NDPGT_BACSU
ID NDPGT_BACSU Reviewed; 392 AA.
AC O34539; Q796N7;
DT 20-JAN-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 116.
DE RecName: Full=NDP-glycosyltransferase YjiC {ECO:0000305};
DE EC=2.4.1.384 {ECO:0000269|PubMed:28315700, ECO:0000269|PubMed:33152360};
DE AltName: Full=UDP-glycosyltransferase YjiC {ECO:0000303|PubMed:33310191};
GN Name=yjiC; OrderedLocusNames=BSU12220;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9579062; DOI=10.1099/00221287-144-4-877;
RA Rivolta C., Soldo B., Lazarevic V., Joris B., Mauel C., Karamata D.;
RT "A 35.7 kb DNA fragment from the Bacillus subtilis chromosome containing a
RT putative 12.3 kb operon involved in hexuronate catabolism and a perfectly
RT symmetrical hypothetical catabolite-responsive element.";
RL Microbiology 144:877-884(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
RC STRAIN=168;
RX PubMed=28315700; DOI=10.1016/j.jbiotec.2017.03.009;
RA Dai L., Li J., Yao P., Zhu Y., Men Y., Zeng Y., Yang J., Sun Y.;
RT "Exploiting the aglycon promiscuity of glycosyltransferase Bs-YjiC from
RT Bacillus subtilis and its application in synthesis of glycosides.";
RL J. Biotechnol. 248:69-76(2017).
RN [4] {ECO:0007744|PDB:6KQW, ECO:0007744|PDB:6KQX}
RP X-RAY CRYSTALLOGRAPHY (2.18 ANGSTROMS) OF 1-387 IN COMPLEX WITH UDP,
RP SUBUNIT, AND DOMAIN.
RX PubMed=33310191; DOI=10.1016/j.bbrc.2020.11.104;
RA Dai L., Qin L., Hu Y., Huang J.W., Hu Z., Min J., Sun Y., Guo R.T.;
RT "Structural dissection of unnatural ginsenoside-biosynthetic UDP-
RT glycosyltransferase Bs-YjiC from Bacillus subtilis for substrate
RT promiscuity.";
RL Biochem. Biophys. Res. Commun. 534:73-78(2021).
RN [5] {ECO:0007744|PDB:7BOV}
RP X-RAY CRYSTALLOGRAPHY (2.29 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, DOMAIN, AND MUTAGENESIS OF HIS-16;
RP ASP-106; PHE-107; VAL-108; SER-128; SER-129; TYR-130; THR-229; SER-277;
RP HIS-293; GLU-301; MET-315; GLU-317; GLN-318 AND LEU-320.
RC STRAIN=168;
RX PubMed=33152360; DOI=10.1016/j.ijbiomac.2020.10.238;
RA Liu B., Zhao C., Xiang Q., Zhao N., Luo Y., Bao R.;
RT "Structural and biochemical studies of the glycosyltransferase Bs-YjiC from
RT Bacillus subtilis.";
RL Int. J. Biol. Macromol. 166:806-817(2021).
CC -!- FUNCTION: Glycosyltransferase that can glycosylate a wide range of
CC substrates, including various flavonoids, phenyl ketones, curcuminoid,
CC lignins, zingerone, triterpenes, stilbene and anthraquinone, using UDP-
CC glucose or ADP-glucose as sugar donor (PubMed:28315700,
CC PubMed:33152360). It also exhibits O-, N- and S-glycosylation
CC activities towards simple aromatics (PubMed:28315700). In vivo, the
CC broad acceptor tolerance of YjiC might function as a detoxification
CC agent against exogenous xenobiotics to make the strain adaptable to the
CC changeable environment (Probable). {ECO:0000269|PubMed:28315700,
CC ECO:0000269|PubMed:33152360, ECO:0000305|PubMed:28315700}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=an NDP-glycose + an acceptor = a glycosylated acceptor + NDP.;
CC EC=2.4.1.384; Evidence={ECO:0000269|PubMed:28315700,
CC ECO:0000269|PubMed:33152360};
CC -!- ACTIVITY REGULATION: Activity is improved in the presence of Mn(2+),
CC Mg(2+) and Ca(2+), and inhibited by Ni(2+), Zn(2+) and Cu(2+).
CC {ECO:0000269|PubMed:28315700}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=19.4 uM for apigenin {ECO:0000269|PubMed:28315700};
CC KM=22.6 uM for genistein {ECO:0000269|PubMed:28315700};
CC KM=6.795 uM for 2-chloro-4-nitrophenyl glycoside
CC {ECO:0000269|PubMed:33152360};
CC Note=kcat is 1.9 sec(-1) with apigenin as substrate. kcat is 1.6
CC sec(-1) with genistein as substrate (PubMed:28315700). kcat is 164
CC min(-1) with 2-chloro-4-nitrophenyl glycoside as substrate
CC (PubMed:33152360). {ECO:0000269|PubMed:28315700,
CC ECO:0000269|PubMed:33152360};
CC pH dependence:
CC Optimum pH is approximately 8.0. {ECO:0000269|PubMed:28315700};
CC Temperature dependence:
CC Optimum temperature is 30-40 degrees Celsius.
CC {ECO:0000269|PubMed:28315700};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:33152360,
CC ECO:0000269|PubMed:33310191}.
CC -!- DOMAIN: Adopts the classical GT-B fold containing the N-terminal and C-
CC terminal domains that accommodate the sugar acceptor and UDP-glucose,
CC respectively (PubMed:33310191, PubMed:33152360). The spacious sugar-
CC acceptor binding pocket might be responsible for the broad substrate
CC spectrum (PubMed:33310191). {ECO:0000269|PubMed:33152360,
CC ECO:0000269|PubMed:33310191}.
CC -!- SIMILARITY: Belongs to the UDP-glycosyltransferase family.
CC {ECO:0000305}.
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DR EMBL; AF015825; AAC46318.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB13079.1; -; Genomic_DNA.
DR PIR; C69851; C69851.
DR RefSeq; NP_389104.1; NC_000964.3.
DR RefSeq; WP_003232783.1; NZ_JNCM01000035.1.
DR PDB; 6KQW; X-ray; 2.18 A; A=1-387.
DR PDB; 6KQX; X-ray; 2.44 A; A=1-392.
DR PDB; 7BOV; X-ray; 2.29 A; A=1-392.
DR PDBsum; 6KQW; -.
DR PDBsum; 6KQX; -.
DR PDBsum; 7BOV; -.
DR AlphaFoldDB; O34539; -.
DR SMR; O34539; -.
DR STRING; 224308.BSU12220; -.
DR CAZy; GT1; Glycosyltransferase Family 1.
DR jPOST; O34539; -.
DR PaxDb; O34539; -.
DR PRIDE; O34539; -.
DR EnsemblBacteria; CAB13079; CAB13079; BSU_12220.
DR GeneID; 939402; -.
DR KEGG; bsu:BSU12220; -.
DR PATRIC; fig|224308.179.peg.1320; -.
DR eggNOG; COG1819; Bacteria.
DR InParanoid; O34539; -.
DR OMA; NIPAYGH; -.
DR PhylomeDB; O34539; -.
DR BioCyc; BSUB:BSU12220-MON; -.
DR BRENDA; 2.4.1.384; 658.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0016758; F:hexosyltransferase activity; IEA:InterPro.
DR GO; GO:0008194; F:UDP-glycosyltransferase activity; IEA:InterPro.
DR CDD; cd03784; GT1_Gtf-like; 1.
DR InterPro; IPR007235; Glyco_trans_28_C.
DR InterPro; IPR002213; UDP_glucos_trans.
DR InterPro; IPR006326; UDPGT_MGT-like.
DR Pfam; PF04101; Glyco_tran_28_C; 1.
DR TIGRFAMs; TIGR01426; MGT; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Glycosyltransferase; Reference proteome; Transferase.
FT CHAIN 1..392
FT /note="NDP-glycosyltransferase YjiC"
FT /id="PRO_0000360169"
FT BINDING 18
FT /ligand="UDP"
FT /ligand_id="ChEBI:CHEBI:58223"
FT /evidence="ECO:0000269|PubMed:33310191,
FT ECO:0007744|PDB:6KQX"
FT BINDING 229
FT /ligand="UDP"
FT /ligand_id="ChEBI:CHEBI:58223"
FT /evidence="ECO:0000269|PubMed:33310191,
FT ECO:0007744|PDB:6KQX"
FT BINDING 255
FT /ligand="UDP"
FT /ligand_id="ChEBI:CHEBI:58223"
FT /evidence="ECO:0000269|PubMed:33310191,
FT ECO:0007744|PDB:6KQX"
FT BINDING 278
FT /ligand="UDP"
FT /ligand_id="ChEBI:CHEBI:58223"
FT /evidence="ECO:0000269|PubMed:33310191,
FT ECO:0007744|PDB:6KQX"
FT BINDING 293
FT /ligand="UDP"
FT /ligand_id="ChEBI:CHEBI:58223"
FT /evidence="ECO:0000269|PubMed:33310191,
FT ECO:0007744|PDB:6KQX"
FT BINDING 297..301
FT /ligand="UDP"
FT /ligand_id="ChEBI:CHEBI:58223"
FT /evidence="ECO:0000269|PubMed:33310191,
FT ECO:0007744|PDB:6KQX"
FT MUTAGEN 16
FT /note="H->A: Drastic loss of activity for both
FT pterostilbene glycosylation and UDP glycosylation."
FT /evidence="ECO:0000269|PubMed:33152360"
FT MUTAGEN 106
FT /note="D->A: Significant decrease in activity for both
FT pterostilbene glycosylation and UDP glycosylation."
FT /evidence="ECO:0000269|PubMed:33152360"
FT MUTAGEN 107
FT /note="F->A: Shows slightly reduced activity."
FT /evidence="ECO:0000269|PubMed:33152360"
FT MUTAGEN 108
FT /note="V->A: Increases pterostilbene glycosylation activity
FT and UDP glycosylation efficiency."
FT /evidence="ECO:0000269|PubMed:33152360"
FT MUTAGEN 128
FT /note="S->A: No change in activity. Dramatic reduction of
FT the catalytic efficiency and glycosylation levels; when
FT associated with A-129."
FT /evidence="ECO:0000269|PubMed:33152360"
FT MUTAGEN 129
FT /note="S->A: No change in activity. Dramatic reduction of
FT the catalytic efficiency and glycosylation levels; when
FT associated with A-128."
FT /evidence="ECO:0000269|PubMed:33152360"
FT MUTAGEN 130
FT /note="Y->A: Significant reduction in catalytic efficiency
FT and glycosylation levels."
FT /evidence="ECO:0000269|PubMed:33152360"
FT MUTAGEN 229
FT /note="T->A: Strong decrease in activity for both
FT pterostilbene glycosylation and UDP glycosylation."
FT /evidence="ECO:0000269|PubMed:33152360"
FT MUTAGEN 277
FT /note="S->F: Significantly enhances the UDP glycosylation
FT efficiency, but shows unchanged or reduced pterostilbene
FT glycosylation when supplied with UDP-glucose and ADP-
FT glucose, respectively."
FT /evidence="ECO:0000269|PubMed:33152360"
FT MUTAGEN 277
FT /note="S->W: Enhances the catalytic efficiency of UDP
FT glycosylation, but reduces the relative activity of
FT pterostilbene glycosylation reaction."
FT /evidence="ECO:0000269|PubMed:33152360"
FT MUTAGEN 293
FT /note="H->A: Strong decrease in activity for both
FT pterostilbene glycosylation and UDP glycosylation."
FT /evidence="ECO:0000269|PubMed:33152360"
FT MUTAGEN 301
FT /note="E->A: Strong decrease in activity for both
FT pterostilbene glycosylation and UDP glycosylation."
FT /evidence="ECO:0000269|PubMed:33152360"
FT MUTAGEN 315
FT /note="M->A: Significant reduction in catalytic efficiency
FT and glycosylation levels."
FT /evidence="ECO:0000269|PubMed:33152360"
FT MUTAGEN 317
FT /note="E->A: Almost abolishes the glycosyltransferase
FT activity."
FT /evidence="ECO:0000269|PubMed:33152360"
FT MUTAGEN 317
FT /note="E->D: Strong decrease in activity for both
FT pterostilbene glycosylation and UDP glycosylation."
FT /evidence="ECO:0000269|PubMed:33152360"
FT MUTAGEN 318
FT /note="Q->A: Leads to about 2-fold decrease in specific
FT activities."
FT /evidence="ECO:0000269|PubMed:33152360"
FT MUTAGEN 320
FT /note="L->A: Increases UDP glycosylation efficiency and
FT enhances pterostilbene glycosylation activity."
FT /evidence="ECO:0000269|PubMed:33152360"
FT STRAND 7..9
FT /evidence="ECO:0007829|PDB:6KQW"
FT HELIX 14..29
FT /evidence="ECO:0007829|PDB:6KQW"
FT STRAND 35..38
FT /evidence="ECO:0007829|PDB:6KQW"
FT TURN 40..42
FT /evidence="ECO:0007829|PDB:6KQW"
FT HELIX 43..48
FT /evidence="ECO:0007829|PDB:6KQW"
FT STRAND 52..55
FT /evidence="ECO:0007829|PDB:6KQW"
FT HELIX 90..94
FT /evidence="ECO:0007829|PDB:6KQW"
FT HELIX 96..98
FT /evidence="ECO:0007829|PDB:6KQX"
FT STRAND 103..106
FT /evidence="ECO:0007829|PDB:6KQW"
FT HELIX 110..114
FT /evidence="ECO:0007829|PDB:6KQW"
FT STRAND 123..129
FT /evidence="ECO:0007829|PDB:6KQW"
FT HELIX 141..145
FT /evidence="ECO:0007829|PDB:7BOV"
FT TURN 146..148
FT /evidence="ECO:0007829|PDB:7BOV"
FT STRAND 176..182
FT /evidence="ECO:0007829|PDB:6KQW"
FT HELIX 184..186
FT /evidence="ECO:0007829|PDB:6KQW"
FT HELIX 190..192
FT /evidence="ECO:0007829|PDB:6KQW"
FT STRAND 197..199
FT /evidence="ECO:0007829|PDB:6KQW"
FT STRAND 222..226
FT /evidence="ECO:0007829|PDB:6KQW"
FT STRAND 229..231
FT /evidence="ECO:0007829|PDB:6KQX"
FT HELIX 235..245
FT /evidence="ECO:0007829|PDB:6KQW"
FT STRAND 251..255
FT /evidence="ECO:0007829|PDB:6KQW"
FT STRAND 258..260
FT /evidence="ECO:0007829|PDB:6KQX"
FT HELIX 262..264
FT /evidence="ECO:0007829|PDB:6KQW"
FT STRAND 265..267
FT /evidence="ECO:0007829|PDB:6KQX"
FT STRAND 272..276
FT /evidence="ECO:0007829|PDB:6KQW"
FT HELIX 280..284
FT /evidence="ECO:0007829|PDB:6KQW"
FT STRAND 288..292
FT /evidence="ECO:0007829|PDB:6KQW"
FT HELIX 296..304
FT /evidence="ECO:0007829|PDB:6KQW"
FT STRAND 309..311
FT /evidence="ECO:0007829|PDB:6KQW"
FT HELIX 316..327
FT /evidence="ECO:0007829|PDB:6KQW"
FT STRAND 330..333
FT /evidence="ECO:0007829|PDB:6KQW"
FT HELIX 336..338
FT /evidence="ECO:0007829|PDB:6KQW"
FT HELIX 341..352
FT /evidence="ECO:0007829|PDB:6KQW"
FT HELIX 355..370
FT /evidence="ECO:0007829|PDB:6KQW"
FT HELIX 373..384
FT /evidence="ECO:0007829|PDB:6KQW"
SQ SEQUENCE 392 AA; 43988 MW; 3830835750C5E896 CRC64;
MKKYHISMIN IPAYGHVNPT LALVEKLCEK GHRVTYATTE EFAPAVQQAG GEALIYHTSL
NIDPKQIREM MEKNDAPLSL LKESLSILPQ LEELYKDDQP DLIIYDFVAL AGKLFAEKLN
VPVIKLCSSY AQNESFQLGN EDMLKKIREA EAEFKAYLEQ EKLPAVSFEQ LAVPEALNIV
FMPKSFQIQH ETFDDRFCFV GPSLGERKEK ESLLIDKDDR PLMLISLGTA FNAWPEFYKM
CIKAFRDSSW QVIMSVGKTI DPESLEDIPA NFTIRQSVPQ LEVLEKADLF ISHGGMNSTM
EAMNAGVPLV VIPQMYEQEL TANRVDELGL GVYLPKEEVT VSSLQEAVQA VSSDQELLSR
VKNMQKDVKE AGGAERAAAE IEAFMKKSAV PQ
