DPGC_STRTO
ID DPGC_STRTO Reviewed; 438 AA.
AC Q8KLK7;
DT 17-FEB-2016, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2002, sequence version 1.
DT 03-AUG-2022, entry version 79.
DE RecName: Full=(3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase {ECO:0000303|PubMed:18004875};
DE EC=1.13.11.80 {ECO:0000269|PubMed:17507985, ECO:0000269|PubMed:18004875};
GN ORFNames=BU52_01220;
OS Streptomyces toyocaensis.
OC Bacteria; Actinobacteria; Streptomycetales; Streptomycetaceae;
OC Streptomyces.
OX NCBI_TaxID=55952;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=NRRL 15009;
RX PubMed=9177243; DOI=10.1073/pnas.94.12.6480;
RA Marshall C.G., Broadhead G., Leskiw B.K., Wright G.D.;
RT "D-Ala-D-Ala ligases from glycopeptide antibiotic-producing organisms are
RT highly homologous to the enterococcal vancomycin-resistance ligases VanA
RT and VanB.";
RL Proc. Natl. Acad. Sci. U.S.A. 94:6480-6483(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=NRRL 15009;
RX PubMed=12060705; DOI=10.1073/pnas.102285099;
RA Pootoolal J., Thomas M.G., Marshall C.G., Neu J.M., Hubbard B.K.,
RA Walsh C.T., Wright G.D.;
RT "Assembling the glycopeptide antibiotic scaffold: the biosynthesis of
RT A47934 from Streptomyces toyocaensis NRRL15009.";
RL Proc. Natl. Acad. Sci. U.S.A. 99:8962-8967(2002).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NRRL 15009;
RA Hong H.-J., Kwun M.J.;
RT "The genome announcement of Streptomyces toyocaensis NRRL15009.";
RL Submitted (FEB-2014) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS) OF 10-426 OF MUTANT LYS-245 IN
RP COMPLEX WITH ANALOG SUBSTRATE, FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF GLU-189; ARG-254; GLU-255 AND
RP GLN-299, ACTIVITY REGULATION, SUBSTRATE SPECIFICITY, AND SUBUNIT.
RX PubMed=18004875; DOI=10.1021/bi701148b;
RA Fielding E.N., Widboom P.F., Bruner S.D.;
RT "Substrate recognition and catalysis by the cofactor-independent
RT dioxygenase DpgC.";
RL Biochemistry 46:13994-14000(2007).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.45 ANGSTROMS) OF 2-438 IN COMPLEX WITH ANALOG
RP SUBSTRATE, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES,
RP MUTAGENESIS OF LEU-237; ILE-324; VAL-425 AND VAL-429, REACTION MECHANISM,
RP AND SUBUNIT.
RX PubMed=17507985; DOI=10.1038/nature05702;
RA Widboom P.F., Fielding E.N., Liu Y., Bruner S.D.;
RT "Structural basis for cofactor-independent dioxygenation in vancomycin
RT biosynthesis.";
RL Nature 447:342-345(2007).
CC -!- FUNCTION: Involved in the biosynthesis of the nonproteinogenic amino
CC acid monomer (S)-3,5-dihydroxyphenylglycine (Dpg) responsible of the
CC production of vancomycin and teicoplanin antibiotics. Catalyzes the
CC unusual conversion 3,5-dihydroxyphenylacetyl-CoA (DPA-CoA) to 3,5-
CC dihydroxyphenylglyoxylate. DpgC performed a net four-electron oxidation
CC of the benzylic carbon of DPA-CoA and the hydrolysis of the thioester
CC bond to generate free CoA (PubMed:18004875, PubMed:17507985). DpgC has
CC the ability to process a diverse range of substituted phenylacetyl-CoA
CC substrates (PubMed:18004875). {ECO:0000269|PubMed:17507985,
CC ECO:0000269|PubMed:18004875}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(3,5-dihydroxyphenyl)acetyl-CoA + O2 = 2-(3,5-
CC dihydroxyphenyl)-2-oxoacetate + CoA + H(+); Xref=Rhea:RHEA:44632,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:15379, ChEBI:CHEBI:57287,
CC ChEBI:CHEBI:75210, ChEBI:CHEBI:84554; EC=1.13.11.80;
CC Evidence={ECO:0000269|PubMed:17507985, ECO:0000269|PubMed:18004875};
CC -!- ACTIVITY REGULATION: Inhibited by DPA-S-(N-acetylcysteamine).
CC {ECO:0000269|PubMed:18004875}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=3.9 uM for DPA-CoA {ECO:0000269|PubMed:17507985};
CC KM=1.7 mM for dioxygen {ECO:0000269|PubMed:17507985,
CC ECO:0000269|PubMed:18004875};
CC Note=kcat is 10.32 min(-1) for dioxygenase activity with DPA-CoA as
CC substrate (PubMed:18004875). kcat is 0.172 sec(-1) for dioxygenase
CC activity with DPA-CoA as substrate (PubMed:17507985).
CC {ECO:0000269|PubMed:17507985, ECO:0000269|PubMed:18004875};
CC -!- SUBUNIT: Homohexamer; dimer of trimers. {ECO:0000269|PubMed:17507985,
CC ECO:0000269|PubMed:18004875}.
CC -!- INTERACTION:
CC Q8KLK7; Q8KLK7: BU52_01220; NbExp=3; IntAct=EBI-15637670, EBI-15637670;
CC -!- SIMILARITY: Belongs to the enoyl-CoA hydratase/isomerase family.
CC {ECO:0000305}.
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DR EMBL; U82965; AAM80546.1; -; Genomic_DNA.
DR EMBL; JFCB01000001; KES08700.1; -; Genomic_DNA.
DR RefSeq; WP_037926382.1; NZ_JFCB01000001.1.
DR PDB; 2NP9; X-ray; 2.45 A; A/B/C=2-438.
DR PDB; 2PG8; X-ray; 3.00 A; A/B/C=10-426.
DR PDB; 4YLH; X-ray; 2.58 A; A/B/C/D/E/F/G/H/I/J/K/L=2-438.
DR PDB; 5KAG; X-ray; 2.46 A; A/B/C/D/E/F/G/H/I/J/K/L=1-438.
DR PDB; 5KAH; X-ray; 2.78 A; A/B/C/D/E/F/G/H/I/J/K/L=1-438.
DR PDB; 5KAJ; X-ray; 2.68 A; A/B/C/D/E/F/G/H/I/J/K/L=1-438.
DR PDBsum; 2NP9; -.
DR PDBsum; 2PG8; -.
DR PDBsum; 4YLH; -.
DR PDBsum; 5KAG; -.
DR PDBsum; 5KAH; -.
DR PDBsum; 5KAJ; -.
DR AlphaFoldDB; Q8KLK7; -.
DR SMR; Q8KLK7; -.
DR DIP; DIP-60298N; -.
DR STRING; 55952.BU52_01220; -.
DR EnsemblBacteria; KES08700; KES08700; BU52_01220.
DR eggNOG; COG1024; Bacteria.
DR OMA; IDQGIFF; -.
DR BRENDA; 1.13.11.80; 6104.
DR EvolutionaryTrace; Q8KLK7; -.
DR Proteomes; UP000028341; Unassembled WGS sequence.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0016702; F:oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen; IDA:UniProtKB.
DR GO; GO:0017000; P:antibiotic biosynthetic process; IEA:UniProtKB-KW.
DR InterPro; IPR029045; ClpP/crotonase-like_dom_sf.
DR InterPro; IPR001753; Enoyl-CoA_hydra/iso.
DR Pfam; PF00378; ECH_1; 1.
DR SUPFAM; SSF52096; SSF52096; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Antibiotic biosynthesis; Oxidoreductase; Reference proteome.
FT CHAIN 1..438
FT /note="(3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase"
FT /id="PRO_0000435521"
FT BINDING 183
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:18004875"
FT BINDING 189
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:18004875"
FT BINDING 222..225
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:18004875"
FT BINDING 233..238
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:18004875"
FT BINDING 296
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:18004875"
FT BINDING 325..327
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:18004875"
FT BINDING 416
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:18004875"
FT MUTAGEN 189
FT /note="E->Q: Strong decrease of affinity and the catalytic
FT efficiency compared to the wild-type."
FT /evidence="ECO:0000269|PubMed:18004875"
FT MUTAGEN 237
FT /note="L->T: Strong decrease of affinity for DPA-CoA and 2-
FT fold decrease of the catalytic efficiency compared to the
FT wild-type. Slight decrease of affinity for dioxygen."
FT /evidence="ECO:0000269|PubMed:17507985"
FT MUTAGEN 254
FT /note="R->K: Strong decrease of affinity and the catalytic
FT efficiency compared to the wild-type."
FT /evidence="ECO:0000269|PubMed:18004875"
FT MUTAGEN 255
FT /note="E->Q: Same affinity and catalytic efficiency
FT compared to the wild-type."
FT /evidence="ECO:0000269|PubMed:18004875"
FT MUTAGEN 299
FT /note="Q->N: Slight increase of the affinity and 2-fold
FT decrease of the catalytic efficiency compared to the wild-
FT type."
FT /evidence="ECO:0000269|PubMed:18004875"
FT MUTAGEN 324
FT /note="I->T: Loss of dioxygenase activity."
FT /evidence="ECO:0000269|PubMed:17507985"
FT MUTAGEN 425
FT /note="V->T: Slight decrease of affinity for DPA-CoA and
FT catalytic efficiency compared to the wild-type. Slight
FT decrease of affinity for dioxygen."
FT /evidence="ECO:0000269|PubMed:17507985"
FT MUTAGEN 429
FT /note="V->T: Slight decrease of affinity for DPA-CoA and
FT catalytic efficiency compared to the wild-type. Slight
FT decrease of affinity for dioxygen."
FT /evidence="ECO:0000269|PubMed:17507985"
FT HELIX 14..31
FT /evidence="ECO:0007829|PDB:2NP9"
FT HELIX 35..37
FT /evidence="ECO:0007829|PDB:5KAG"
FT HELIX 40..72
FT /evidence="ECO:0007829|PDB:2NP9"
FT TURN 73..77
FT /evidence="ECO:0007829|PDB:2NP9"
FT HELIX 82..92
FT /evidence="ECO:0007829|PDB:2NP9"
FT TURN 94..96
FT /evidence="ECO:0007829|PDB:4YLH"
FT HELIX 100..106
FT /evidence="ECO:0007829|PDB:2NP9"
FT TURN 111..113
FT /evidence="ECO:0007829|PDB:2NP9"
FT HELIX 118..130
FT /evidence="ECO:0007829|PDB:2NP9"
FT HELIX 134..143
FT /evidence="ECO:0007829|PDB:2NP9"
FT HELIX 147..159
FT /evidence="ECO:0007829|PDB:2NP9"
FT STRAND 160..163
FT /evidence="ECO:0007829|PDB:2NP9"
FT STRAND 165..172
FT /evidence="ECO:0007829|PDB:2NP9"
FT STRAND 175..180
FT /evidence="ECO:0007829|PDB:2NP9"
FT TURN 183..187
FT /evidence="ECO:0007829|PDB:2NP9"
FT HELIX 191..206
FT /evidence="ECO:0007829|PDB:2NP9"
FT STRAND 211..217
FT /evidence="ECO:0007829|PDB:2NP9"
FT TURN 223..227
FT /evidence="ECO:0007829|PDB:2NP9"
FT HELIX 237..241
FT /evidence="ECO:0007829|PDB:2NP9"
FT TURN 247..250
FT /evidence="ECO:0007829|PDB:2NP9"
FT HELIX 251..256
FT /evidence="ECO:0007829|PDB:2NP9"
FT HELIX 258..264
FT /evidence="ECO:0007829|PDB:2NP9"
FT TURN 273..277
FT /evidence="ECO:0007829|PDB:2NP9"
FT STRAND 279..281
FT /evidence="ECO:0007829|PDB:5KAG"
FT STRAND 285..289
FT /evidence="ECO:0007829|PDB:2NP9"
FT STRAND 291..294
FT /evidence="ECO:0007829|PDB:2NP9"
FT HELIX 296..300
FT /evidence="ECO:0007829|PDB:2NP9"
FT HELIX 301..303
FT /evidence="ECO:0007829|PDB:2NP9"
FT STRAND 305..310
FT /evidence="ECO:0007829|PDB:2NP9"
FT STRAND 314..316
FT /evidence="ECO:0007829|PDB:2NP9"
FT TURN 320..322
FT /evidence="ECO:0007829|PDB:2NP9"
FT HELIX 329..348
FT /evidence="ECO:0007829|PDB:2NP9"
FT STRAND 351..353
FT /evidence="ECO:0007829|PDB:5KAJ"
FT HELIX 357..361
FT /evidence="ECO:0007829|PDB:2NP9"
FT STRAND 364..367
FT /evidence="ECO:0007829|PDB:2NP9"
FT HELIX 369..381
FT /evidence="ECO:0007829|PDB:2NP9"
FT HELIX 386..399
FT /evidence="ECO:0007829|PDB:2NP9"
FT HELIX 402..420
FT /evidence="ECO:0007829|PDB:2NP9"
FT HELIX 423..430
FT /evidence="ECO:0007829|PDB:2NP9"
SQ SEQUENCE 438 AA; 48174 MW; A4C17DCE5E5F3F26 CRC64;
MTTVLPPLED TDGLWAALTE AAASVEKLLA TLPEHGARSS AERAEIAAAH DAARALRVRF
LDTHADAVYD RLTDHRRVHL RLAELVEAAA TAFPGLVPTQ QQLAVERSLP QAAKEGHEID
QGIFLRAVLR SPLAGPHLLD AMLRPTPRAL ELLPEFVRTG EVEMEAVHLE RRDGVARLTM
CRDDRLNAED GQQVDDMETA VDLALLDPGV RVGLLRGGVM SHPRYRGKRV FSAGINLKYL
SQGGISLVDF LMRRELGYIH KLVRGVLTND DRPGWWHSPR IEKPWVAAVD GFAIGGGAQL
LLVFDRVLAS SDAYFSLPAA KEGIIPGAAN LRLGRFAGPR VSRQVILEGR RIWAKEPEAR
LLVDEVVEPD ELDAAIERSL TRLDGDAVLA NRRMLNLADE SPDGFRAYMA EFALMQALRL
YGHDVIDKVG RFGGRPPA
