VLDW_STRHL
ID VLDW_STRHL Reviewed; 365 AA.
AC Q15JG7;
DT 12-SEP-2018, integrated into UniProtKB/Swiss-Prot.
DT 25-JUL-2006, sequence version 1.
DT 03-AUG-2022, entry version 59.
DE RecName: Full=Validamycin A dioxygenase {ECO:0000303|PubMed:22961651};
DE EC=1.14.11.52 {ECO:0000269|PubMed:22961651};
DE AltName: Full=Alpha-ketoglutarate/Fe(II)-dependent dioxygenase VldW {ECO:0000303|PubMed:22961651};
DE AltName: Full=Validamycin B synthase {ECO:0000303|PubMed:22961651};
GN Name=vldW {ECO:0000303|PubMed:16725283};
GN ORFNames=SHL15_8012 {ECO:0000312|EMBL:ALO98989.1};
OS Streptomyces hygroscopicus subsp. limoneus.
OC Bacteria; Actinobacteria; Streptomycetales; Streptomycetaceae;
OC Streptomyces; Streptomyces violaceusniger group.
OX NCBI_TaxID=264445;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 21432 / NBRC 12704 / KCTC 1717 / KCCM 11405
RC {ECO:0000312|EMBL:ABC67263.1};
RX PubMed=16725283; DOI=10.1016/j.gene.2005.12.035;
RA Singh D., Seo M.J., Kwon H.J., Rajkarnikar A., Kim K.R., Kim S.O.,
RA Suh J.W.;
RT "Genetic localization and heterologous expression of validamycin
RT biosynthetic gene cluster isolated from Streptomyces hygroscopicus var.
RT limoneus KCCM 11405 (IFO 12704).";
RL Gene 376:13-23(2006).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 21432 / NBRC 12704 / KCTC 1717 / KCCM 11405
RC {ECO:0000312|Proteomes:UP000057753}, and
RC KCTC 1717 {ECO:0000312|EMBL:ALO98989.1};
RA Kim K.M.;
RL Submitted (NOV-2015) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, PATHWAY,
RP COFACTOR, AND SUBSTRATE SPECIFICITY.
RX PubMed=22961651; DOI=10.1002/cbic.201200464;
RA Almabruk K.H., Asamizu S., Chang A., Varghese S.G., Mahmud T.;
RT "The alpha-ketoglutarate/Fe(II)-dependent dioxygenase VldW is responsible
RT for the formation of validamycin B.";
RL ChemBioChem 13:2209-2211(2012).
CC -!- FUNCTION: Involved in the biosynthesis of validamycin B, a component of
CC the antifungal and antibiotic validamycin complex used as a crop
CC protectant. Catalyzes the regioselective hydroxylation of validamycin A
CC (4-O-beta-D-glucopyranosyl-validoxylamine A) at the C-6 position to
CC yield validamycin B. To a lesser extent, also able to convert
CC validoxylamine A to its hydroxylated derivative.
CC {ECO:0000269|PubMed:22961651}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-oxoglutarate + O2 + validamycin A = CO2 + H(+) + succinate +
CC validamycin B; Xref=Rhea:RHEA:48752, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:15379, ChEBI:CHEBI:16526, ChEBI:CHEBI:16810,
CC ChEBI:CHEBI:30031, ChEBI:CHEBI:90868, ChEBI:CHEBI:90869;
CC EC=1.14.11.52; Evidence={ECO:0000269|PubMed:22961651};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-oxoglutarate + O2 + validoxylamine A = CO2 + H(+) +
CC succinate + validoxylamine B; Xref=Rhea:RHEA:55648,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:16810, ChEBI:CHEBI:30031, ChEBI:CHEBI:111505,
CC ChEBI:CHEBI:141057; Evidence={ECO:0000269|PubMed:22961651};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000305|PubMed:22961651};
CC Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000255|PROSITE-
CC ProRule:PRU00805};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=19 uM for 2-oxoglutarate (at pH 7.2)
CC {ECO:0000269|PubMed:22961651};
CC KM=303 uM for validamycin A (at pH 7.2)
CC {ECO:0000269|PubMed:22961651};
CC Note=kcat is 0.97 min(-1) for validamycin A as substrate (at pH 7.2).
CC {ECO:0000269|PubMed:22961651};
CC pH dependence:
CC Optimum pH is 7.2. {ECO:0000269|PubMed:22961651};
CC -!- PATHWAY: Antibiotic biosynthesis. {ECO:0000305|PubMed:22961651}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene are still able to produce
CC the aminoglycoside antibiotic validamycin A, but not validamycin B.
CC {ECO:0000269|PubMed:16725283}.
CC -!- SIMILARITY: Belongs to the iron/ascorbate-dependent oxidoreductase
CC family. {ECO:0000305}.
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DR EMBL; DQ223652; ABC67263.1; -; Genomic_DNA.
DR EMBL; CP013220; ALO98989.1; -; Genomic_DNA.
DR AlphaFoldDB; Q15JG7; -.
DR SMR; Q15JG7; -.
DR EnsemblBacteria; ALO98989; ALO98989; SHL15_8012.
DR KEGG; ag:ABC67263; -.
DR PATRIC; fig|264445.3.peg.8527; -.
DR BioCyc; MetaCyc:MON-19692; -.
DR BRENDA; 1.14.11.52; 14504.
DR Proteomes; UP000057753; Chromosome II.
DR GO; GO:0051213; F:dioxygenase activity; IDA:UniProtKB.
DR GO; GO:0005506; F:iron ion binding; TAS:UniProtKB.
DR GO; GO:0017000; P:antibiotic biosynthetic process; IEA:UniProtKB-KW.
DR Gene3D; 2.60.120.330; -; 1.
DR InterPro; IPR026992; DIOX_N.
DR InterPro; IPR044861; IPNS-like_FE2OG_OXY.
DR InterPro; IPR027443; IPNS-like_sf.
DR InterPro; IPR005123; Oxoglu/Fe-dep_dioxygenase.
DR Pfam; PF03171; 2OG-FeII_Oxy; 1.
DR Pfam; PF14226; DIOX_N; 1.
DR PROSITE; PS51471; FE2OG_OXY; 1.
PE 1: Evidence at protein level;
KW Antibiotic biosynthesis; Dioxygenase; Iron; Metal-binding; Oxidoreductase.
FT CHAIN 1..365
FT /note="Validamycin A dioxygenase"
FT /id="PRO_0000444994"
FT DOMAIN 174..284
FT /note="Fe2OG dioxygenase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00805"
FT REGION 331..365
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 203
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00805"
FT BINDING 205
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00805"
FT BINDING 261
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00805"
SQ SEQUENCE 365 AA; 39638 MW; 41104A70506B6660 CRC64;
MTGSVPIVDL EAWRAADEEN RASLAEIIDG ALHTVGTFLL AGHGVPAELT ARMRTAGRSF
FDLPWEKKEP HAVQRPHDNG WRGLVKHRTD TIEGTGGAPD LHEAFHMGPT HRTGDDAFDA
LYYPANKWPA ELPELRETAL AYTAHMTRVA GAVMEMLAGV LGLEPAFFTS RCEHATWTQS
VNWYPSLDTV GQTAEGQMRV GPHTDFGTIT LLDRQQGVSG LEVWSEEDGW FAPPFVEGTL
LVNLGDLMHQ WTDGRWRSLR HRVLAPSASA PQEELVSLVY FFDADPEAEL VPLAAPVGGG
AGMPTVNVGE TILKKNIQML TDLKGHGLFQ GELSLSRPGS ADSPGSSPAD DHPSRPGRHP
AQGPQ
