SDHD_ECOLI
ID SDHD_ECOLI Reviewed; 442 AA.
AC P00926; P78303;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 3.
DT 03-AUG-2022, entry version 170.
DE RecName: Full=D-serine dehydratase;
DE EC=4.3.1.18;
DE AltName: Full=D-serine deaminase;
DE Short=DSD;
GN Name=dsdA; OrderedLocusNames=b2366, JW2363;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=3053699; DOI=10.1016/s0021-9258(18)37480-5;
RA Marceau M., McFall E., Lewis S.D., Shafer J.A.;
RT "D-serine dehydratase from Escherichia coli. DNA sequence and
RT identification of catalytically inactive glycine to aspartic acid
RT variants.";
RL J. Biol. Chem. 263:16926-16933(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9205837; DOI=10.1093/dnares/4.2.91;
RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K.,
RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S.,
RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H.,
RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12
RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of
RT its sequence features.";
RL DNA Res. 4:91-113(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP PROTEIN SEQUENCE.
RC STRAIN=K12 / mutant C6;
RX PubMed=9222324; DOI=10.1016/0014-5793(81)80550-9;
RA Schiltz E., Schmitt W.;
RT "Sequence of Escherichia coli D-serine dehydratase. Location of the
RT pyridoxal-phosphate binding site.";
RL FEBS Lett. 134:57-62(1981).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-195.
RX PubMed=6343359; DOI=10.1128/jb.154.3.1508-1512.1983;
RA McFall E., Runkel L.;
RT "DNA sequences of the D-serine deaminase control region and N-terminal
RT portion of the structural gene.";
RL J. Bacteriol. 154:1508-1512(1983).
RN [7]
RP PROTEIN SEQUENCE OF 1-23 AND 107-120.
RX PubMed=795658; DOI=10.1111/j.1432-1033.1976.tb11095.x;
RA Schiltz E., Schnackerz K.D.;
RT "Sequence studies on D-serine dehydratase of Escherichia coli. Primary
RT structure of the tryptic phosphopyridoxyl peptide and of the N-terminus.";
RL Eur. J. Biochem. 71:109-116(1976).
RN [8]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-10.
RC STRAIN=K12;
RA Brannigan J.A.;
RL Submitted (APR-1995) to the EMBL/GenBank/DDBJ databases.
RN [9]
RP INDUCTION BY D-SERINE.
RC STRAIN=K12;
RX PubMed=7592420; DOI=10.1128/jb.177.22.6456-6461.1995;
RA Noerregaard-Madsen M., McFall E., Valentin-Hansen P.;
RT "Organization and transcriptional regulation of the Escherichia coli K-12
RT D-serine tolerance locus.";
RL J. Bacteriol. 177:6456-6461(1995).
RN [10] {ECO:0007744|PDB:3SS7, ECO:0007744|PDB:3SS9}
RP X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL PHOSPHATE
RP IN OPEN AND CLOSED CONFORMATION, COFACTOR, SUBUNIT, AND DOMAIN.
RX PubMed=22197591; DOI=10.1016/j.bbapap.2011.10.017;
RA Urusova D.V., Isupov M.N., Antonyuk S., Kachalova G.S., Obmolova G.,
RA Vagin A.A., Lebedev A.A., Burenkov G.P., Dauter Z., Bartunik H.D.,
RA Lamzin V.S., Melik-Adamyan W.R., Mueller T.D., Schnackerz K.D.;
RT "Crystal structure of D-serine dehydratase from Escherichia coli.";
RL Biochim. Biophys. Acta 1824:422-432(2012).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-serine = NH4(+) + pyruvate; Xref=Rhea:RHEA:13977,
CC ChEBI:CHEBI:15361, ChEBI:CHEBI:28938, ChEBI:CHEBI:35247; EC=4.3.1.18;
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000269|PubMed:22197591};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:22197591}.
CC -!- INDUCTION: By growth in D-serine. {ECO:0000269|PubMed:7592420}.
CC -!- DOMAIN: Crystal structures show a large (N-terminal) and small (C-
CC terminal) domain; the C-terminal domain is mobile and can block access
CC to the active site. {ECO:0000269|PubMed:22197591}.
CC -!- SIMILARITY: Belongs to the serine/threonine dehydratase family. DsdA
CC subfamily. {ECO:0000305}.
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DR EMBL; J01603; AAA87975.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75425.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA16229.1; -; Genomic_DNA.
DR EMBL; X86379; CAA60139.1; -; Genomic_DNA.
DR PIR; C65010; DWECS.
DR RefSeq; NP_416867.1; NC_000913.3.
DR RefSeq; WP_000426427.1; NZ_STEB01000008.1.
DR PDB; 3SS7; X-ray; 1.55 A; X=1-442.
DR PDB; 3SS9; X-ray; 1.97 A; X=1-442.
DR PDBsum; 3SS7; -.
DR PDBsum; 3SS9; -.
DR AlphaFoldDB; P00926; -.
DR SMR; P00926; -.
DR BioGRID; 4260555; 10.
DR BioGRID; 851178; 1.
DR IntAct; P00926; 4.
DR STRING; 511145.b2366; -.
DR jPOST; P00926; -.
DR PaxDb; P00926; -.
DR PRIDE; P00926; -.
DR EnsemblBacteria; AAC75425; AAC75425; b2366.
DR EnsemblBacteria; BAA16229; BAA16229; BAA16229.
DR GeneID; 946837; -.
DR KEGG; ecj:JW2363; -.
DR KEGG; eco:b2366; -.
DR PATRIC; fig|1411691.4.peg.4363; -.
DR EchoBASE; EB0245; -.
DR eggNOG; COG3048; Bacteria.
DR HOGENOM; CLU_035707_0_0_6; -.
DR InParanoid; P00926; -.
DR OMA; ESDPNCF; -.
DR PhylomeDB; P00926; -.
DR BioCyc; EcoCyc:DSERDEAM-MON; -.
DR BioCyc; MetaCyc:DSERDEAM-MON; -.
DR BRENDA; 4.3.1.18; 2026.
DR PRO; PR:P00926; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IDA:EcoliWiki.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0008721; F:D-serine ammonia-lyase activity; IDA:CACAO.
DR GO; GO:0016836; F:hydro-lyase activity; IDA:EcoliWiki.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IDA:EcoCyc.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; IEP:EcoliWiki.
DR GO; GO:0036088; P:D-serine catabolic process; IDA:EcoCyc.
DR GO; GO:0070178; P:D-serine metabolic process; IDA:EcoliWiki.
DR GO; GO:0051410; P:detoxification of nitrogen compound; IMP:EcoCyc.
DR GO; GO:0009097; P:isoleucine biosynthetic process; IBA:GO_Central.
DR Gene3D; 3.40.50.1100; -; 2.
DR HAMAP; MF_01030; D_Ser_dehydrat; 1.
DR InterPro; IPR011780; D_Ser_am_lyase.
DR InterPro; IPR001926; PLP-dep.
DR InterPro; IPR000634; Ser/Thr_deHydtase_PyrdxlP-BS.
DR InterPro; IPR036052; Trypto_synt_PLP_dependent.
DR PANTHER; PTHR48078:SF9; PTHR48078:SF9; 1.
DR Pfam; PF00291; PALP; 1.
DR SUPFAM; SSF53686; SSF53686; 1.
DR TIGRFAMs; TIGR02035; D_Ser_am_lyase; 1.
DR PROSITE; PS00165; DEHYDRATASE_SER_THR; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Lyase; Pyridoxal phosphate;
KW Reference proteome.
FT CHAIN 1..442
FT /note="D-serine dehydratase"
FT /id="PRO_0000185611"
FT MOD_RES 118
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000269|PubMed:22197591,
FT ECO:0007744|PDB:3SS7, ECO:0007744|PDB:3SS9"
FT CONFLICT 34
FT /note="S -> T (in Ref. 5; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 85
FT /note="P -> R (in Ref. 1; AAA87975)"
FT /evidence="ECO:0000305"
FT CONFLICT 204
FT /note="S -> T (in Ref. 1; AAA87975)"
FT /evidence="ECO:0000305"
FT HELIX 7..12
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 15..20
FT /evidence="ECO:0007829|PDB:3SS7"
FT STRAND 26..28
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 35..38
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 39..41
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 46..66
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 68..73
FT /evidence="ECO:0007829|PDB:3SS7"
FT STRAND 81..83
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 85..95
FT /evidence="ECO:0007829|PDB:3SS7"
FT STRAND 101..107
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 108..110
FT /evidence="ECO:0007829|PDB:3SS7"
FT TURN 112..114
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 118..136
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 146..150
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 152..159
FT /evidence="ECO:0007829|PDB:3SS7"
FT STRAND 161..166
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 170..182
FT /evidence="ECO:0007829|PDB:3SS7"
FT STRAND 185..191
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 196..204
FT /evidence="ECO:0007829|PDB:3SS7"
FT STRAND 208..214
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 216..228
FT /evidence="ECO:0007829|PDB:3SS7"
FT STRAND 233..235
FT /evidence="ECO:0007829|PDB:3SS7"
FT TURN 238..240
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 242..249
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 251..262
FT /evidence="ECO:0007829|PDB:3SS7"
FT STRAND 272..277
FT /evidence="ECO:0007829|PDB:3SS7"
FT STRAND 279..281
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 282..295
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 296..298
FT /evidence="ECO:0007829|PDB:3SS7"
FT STRAND 299..306
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 311..318
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 321..323
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 326..329
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 338..340
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 349..353
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 354..356
FT /evidence="ECO:0007829|PDB:3SS7"
FT STRAND 359..363
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 365..379
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 385..392
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 393..399
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 401..407
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 411..415
FT /evidence="ECO:0007829|PDB:3SS7"
FT STRAND 418..423
FT /evidence="ECO:0007829|PDB:3SS7"
FT HELIX 431..440
FT /evidence="ECO:0007829|PDB:3SS7"
SQ SEQUENCE 442 AA; 47901 MW; 3BCB9397AC8C7971 CRC64;
MENAKMNSLI AQYPLVKDLV ALKETTWFNP GTTSLAEGLP YVGLTEQDVQ DAHARLSRFA
PYLAKAFPET AATGGIIESE LVAIPAMQKR LEKEYQQPIS GQLLLKKDSH LPISGSIKAR
GGIYEVLAHA EKLALEAGLL TLDDDYSKLL SPEFKQFFSQ YSIAVGSTGN LGLSIGIMSA
RIGFKVTVHM SADARAWKKA KLRSHGVTVV EYEQDYGVAV EEGRKAAQSD PNCFFIDDEN
SRTLFLGYSV AGQRLKAQFA QQGRIVDADN PLFVYLPCGV GGGPGGVAFG LKLAFGDHVH
CFFAEPTHSP CMLLGVHTGL HDQISVQDIG IDNLTAADGL AVGRASGFVG RAMERLLDGF
YTLSDQTMYD MLGWLAQEEG IRLEPSALAG MAGPQRVCAS VSYQQMHGFS AEQLRNTTHL
VWATGGGMVP EEEMNQYLAK GR
