ARGHX_STRVI
ID ARGHX_STRVI Reviewed; 358 AA.
AC Q6WZB0;
DT 22-JAN-2014, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 55.
DE RecName: Full=Alpha-ketoglutarate-dependent L-arginine hydroxylase;
DE EC=1.14.11.41;
DE AltName: Full=Viomycin biosynthesis protein C;
GN Name=vioC;
OS Streptomyces vinaceus.
OC Bacteria; Actinobacteria; Streptomycetales; Streptomycetaceae;
OC Streptomyces.
OX NCBI_TaxID=1960;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 11861;
RX PubMed=12936980; DOI=10.1128/aac.47.9.2823-2830.2003;
RA Thomas M.G., Chan Y.A., Ozanick S.G.;
RT "Deciphering tuberactinomycin biosynthesis: isolation, sequencing, and
RT annotation of the viomycin biosynthetic gene cluster.";
RL Antimicrob. Agents Chemother. 47:2823-2830(2003).
RN [2]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=15368580; DOI=10.1002/cbic.200400082;
RA Yin X., Zabriskie T.M.;
RT "VioC is a non-heme iron, alpha-ketoglutarate-dependent oxygenase that
RT catalyzes the formation of 3S-hydroxy-L-arginine during viomycin
RT biosynthesis.";
RL ChemBioChem 5:1274-1277(2004).
RN [3]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RC STRAIN=ATCC 11861;
RX PubMed=15368582; DOI=10.1002/cbic.200400136;
RA Ju J., Ozanick S.G., Shen B., Thomas M.G.;
RT "Conversion of (2S)-arginine to (2S,3R)-capreomycidine by VioC and VioD
RT from the viomycin biosynthetic pathway of Streptomyces sp. strain ATCC
RT 11861.";
RL ChemBioChem 5:1281-1285(2004).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.10 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS
RP AND IRON ION, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL
RP PROPERTIES, AND SUBSTRATE SPECIFICITY.
RX PubMed=19490124; DOI=10.1111/j.1742-4658.2009.07085.x;
RA Helmetag V., Samel S.A., Thomas M.G., Marahiel M.A., Essen L.O.;
RT "Structural basis for the erythro-stereospecificity of the L-arginine
RT oxygenase VioC in viomycin biosynthesis.";
RL FEBS J. 276:3669-3682(2009).
CC -!- FUNCTION: Involved in the biosynthesis of capreomycidine, an unusual
CC amino acid used by non-ribosomal peptide synthases (NRPS) to make the
CC tuberactinomycin class of peptide antibiotics such as viomycin and
CC capreomycin. Catalyzes the stereospecific hydroxylation of the C3 of
CC (2S)-arginine to generate (3S)-hydroxy-(2S)-arginine. Usually
CC clavaminic acid synthase-like oxygenases catalyze the formation of
CC threo diastereomers, however VioC produces the erythro diastereomer of
CC beta-carbon-hydroxylated L-arginine. It exerts a broad substrate
CC specificity by accepting the analogs L-homoarginine and L-canavanine
CC for the beta-carbon hydroxylation. {ECO:0000269|PubMed:15368580,
CC ECO:0000269|PubMed:15368582, ECO:0000269|PubMed:19490124}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-oxoglutarate + L-arginine + O2 = (2S,3S)-hydroxyarginine +
CC CO2 + succinate; Xref=Rhea:RHEA:36607, ChEBI:CHEBI:15379,
CC ChEBI:CHEBI:16526, ChEBI:CHEBI:16810, ChEBI:CHEBI:30031,
CC ChEBI:CHEBI:32682, ChEBI:CHEBI:73938; EC=1.14.11.41;
CC Evidence={ECO:0000269|PubMed:15368580, ECO:0000269|PubMed:15368582,
CC ECO:0000269|PubMed:19490124};
CC -!- COFACTOR:
CC Name=Fe cation; Xref=ChEBI:CHEBI:24875;
CC Evidence={ECO:0000269|PubMed:19490124};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.16 mM for L-canavanine (at pH 8 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:19490124};
CC KM=3.4 mM for L-arginine (at pH 8 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:19490124};
CC KM=7.05 mM for L-homoarginine (at pH 8 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:19490124};
CC Note=kcat is 2611 min(-1), 831 min(-1) and 73.2 min(-1) for L-
CC arginine, L-homoarginine and L-canavanine, respectively (at pH 8 and
CC 30 degrees Celsius).;
CC -!- PATHWAY: Antibiotic biosynthesis.
CC -!- SUBCELLULAR LOCATION: Membrane {ECO:0000305}; Single-pass membrane
CC protein {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the clavaminate synthase family. {ECO:0000305}.
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DR EMBL; AY263398; AAP92493.1; -; Genomic_DNA.
DR PDB; 2WBO; X-ray; 1.30 A; A=1-358.
DR PDB; 2WBP; X-ray; 1.16 A; A=1-358.
DR PDB; 2WBQ; X-ray; 1.10 A; A=1-358.
DR PDB; 6ALM; X-ray; 1.60 A; A=1-358.
DR PDB; 6ALN; X-ray; 1.80 A; A=1-358.
DR PDB; 6ALO; X-ray; 1.79 A; A=1-358.
DR PDB; 6ALP; X-ray; 1.99 A; A=1-358.
DR PDB; 6ALQ; X-ray; 1.67 A; A=1-358.
DR PDB; 6ALR; X-ray; 1.55 A; A=1-358.
DR PDB; 6DAX; X-ray; 1.70 A; A=21-358.
DR PDB; 6DAZ; X-ray; 1.94 A; A=23-358.
DR PDB; 6DB2; X-ray; 1.70 A; A=23-358.
DR PDB; 6MP8; X-ray; 1.89 A; A=21-358.
DR PDB; 6MP9; X-ray; 1.89 A; A=22-358.
DR PDB; 6Y0N; X-ray; 1.86 A; A=1-358.
DR PDB; 6Y12; X-ray; 1.70 A; A=1-358.
DR PDBsum; 2WBO; -.
DR PDBsum; 2WBP; -.
DR PDBsum; 2WBQ; -.
DR PDBsum; 6ALM; -.
DR PDBsum; 6ALN; -.
DR PDBsum; 6ALO; -.
DR PDBsum; 6ALP; -.
DR PDBsum; 6ALQ; -.
DR PDBsum; 6ALR; -.
DR PDBsum; 6DAX; -.
DR PDBsum; 6DAZ; -.
DR PDBsum; 6DB2; -.
DR PDBsum; 6MP8; -.
DR PDBsum; 6MP9; -.
DR PDBsum; 6Y0N; -.
DR PDBsum; 6Y12; -.
DR AlphaFoldDB; Q6WZB0; -.
DR SMR; Q6WZB0; -.
DR KEGG; ag:AAP92493; -.
DR BRENDA; 1.14.11.41; 6110.
DR EvolutionaryTrace; Q6WZB0; -.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0102525; F:2-oxoglutarate, L-arginine oxygenase (succinate-forming) activity; IEA:UniProtKB-EC.
DR GO; GO:0016706; F:2-oxoglutarate-dependent dioxygenase activity; IDA:UniProtKB.
DR GO; GO:0005506; F:iron ion binding; IEA:InterPro.
DR GO; GO:0017000; P:antibiotic biosynthetic process; IDA:UniProtKB.
DR Gene3D; 3.60.130.10; -; 1.
DR InterPro; IPR023966; Arginine_beta-hydroxylase.
DR InterPro; IPR014503; Clavaminate_syn-like.
DR InterPro; IPR042098; TauD-like_sf.
DR InterPro; IPR003819; TauD/TfdA-like.
DR Pfam; PF02668; TauD; 1.
DR PIRSF; PIRSF019543; Clavaminate_syn; 1.
DR TIGRFAMs; TIGR03946; viomycin_VioC; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Antibiotic biosynthesis; Iron; Membrane; Metal-binding;
KW Oxidoreductase; Transmembrane; Transmembrane helix.
FT CHAIN 1..358
FT /note="Alpha-ketoglutarate-dependent L-arginine
FT hydroxylase"
FT /id="PRO_0000424865"
FT TRANSMEM 117..135
FT /note="Helical"
FT /evidence="ECO:0000255"
FT REGION 1..21
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 156..158
FT /ligand="L-arginine"
FT /ligand_id="ChEBI:CHEBI:32682"
FT BINDING 168
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT BINDING 170
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT BINDING 194
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT BINDING 268..270
FT /ligand="L-arginine"
FT /ligand_id="ChEBI:CHEBI:32682"
FT BINDING 316
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT BINDING 330
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT BINDING 334
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT BINDING 334
FT /ligand="L-arginine"
FT /ligand_id="ChEBI:CHEBI:32682"
FT STRAND 23..28
FT /evidence="ECO:0007829|PDB:2WBQ"
FT HELIX 31..47
FT /evidence="ECO:0007829|PDB:2WBQ"
FT STRAND 51..53
FT /evidence="ECO:0007829|PDB:6DAZ"
FT HELIX 54..63
FT /evidence="ECO:0007829|PDB:2WBQ"
FT HELIX 64..66
FT /evidence="ECO:0007829|PDB:2WBQ"
FT HELIX 69..78
FT /evidence="ECO:0007829|PDB:2WBQ"
FT STRAND 85..90
FT /evidence="ECO:0007829|PDB:2WBQ"
FT HELIX 96..99
FT /evidence="ECO:0007829|PDB:2WBQ"
FT STRAND 104..106
FT /evidence="ECO:0007829|PDB:2WBQ"
FT HELIX 112..114
FT /evidence="ECO:0007829|PDB:2WBQ"
FT HELIX 115..126
FT /evidence="ECO:0007829|PDB:2WBQ"
FT STRAND 130..134
FT /evidence="ECO:0007829|PDB:2WBQ"
FT HELIX 138..140
FT /evidence="ECO:0007829|PDB:2WBQ"
FT STRAND 142..146
FT /evidence="ECO:0007829|PDB:2WBQ"
FT STRAND 155..157
FT /evidence="ECO:0007829|PDB:2WBQ"
FT STRAND 165..168
FT /evidence="ECO:0007829|PDB:2WBQ"
FT TURN 170..173
FT /evidence="ECO:0007829|PDB:2WBQ"
FT STRAND 179..187
FT /evidence="ECO:0007829|PDB:2WBQ"
FT STRAND 193..198
FT /evidence="ECO:0007829|PDB:2WBQ"
FT TURN 201..203
FT /evidence="ECO:0007829|PDB:2WBQ"
FT HELIX 206..212
FT /evidence="ECO:0007829|PDB:2WBQ"
FT STRAND 217..219
FT /evidence="ECO:0007829|PDB:2WBO"
FT HELIX 223..225
FT /evidence="ECO:0007829|PDB:2WBQ"
FT HELIX 227..229
FT /evidence="ECO:0007829|PDB:2WBQ"
FT STRAND 232..236
FT /evidence="ECO:0007829|PDB:2WBO"
FT HELIX 239..248
FT /evidence="ECO:0007829|PDB:2WBQ"
FT STRAND 255..259
FT /evidence="ECO:0007829|PDB:2WBQ"
FT STRAND 262..265
FT /evidence="ECO:0007829|PDB:2WBQ"
FT TURN 269..271
FT /evidence="ECO:0007829|PDB:2WBQ"
FT STRAND 273..275
FT /evidence="ECO:0007829|PDB:2WBQ"
FT HELIX 279..295
FT /evidence="ECO:0007829|PDB:2WBQ"
FT STRAND 297..300
FT /evidence="ECO:0007829|PDB:2WBQ"
FT STRAND 306..310
FT /evidence="ECO:0007829|PDB:2WBQ"
FT TURN 311..313
FT /evidence="ECO:0007829|PDB:2WBQ"
FT STRAND 314..318
FT /evidence="ECO:0007829|PDB:2WBQ"
FT STRAND 331..339
FT /evidence="ECO:0007829|PDB:2WBQ"
FT HELIX 341..347
FT /evidence="ECO:0007829|PDB:2WBQ"
FT STRAND 348..351
FT /evidence="ECO:0007829|PDB:2WBQ"
SQ SEQUENCE 358 AA; 39427 MW; B780A4AA68603122 CRC64;
MTESPTTHHG AAPPDSVATP VRPWSEFRLT PAEAAAAAAL AARCAQRYDE TDGPEFLLDA
PVIAHELPRR LRTFMARARL DAWPHALVVR GNPVDDAALG STPVHWRTAR TPGSRPLSFL
LMLYAGLLGD VFGWATQQDG RVVTDVLPIK GGEHTLVSSS SRQELGWHTE DAFSPYRADY
VGLLSLRNPD GVATTLAGVP LDDLDERTLD VLFQERFLIR PDDSHLQVNN STAQQGRVEF
EGIAQAADRP EPVAILTGHR AAPHLRVDGD FSAPAEGDEE AAAALGTLRK LIDASLYELV
LDQGDVAFID NRRAVHGRRA FQPRYDGRDR WLKRINITRD LHRSRKAWAG DSRVLGQR
