DOIS_NIACI
ID DOIS_NIACI Reviewed; 368 AA.
AC Q9S5E2;
DT 02-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 89.
DE RecName: Full=2-deoxy-scyllo-inosose synthase;
DE Short=DOI synthase;
DE Short=DOIS;
DE EC=4.2.3.124;
GN Name=btrC;
OS Niallia circulans (Bacillus circulans).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Niallia.
OX NCBI_TaxID=1397;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 1-22.
RC STRAIN=SANK 72073;
RX PubMed=10470681; DOI=10.7164/antibiotics.52.559;
RA Kudo F., Tamegai H., Fujiwara T., Tagami U., Hirayama K., Kakinuma K.;
RT "Molecular cloning of the gene for the key carbocycle-forming enzyme in the
RT biosynthesis of 2-deoxystreptamine-containing aminocyclitol antibiotics and
RT its comparison with dehydroquinate synthase.";
RL J. Antibiot. 52:559-571(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 21557 / NCIMB 12336 / BU-1709-YQW-B6;
RA Aboshanab K.M.A., Schmidt-Beissner H., Wehmeier U.F., Welzel K., Vente A.,
RA Piepersberg W.;
RT "Analysis and comparison of the biosynthetic gene clusters for the 2-
RT deoxystreptamine-containing aminoglycoside antibiotics ribostamycin,
RT neomycin, lividomycin, paromomycin and butirosin.";
RL Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=SANK 72073;
RX PubMed=16156513; DOI=10.1038/ja.2005.47;
RA Kudo F., Numakura M., Tamegai H., Yamamoto H., Eguchi T., Kakinuma K.;
RT "Extended sequence and functional analysis of the butirosin biosynthetic
RT gene cluster in Bacillus circulans SANK 72073.";
RL J. Antibiot. 58:373-379(2005).
RN [4]
RP CATALYTIC ACTIVITY, REACTION MECHANISM, AND COFACTOR.
RC STRAIN=SANK 72073;
RX PubMed=9207913; DOI=10.7164/antibiotics.50.424;
RA Kudo F., Yamauchi N., Suzuki R., Kakinuma K.;
RT "Kinetic isotope effect and reaction mechanism of 2-deoxy-scyllo-inosose
RT synthase derived from butirosin-producing Bacillus circulans.";
RL J. Antibiot. 50:424-428(1997).
RN [5]
RP CATALYTIC ACTIVITY, AND REACTION MECHANISM.
RC STRAIN=SANK 72073;
RX PubMed=9972266; DOI=10.1271/bbb.62.2396;
RA Iwase N., Kudo F., Yamauchi N., Kakinuma K.;
RT "Substrate specificity of 2-deoxy-scyllo-inosose synthase, the starter
RT enzyme for 2-deoxystreptamine biosynthesis, toward deoxyglucose-6-
RT phosphates and proposed mechanism.";
RL Biosci. Biotechnol. Biochem. 62:2396-2407(1998).
RN [6]
RP CHARACTERIZATION, COFACTOR, SUBUNIT, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=SANK 72073;
RX PubMed=10344560; DOI=10.7164/antibiotics.52.81;
RA Kudo F., Hosomi Y., Tamegai H., Kakinuma K.;
RT "Purification and characterization of 2-deoxy-scyllo-inosose synthase
RT derived from Bacillus circulans. A crucial carbocyclization enzyme in the
RT biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics.";
RL J. Antibiot. 52:81-88(1999).
RN [7]
RP INVOLVEMENT OF LYS-141 IN REACTION CATALYSIS.
RC STRAIN=SANK 72073;
RX PubMed=14750780; DOI=10.1021/jo034706y;
RA Nango E., Eguchi T., Kakinuma K.;
RT "Active site mapping of 2-deoxy-scyllo-inosose synthase, the key starter
RT enzyme for the biosynthesis of 2-deoxystreptamine. Mechanism-based
RT inhibition and identification of Lysine-141 as the entrapped nucleophile.";
RL J. Org. Chem. 69:593-600(2004).
RN [8]
RP CRYSTALLIZATION.
RC STRAIN=SANK 72073;
RX PubMed=16511136; DOI=10.1107/s1744309105018841;
RA Nango E., Kumasaka T., Sato T., Tanaka N., Kakinuma K., Eguchi T.;
RT "Crystallization and X-ray analysis of 2-deoxy-scyllo-inosose synthase, the
RT key enzyme in the biosynthesis of 2-deoxystreptamine-containing
RT aminoglycoside antibiotics.";
RL Acta Crystallogr. F 61:709-711(2005).
RN [9]
RP CATALYTIC ACTIVITY, AND REACTION STEREOCHEMISTRY.
RC STRAIN=SANK 72073;
RX PubMed=15788164; DOI=10.1016/j.bioorg.2004.09.002;
RA Huang Z., Kakinuma K., Eguchi T.;
RT "Stereospecificity of hydride transfer in NAD+-catalyzed 2-deoxy-scyllo-
RT inosose synthase, the key enzyme in the biosynthesis of 2-deoxystreptamine-
RT containing aminocyclitol antibiotics.";
RL Bioorg. Chem. 33:82-89(2005).
RN [10] {ECO:0007744|PDB:2D2X, ECO:0007744|PDB:2GRU}
RP X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) IN COMPLEX WITH NAD; COBALT AND
RP INHIBITOR, COFACTOR, SUBUNIT, AND ACTIVE SITE.
RX PubMed=17879343; DOI=10.1002/prot.21526;
RA Nango E., Kumasaka T., Hirayama T., Tanaka N., Eguchi T.;
RT "Structure of 2-deoxy-scyllo-inosose synthase, a key enzyme in the
RT biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics,
RT in complex with a mechanism-based inhibitor and NAD+.";
RL Proteins 70:517-527(2008).
CC -!- FUNCTION: Catalyzes the intramolecular carbocycle formation from D-
CC glucose-6-phosphate to 2-deoxy-scyllo-inosose (DOI).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-glucose 6-phosphate = 2-deoxy-L-scyllo-inosose + phosphate;
CC Xref=Rhea:RHEA:33071, ChEBI:CHEBI:43474, ChEBI:CHEBI:61548,
CC ChEBI:CHEBI:64796; EC=4.2.3.124;
CC Evidence={ECO:0000269|PubMed:15788164, ECO:0000269|PubMed:9207913,
CC ECO:0000269|PubMed:9972266};
CC -!- COFACTOR:
CC Name=NAD(+); Xref=ChEBI:CHEBI:57540;
CC Evidence={ECO:0000269|PubMed:17879343};
CC -!- COFACTOR:
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:17879343};
CC Note=Binds 1 Co(2+) ion per subunit. {ECO:0000269|PubMed:17879343};
CC -!- ACTIVITY REGULATION: Strongly inhibited by EDTA, zinc and Cu(2+).
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=900 uM for glucose-6-phosphate (at pH 7.7 and 46 degrees Celsius)
CC {ECO:0000269|PubMed:10344560};
CC KM=170 uM for NAD(+) (at pH 7.7 and 46 degrees Celsius)
CC {ECO:0000269|PubMed:10344560};
CC pH dependence:
CC Optimum pH is 7.5-8.5. {ECO:0000269|PubMed:10344560};
CC Temperature dependence:
CC Optimum temperature is 46 degrees Celsius.
CC {ECO:0000269|PubMed:10344560};
CC -!- PATHWAY: Metabolic intermediate biosynthesis; 2-deoxystreptamine
CC biosynthesis; 2-deoxystreptamine from D-glucose 6-phosphate: step 1/4.
CC -!- PATHWAY: Antibiotic biosynthesis; butirosin biosynthesis.
CC -!- SUBUNIT: Was isolated as a heterodimeric enzyme comprising of BtrC and
CC a smaller polypeptide further identified as PdxT by sequence homology
CC (PubMed:10344560). Homodimer in solution (PubMed:17879343).
CC {ECO:0000269|PubMed:10344560, ECO:0000269|PubMed:17879343}.
CC -!- SIMILARITY: Belongs to the sugar phosphate cyclases superfamily. DOI
CC synthase family. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AB019237; BAA83344.1; -; Genomic_DNA.
DR EMBL; AJ781030; CAG77421.1; -; Genomic_DNA.
DR EMBL; AB097196; BAE07067.1; -; Genomic_DNA.
DR PDB; 2D2X; X-ray; 2.30 A; A/B=1-368.
DR PDB; 2GRU; X-ray; 2.15 A; A/B=1-368.
DR PDBsum; 2D2X; -.
DR PDBsum; 2GRU; -.
DR AlphaFoldDB; Q9S5E2; -.
DR SMR; Q9S5E2; -.
DR KEGG; ag:BAE07067; -.
DR KEGG; ag:BAE07068; -.
DR BioCyc; MetaCyc:MON-17225; -.
DR BRENDA; 4.2.3.124; 649.
DR SABIO-RK; Q9S5E2; -.
DR UniPathway; UPA00907; UER00921.
DR UniPathway; UPA00964; -.
DR EvolutionaryTrace; Q9S5E2; -.
DR GO; GO:0016838; F:carbon-oxygen lyase activity, acting on phosphates; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0017000; P:antibiotic biosynthetic process; IEA:UniProtKB-KW.
DR GO; GO:0009073; P:aromatic amino acid family biosynthetic process; IEA:InterPro.
DR InterPro; IPR030963; DHQ_synth_fam.
DR InterPro; IPR030960; DHQS/DOIS.
DR Pfam; PF01761; DHQ_synthase; 1.
DR PIRSF; PIRSF001455; DHQ_synth; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Antibiotic biosynthesis; Cobalt; Direct protein sequencing;
KW Lyase; Metal-binding; NAD.
FT CHAIN 1..368
FT /note="2-deoxy-scyllo-inosose synthase"
FT /id="PRO_0000234034"
FT ACT_SITE 141
FT /evidence="ECO:0000305|PubMed:17879343"
FT ACT_SITE 243
FT /evidence="ECO:0000305|PubMed:17879343"
FT BINDING 42
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:17879343"
FT BINDING 72..75
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:17879343"
FT BINDING 104..108
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:17879343"
FT BINDING 128..129
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:17879343"
FT BINDING 139..141
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:17879343"
FT BINDING 150..151
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:17879343"
FT BINDING 176
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:17879343"
FT BINDING 183
FT /ligand="Co(2+)"
FT /ligand_id="ChEBI:CHEBI:48828"
FT /evidence="ECO:0000269|PubMed:17879343"
FT BINDING 246
FT /ligand="Co(2+)"
FT /ligand_id="ChEBI:CHEBI:48828"
FT /evidence="ECO:0000269|PubMed:17879343"
FT BINDING 262
FT /ligand="Co(2+)"
FT /ligand_id="ChEBI:CHEBI:48828"
FT /evidence="ECO:0000269|PubMed:17879343"
FT STRAND 3..8
FT /evidence="ECO:0007829|PDB:2GRU"
FT STRAND 11..18
FT /evidence="ECO:0007829|PDB:2GRU"
FT HELIX 22..27
FT /evidence="ECO:0007829|PDB:2GRU"
FT STRAND 35..42
FT /evidence="ECO:0007829|PDB:2GRU"
FT HELIX 47..57
FT /evidence="ECO:0007829|PDB:2GRU"
FT TURN 58..60
FT /evidence="ECO:0007829|PDB:2GRU"
FT STRAND 63..68
FT /evidence="ECO:0007829|PDB:2GRU"
FT HELIX 72..74
FT /evidence="ECO:0007829|PDB:2GRU"
FT HELIX 77..89
FT /evidence="ECO:0007829|PDB:2GRU"
FT STRAND 96..103
FT /evidence="ECO:0007829|PDB:2GRU"
FT HELIX 104..116
FT /evidence="ECO:0007829|PDB:2GRU"
FT STRAND 122..127
FT /evidence="ECO:0007829|PDB:2GRU"
FT HELIX 130..134
FT /evidence="ECO:0007829|PDB:2GRU"
FT TURN 135..137
FT /evidence="ECO:0007829|PDB:2GRU"
FT STRAND 141..146
FT /evidence="ECO:0007829|PDB:2GRU"
FT STRAND 149..156
FT /evidence="ECO:0007829|PDB:2GRU"
FT STRAND 160..165
FT /evidence="ECO:0007829|PDB:2GRU"
FT HELIX 166..170
FT /evidence="ECO:0007829|PDB:2GRU"
FT HELIX 174..190
FT /evidence="ECO:0007829|PDB:2GRU"
FT HELIX 200..202
FT /evidence="ECO:0007829|PDB:2GRU"
FT HELIX 211..229
FT /evidence="ECO:0007829|PDB:2GRU"
FT STRAND 235..237
FT /evidence="ECO:0007829|PDB:2GRU"
FT HELIX 238..243
FT /evidence="ECO:0007829|PDB:2GRU"
FT HELIX 246..255
FT /evidence="ECO:0007829|PDB:2GRU"
FT TURN 256..258
FT /evidence="ECO:0007829|PDB:2GRU"
FT HELIX 262..279
FT /evidence="ECO:0007829|PDB:2GRU"
FT HELIX 285..297
FT /evidence="ECO:0007829|PDB:2GRU"
FT TURN 298..302
FT /evidence="ECO:0007829|PDB:2GRU"
FT HELIX 310..318
FT /evidence="ECO:0007829|PDB:2GRU"
FT STRAND 322..327
FT /evidence="ECO:0007829|PDB:2GRU"
FT STRAND 329..335
FT /evidence="ECO:0007829|PDB:2GRU"
FT STRAND 338..340
FT /evidence="ECO:0007829|PDB:2GRU"
FT STRAND 353..356
FT /evidence="ECO:0007829|PDB:2GRU"
FT HELIX 357..366
FT /evidence="ECO:0007829|PDB:2GRU"
SQ SEQUENCE 368 AA; 40747 MW; 88391DD153B67671 CRC64;
MTTKQICFAD RCFNFAFGEH VLESVESYIP RDEFDQYIMI SDSGVPDSIV HYAAEYFGKL
APVHILRFQG GEEYKTLSTV TNLQERAIAL GANRRTAIVA VGGGLTGNVA GVAAGMMFRG
IALIHVPTTF LAASDSVLSI KQAVNLTSGK NLVGFYYPPR FVFADTRILS ESPPRQVKAG
MCELVKNMLI LENDNKEFTE DDLNSANVYS PKQLETFINF CISAKMSVLS EDIYEKKKGL
IFEYGHTIGH AIELAEQGGI THGEAIAVGM IYAAKIANRM NLMPEHDVSA HYWLLNKIGA
LQDIPLKSDP DSIFHYLIHD NKRGYIKLDE DNLGMILLSG VGKPAMYNQT LLTPVRKTLI
KEVIREGL
