Length:250
    Mass (Da):28,456
    Last modified:March 1, 2003 - v1
    Checksum:i30C113758BC60830
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB097196 Genomic DNA. Translation: BAE07062.1.
    AJ494863 Genomic DNA. Translation: CAD41948.1.

    Genome annotation databases

    KEGGiag:BAE07062.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB097196 Genomic DNA. Translation: BAE07062.1.
    AJ494863 Genomic DNA. Translation: CAD41948.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4M7SX-ray2.02A1-250[»]
    4M7TX-ray1.56A1-250[»]
    ProteinModelPortaliQ8G907.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    KEGGiag:BAE07062.

    Phylogenomic databases

    KOiK13549.

    Enzyme and pathway databases

    UniPathwayiUPA00964.
    BioCyciMetaCyc:MONOMER-17280.
    BRENDAi1.1.99.38. 649.

    Family and domain databases

    Gene3Di3.20.20.70. 2 hits.
    InterProiIPR023885. 4Fe4S-binding_SPASM_dom.
    IPR013785. Aldolase_TIM.
    [Graphical view]
    PfamiPF13186. SPASM. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR04085. rSAM_more_4Fe4S. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    1. "Butirosin-biosynthetic gene cluster from Bacillus circulans."
      Ota Y., Tamegai H., Kudo F., Kuriki H., Koike-Takeshita A., Eguchi T., Kakinuma K.
      J. Antibiot. 53:1158-1167(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. Huang F.
      Submitted (JUL-2002) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    3. "Characterization and mechanistic study of a radical SAM dehydrogenase in the biosynthesis of butirosin."
      Yokoyama K., Numakura M., Kudo F., Ohmori D., Eguchi T.
      J. Am. Chem. Soc. 129:15147-15155(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, PATHWAY.
    4. "Mechanistic study on the reaction of a radical SAM dehydrogenase BtrN by electron paramagnetic resonance spectroscopy."
      Yokoyama K., Ohmori D., Kudo F., Eguchi T.
      Biochemistry 47:8950-8960(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: CATALYTIC ACTIVITY, COFACTOR.
    5. "A consensus mechanism for Radical SAM-dependent dehydrogenation? BtrN contains two [4Fe-4S] clusters."
      Grove T.L., Ahlum J.H., Sharma P., Krebs C., Booker S.J.
      Biochemistry 49:3783-3785(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: COFACTOR, MUTAGENESIS OF CYS-16; CYS-20; CYS-23; CYS-68; CYS-169; CYS-187; CYS-232 AND CYS-235.

    Entry informationi

    Entry nameiBTRN_BACCI
    AccessioniPrimary (citable) accession number: Q8G907
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 16, 2013
    Last sequence update: March 1, 2003
    Last modified: December 9, 2015
    This is version 53 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. 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.