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Protein

2-deoxy-scyllo-inosose synthase

Gene

btrC

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

Functioni

Catalyzes the intramolecular carbocycle formation from D-glucose-6-phosphate to 2-deoxy-scyllo-inosose (DOI).

Catalytic activityi

D-glucose-6-phosphate = 2-deoxy-L-scyllo-inosose + phosphate.3 Publications

Cofactori

Protein has several cofactor binding sites:
  • NAD+
  • Co2+Note: Binds 1 Co2+ ion per subunit.

Enzyme regulationi

Strongly inhibited by EDTA, zinc and Cu2+.

Kineticsi

  1. KM=900 µM for glucose-6-phosphate (at pH 7.7 and 46 degrees Celsius)1 Publication
  2. KM=170 µM for NAD+ (at pH 7.7 and 46 degrees Celsius)1 Publication

    pH dependencei

    Optimum pH is 7.5-8.5.1 Publication

    Temperature dependencei

    Optimum temperature is 46 degrees Celsius.1 Publication

    Pathwayi: 2-deoxystreptamine biosynthesis

    This protein is involved in step 1 of the subpathway that synthesizes 2-deoxystreptamine from D-glucose 6-phosphate.
    Proteins known to be involved in the 4 steps of the subpathway in this organism are:
    1. 2-deoxy-scyllo-inosose synthase (btrC)
    2. L-glutamine:2-deoxy-scyllo-inosose aminotransferase (btrR)
    3. no protein annotated in this organism
    4. L-glutamine:2-deoxy-scyllo-inosose aminotransferase (btrR)
    This subpathway is part of the pathway 2-deoxystreptamine biosynthesis, which is itself part of Metabolic intermediate biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes 2-deoxystreptamine from D-glucose 6-phosphate, the pathway 2-deoxystreptamine biosynthesis and in Metabolic intermediate biosynthesis.

    Pathwayi: butirosin biosynthesis

    This protein is involved in the pathway butirosin biosynthesis, which is part of Antibiotic biosynthesis.
    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)DescriptionActionsGraphical viewLength
    Active sitei141Curated1
    Metal bindingi183CobaltSequence analysis1
    Metal bindingi246CobaltSequence analysis1
    Metal bindingi262CobaltSequence analysis1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi102 – 111NADSequence analysis10

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Biological processi

    Antibiotic biosynthesis

    Keywords - Ligandi

    Cobalt, Metal-binding, NAD

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-17225.
    BRENDAi4.2.3.124. 649.
    SABIO-RKQ9S5E2.
    UniPathwayiUPA00907; UER00921.
    UPA00964.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    2-deoxy-scyllo-inosose synthase (EC:4.2.3.124)
    Short name:
    DOI synthase
    Short name:
    DOIS
    Gene namesi
    Name:btrC
    OrganismiBacillus circulans
    Taxonomic identifieri1397 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00002340341 – 3682-deoxy-scyllo-inosose synthaseAdd BLAST368

    Interactioni

    Subunit structurei

    Was isolated as a heterodimeric enzyme comprising of BtrC and a smaller polypeptide further identified as PdxT by sequence homology.1 Publication

    Structurei

    Secondary structure

    1368
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi3 – 8Combined sources6
    Beta strandi11 – 18Combined sources8
    Helixi22 – 27Combined sources6
    Beta strandi35 – 42Combined sources8
    Helixi47 – 57Combined sources11
    Turni58 – 60Combined sources3
    Beta strandi63 – 68Combined sources6
    Helixi72 – 74Combined sources3
    Helixi77 – 89Combined sources13
    Beta strandi96 – 103Combined sources8
    Helixi104 – 116Combined sources13
    Beta strandi122 – 127Combined sources6
    Helixi130 – 134Combined sources5
    Turni135 – 137Combined sources3
    Beta strandi141 – 146Combined sources6
    Beta strandi149 – 156Combined sources8
    Beta strandi160 – 165Combined sources6
    Helixi166 – 170Combined sources5
    Helixi174 – 190Combined sources17
    Helixi200 – 202Combined sources3
    Helixi211 – 229Combined sources19
    Beta strandi235 – 237Combined sources3
    Helixi238 – 243Combined sources6
    Helixi246 – 255Combined sources10
    Turni256 – 258Combined sources3
    Helixi262 – 279Combined sources18
    Helixi285 – 297Combined sources13
    Turni298 – 302Combined sources5
    Helixi310 – 318Combined sources9
    Beta strandi322 – 327Combined sources6
    Beta strandi329 – 335Combined sources7
    Beta strandi338 – 340Combined sources3
    Beta strandi353 – 356Combined sources4
    Helixi357 – 366Combined sources10

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2D2XX-ray2.30A/B1-368[»]
    2GRUX-ray2.15A/B1-368[»]
    ProteinModelPortaliQ9S5E2.
    SMRiQ9S5E2.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9S5E2.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    KOiK13546.
    K13551.

    Family and domain databases

    InterProiIPR030963. DHQ_synth_fam.
    IPR030960. DHQS/DOIS.
    [Graphical view]
    PfamiPF01761. DHQ_synthase. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001455. DHQ_synth. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q9S5E2-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MTTKQICFAD RCFNFAFGEH VLESVESYIP RDEFDQYIMI SDSGVPDSIV
    60 70 80 90 100
    HYAAEYFGKL APVHILRFQG GEEYKTLSTV TNLQERAIAL GANRRTAIVA
    110 120 130 140 150
    VGGGLTGNVA GVAAGMMFRG IALIHVPTTF LAASDSVLSI KQAVNLTSGK
    160 170 180 190 200
    NLVGFYYPPR FVFADTRILS ESPPRQVKAG MCELVKNMLI LENDNKEFTE
    210 220 230 240 250
    DDLNSANVYS PKQLETFINF CISAKMSVLS EDIYEKKKGL IFEYGHTIGH
    260 270 280 290 300
    AIELAEQGGI THGEAIAVGM IYAAKIANRM NLMPEHDVSA HYWLLNKIGA
    310 320 330 340 350
    LQDIPLKSDP DSIFHYLIHD NKRGYIKLDE DNLGMILLSG VGKPAMYNQT
    360
    LLTPVRKTLI KEVIREGL
    Length:368
    Mass (Da):40,747
    Last modified:May 1, 2000 - v1
    Checksum:i88391DD153B67671
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB019237 Genomic DNA. Translation: BAA83344.1.
    AJ781030 Genomic DNA. Translation: CAG77421.1.
    AB097196 Genomic DNA. Translation: BAE07067.1.

    Genome annotation databases

    KEGGiag:BAE07067.
    ag:BAE07068.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB019237 Genomic DNA. Translation: BAA83344.1.
    AJ781030 Genomic DNA. Translation: CAG77421.1.
    AB097196 Genomic DNA. Translation: BAE07067.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2D2XX-ray2.30A/B1-368[»]
    2GRUX-ray2.15A/B1-368[»]
    ProteinModelPortaliQ9S5E2.
    SMRiQ9S5E2.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    KEGGiag:BAE07067.
    ag:BAE07068.

    Phylogenomic databases

    KOiK13546.
    K13551.

    Enzyme and pathway databases

    UniPathwayiUPA00907; UER00921.
    UPA00964.
    BioCyciMetaCyc:MONOMER-17225.
    BRENDAi4.2.3.124. 649.
    SABIO-RKQ9S5E2.

    Miscellaneous databases

    EvolutionaryTraceiQ9S5E2.

    Family and domain databases

    InterProiIPR030963. DHQ_synth_fam.
    IPR030960. DHQS/DOIS.
    [Graphical view]
    PfamiPF01761. DHQ_synthase. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001455. DHQ_synth. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiDOIS_BACCI
    AccessioniPrimary (citable) accession number: Q9S5E2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 2, 2006
    Last sequence update: May 1, 2000
    Last modified: November 2, 2016
    This is version 73 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.