DCSC_STRLA
ID DCSC_STRLA Reviewed; 287 AA.
AC D2Z026;
DT 16-OCT-2013, integrated into UniProtKB/Swiss-Prot.
DT 23-MAR-2010, sequence version 1.
DT 03-AUG-2022, entry version 38.
DE RecName: Full=O-ureido-serine racemase {ECO:0000303|PubMed:20086163};
DE EC=5.1.1.19 {ECO:0000269|PubMed:22307920, ECO:0000269|PubMed:23529730};
GN Name=dcsC {ECO:0000303|PubMed:20086163}; Synonyms=dapF;
OS Streptomyces lavendulae.
OC Bacteria; Actinobacteria; Streptomycetales; Streptomycetaceae;
OC Streptomyces.
OX NCBI_TaxID=1914;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
RC STRAIN=ATCC 11924;
RX PubMed=20086163; DOI=10.1128/aac.01226-09;
RA Kumagai T., Koyama Y., Oda K., Noda M., Matoba Y., Sugiyama M.;
RT "Molecular cloning and heterologous expression of a biosynthetic gene
RT cluster for the antitubercular agent D-cycloserine produced by Streptomyces
RT lavendulae.";
RL Antimicrob. Agents Chemother. 54:1132-1139(2010).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY
RP REGULATION, REACTION MECHANISM, AND MASS SPECTROMETRY.
RX PubMed=22307920; DOI=10.1039/c2ob06864h;
RA Dietrich D., van Belkum M.J., Vederas J.C.;
RT "Characterization of DcsC, a PLP-independent racemase involved in the
RT biosynthesis of D-cycloserine.";
RL Org. Biomol. Chem. 10:2248-2254(2012).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, AND SUBUNIT.
RX PubMed=23529730; DOI=10.1128/aac.02291-12;
RA Uda N., Matoba Y., Kumagai T., Oda K., Noda M., Sugiyama M.;
RT "Establishment of an in vitro D-cycloserine-synthesizing system by using O-
RT ureido-L-serine synthase and D-cycloserine synthetase found in the
RT biosynthetic pathway.";
RL Antimicrob. Agents Chemother. 57:2603-2612(2013).
CC -!- FUNCTION: Involved in the biosynthesis of the antibiotic D-cycloserine
CC (DCS), a cyclic structural analog of D-alanine, used as an
CC antitubercular agent. Catalyzes the stereoinversion of O-ureido-L-
CC serine to O-ureido-D-serine. {ECO:0000269|PubMed:20086163,
CC ECO:0000269|PubMed:22307920, ECO:0000269|PubMed:23529730}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=O-ureido-L-serine = O-ureido-D-serine; Xref=Rhea:RHEA:36707,
CC ChEBI:CHEBI:73389, ChEBI:CHEBI:74158; EC=5.1.1.19;
CC Evidence={ECO:0000269|PubMed:22307920, ECO:0000269|PubMed:23529730};
CC -!- ACTIVITY REGULATION: Inhibited by thiol-inactivating reagents such as
CC iodoacetamide and Hg(2+) ions. {ECO:0000269|PubMed:22307920}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=17 mM for O-ureido-D-serine (at 30 degrees Celsius)
CC {ECO:0000269|PubMed:22307920};
CC KM=110 mM for O-ureido-L-serine (at 30 degrees Celsius)
CC {ECO:0000269|PubMed:22307920};
CC Note=kcat is 158 sec(-1) and 29 sec(-1) for O-ureido-L-serine and O-
CC ureido-D-serine, respectively (at 30 degrees Celsius).
CC {ECO:0000269|PubMed:22307920};
CC pH dependence:
CC Optimum pH is 7.9. {ECO:0000269|PubMed:22307920};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:23529730}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
CC -!- MASS SPECTROMETRY: Mass=31205; Method=Electrospray;
CC Evidence={ECO:0000269|PubMed:22307920};
CC -!- MISCELLANEOUS: It employs a two-base mechanism, with a thiolate-thiol
CC pair in the active site. {ECO:0000305|PubMed:22307920}.
CC -!- SIMILARITY: Belongs to the diaminopimelate epimerase family.
CC {ECO:0000305}.
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DR EMBL; AB516431; BAI70377.1; -; Genomic_DNA.
DR PDB; 7VDY; X-ray; 2.12 A; A/B=1-287.
DR PDBsum; 7VDY; -.
DR AlphaFoldDB; D2Z026; -.
DR SMR; D2Z026; -.
DR KEGG; ag:BAI70377; -.
DR BioCyc; MetaCyc:MON-18018; -.
DR BRENDA; 5.1.1.19; 13336.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0008837; F:diaminopimelate epimerase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0016855; F:racemase and epimerase activity, acting on amino acids and derivatives; IDA:UniProtKB.
DR GO; GO:0017000; P:antibiotic biosynthetic process; IEA:UniProtKB-KW.
DR GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IEA:UniProtKB-UniRule.
DR HAMAP; MF_00197; DAP_epimerase; 1.
DR InterPro; IPR001653; DAP_epimerase_DapF.
DR PANTHER; PTHR31689; PTHR31689; 1.
DR Pfam; PF01678; DAP_epimerase; 2.
DR TIGRFAMs; TIGR00652; DapF; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Antibiotic biosynthesis; Cytoplasm; Isomerase.
FT CHAIN 1..287
FT /note="O-ureido-serine racemase"
FT /id="PRO_0000424062"
FT ACT_SITE 81
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:P44859"
FT ACT_SITE 227
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:P44859"
FT BINDING 20
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P44859"
FT BINDING 82..83
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P44859"
FT BINDING 167
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P44859"
FT BINDING 200
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P44859"
FT BINDING 218..219
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P44859"
FT BINDING 228..229
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P44859"
FT SITE 169
FT /note="Could be important to modulate the pK values of the
FT two catalytic cysteine residues"
FT /evidence="ECO:0000250|UniProtKB:P44859"
FT SITE 218
FT /note="Could be important to modulate the pK values of the
FT two catalytic cysteine residues"
FT /evidence="ECO:0000250|UniProtKB:P44859"
FT SITE 278
FT /note="Important for dimerization"
FT /evidence="ECO:0000250|UniProtKB:P0A6K1"
FT STRAND 10..17
FT /evidence="ECO:0007829|PDB:7VDY"
FT STRAND 20..26
FT /evidence="ECO:0007829|PDB:7VDY"
FT HELIX 35..42
FT /evidence="ECO:0007829|PDB:7VDY"
FT TURN 44..46
FT /evidence="ECO:0007829|PDB:7VDY"
FT STRAND 51..57
FT /evidence="ECO:0007829|PDB:7VDY"
FT STRAND 61..63
FT /evidence="ECO:0007829|PDB:7VDY"
FT STRAND 65..72
FT /evidence="ECO:0007829|PDB:7VDY"
FT HELIX 83..94
FT /evidence="ECO:0007829|PDB:7VDY"
FT STRAND 100..107
FT /evidence="ECO:0007829|PDB:7VDY"
FT STRAND 110..118
FT /evidence="ECO:0007829|PDB:7VDY"
FT STRAND 121..125
FT /evidence="ECO:0007829|PDB:7VDY"
FT TURN 133..137
FT /evidence="ECO:0007829|PDB:7VDY"
FT STRAND 148..151
FT /evidence="ECO:0007829|PDB:7VDY"
FT STRAND 157..173
FT /evidence="ECO:0007829|PDB:7VDY"
FT HELIX 177..179
FT /evidence="ECO:0007829|PDB:7VDY"
FT HELIX 182..191
FT /evidence="ECO:0007829|PDB:7VDY"
FT STRAND 193..195
FT /evidence="ECO:0007829|PDB:7VDY"
FT STRAND 200..208
FT /evidence="ECO:0007829|PDB:7VDY"
FT STRAND 211..218
FT /evidence="ECO:0007829|PDB:7VDY"
FT TURN 219..221
FT /evidence="ECO:0007829|PDB:7VDY"
FT HELIX 228..240
FT /evidence="ECO:0007829|PDB:7VDY"
FT STRAND 246..251
FT /evidence="ECO:0007829|PDB:7VDY"
FT STRAND 256..260
FT /evidence="ECO:0007829|PDB:7VDY"
FT STRAND 269..273
FT /evidence="ECO:0007829|PDB:7VDY"
FT STRAND 275..284
FT /evidence="ECO:0007829|PDB:7VDY"
SQ SEQUENCE 287 AA; 30382 MW; 618C5B1B472E1D06 CRC64;
MIRMRTPSTL PFTKMHGAGN DFVVLDLRDG PDPSPELCRA LADRHKGVGC DLVLGIREPR
SARAVAAFDI WTADGSRSAQ CGNGARCVAA WAVRAGLARG PRFALDSPSG THEVDVLDAD
TFRVALAVPR FAPESIPLFG HDGEQDLYEA DLGDGTRVRF AAVSMGNPHA VIEVDDTATA
PVARVGRAVQ ASGLFLPTVN VGFARVESRD RVHLRVHEYG AGETLACGSG ACAAAAVLMR
RGRVDRNVSV VLPGGELRIS WPDDAADVLM TGPAAFVYEG TFLHASV
