SRR_SCHPO
ID SRR_SCHPO Reviewed; 323 AA.
AC O59791;
DT 31-JAN-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 148.
DE RecName: Full=Serine racemase;
DE EC=4.3.1.17;
DE EC=4.3.1.18;
DE EC=5.1.1.18;
DE AltName: Full=D-serine ammonia-lyase;
DE AltName: Full=D-serine dehydratase;
DE AltName: Full=L-serine ammonia-lyase;
DE AltName: Full=L-serine dehydratase;
GN Name=SRR; ORFNames=SPCC320.14, SPCC330.15c;
OS Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina;
OC Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae;
OC Schizosaccharomyces.
OX NCBI_TaxID=284812;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=972 / ATCC 24843;
RX PubMed=11859360; DOI=10.1038/nature724;
RA Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A.,
RA Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S.,
RA Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.,
RA Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S.,
RA Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S.,
RA Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D.,
RA Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P.,
RA Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K.,
RA O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M.,
RA Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N.,
RA Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A.,
RA Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R.,
RA Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M.,
RA Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A.,
RA Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A.,
RA Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H.,
RA Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S.,
RA Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C.,
RA Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A.,
RA Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M.,
RA del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S.,
RA Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R.,
RA Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G.,
RA Nurse P.;
RT "The genome sequence of Schizosaccharomyces pombe.";
RL Nature 415:871-880(2002).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL PHOSPHATE
RP AND MAGNESIUM IONS, COFACTOR, ACTIVITY REGULATION, ACTIVE SITE, PYRIDOXAL
RP PHOSPHATE AT LYS-57, SUBUNIT, IDENTIFICATION BY MASS SPECTROMETRY, AND
RP LYSINO-D-ALANINE AT LYS-57.
RX PubMed=19155267; DOI=10.1093/jb/mvp010;
RA Yamauchi T., Goto M., Wu H.Y., Uo T., Yoshimura T., Mihara H., Kurihara T.,
RA Miyahara I., Hirotsu K., Esaki N.;
RT "Serine racemase with catalytically active lysinoalanyl residue.";
RL J. Biochem. 145:421-424(2009).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL PHOSPHATE;
RP SERINE; ATP ANALOG AND MAGNESIUM IONS, CATALYTIC ACTIVITY, FUNCTION,
RP COFACTOR, ACTIVE SITE, PYRIDOXAL PHOSPHATE AT LYS-57, LYSINO-D-ALANINE AT
RP LYS-57, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, ACTIVITY REGULATION, AND
RP MUTAGENESIS OF SER-82.
RX PubMed=19640845; DOI=10.1074/jbc.m109.010470;
RA Goto M., Yamauchi T., Kamiya N., Miyahara I., Yoshimura T., Mihara H.,
RA Kurihara T., Hirotsu K., Esaki N.;
RT "Crystal structure of a homolog of mammalian serine racemase from
RT Schizosaccharomyces pombe.";
RL J. Biol. Chem. 284:25944-25952(2009).
CC -!- FUNCTION: Catalyzes the synthesis of D-serine from L-serine. Has
CC dehydratase activity towards both L-serine and D-serine.
CC {ECO:0000269|PubMed:19640845}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-serine = D-serine; Xref=Rhea:RHEA:10980, ChEBI:CHEBI:33384,
CC ChEBI:CHEBI:35247; EC=5.1.1.18;
CC Evidence={ECO:0000269|PubMed:19640845};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-serine = NH4(+) + pyruvate; Xref=Rhea:RHEA:19169,
CC ChEBI:CHEBI:15361, ChEBI:CHEBI:28938, ChEBI:CHEBI:33384; EC=4.3.1.17;
CC Evidence={ECO:0000269|PubMed:19640845};
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 Evidence={ECO:0000269|PubMed:19640845};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000269|PubMed:19155267, ECO:0000269|PubMed:19640845};
CC -!- ACTIVITY REGULATION: Allosterically activated by ATP, by magnesium, and
CC possibly also by other divalent metal cations.
CC {ECO:0000269|PubMed:19155267, ECO:0000269|PubMed:19640845}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=36 mM for serine {ECO:0000269|PubMed:19640845};
CC Vmax=870 nmol/min/mg enzyme {ECO:0000269|PubMed:19640845};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:19155267,
CC ECO:0000269|PubMed:19640845}.
CC -!- PTM: Modification of the active site Lys by its substrate Ser to
CC lysino-D-alanine reduces but does not abolish enzyme activity.
CC -!- SIMILARITY: Belongs to the serine/threonine dehydratase family.
CC {ECO:0000305}.
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DR EMBL; CU329672; CAA20920.1; -; Genomic_DNA.
DR PIR; T41297; T41297.
DR RefSeq; NP_587715.1; NM_001022710.2.
DR PDB; 1V71; X-ray; 1.70 A; A=1-323.
DR PDB; 1WTC; X-ray; 1.90 A; A=1-323.
DR PDB; 2ZPU; X-ray; 1.70 A; A=1-323.
DR PDB; 2ZR8; X-ray; 2.20 A; A=1-323.
DR PDBsum; 1V71; -.
DR PDBsum; 1WTC; -.
DR PDBsum; 2ZPU; -.
DR PDBsum; 2ZR8; -.
DR AlphaFoldDB; O59791; -.
DR SMR; O59791; -.
DR BioGRID; 275321; 6.
DR STRING; 4896.SPCC320.14.1; -.
DR BindingDB; O59791; -.
DR ChEMBL; CHEMBL3097984; -.
DR iPTMnet; O59791; -.
DR MaxQB; O59791; -.
DR PaxDb; O59791; -.
DR PRIDE; O59791; -.
DR EnsemblFungi; SPCC320.14.1; SPCC320.14.1:pep; SPCC320.14.
DR GeneID; 2538738; -.
DR KEGG; spo:SPCC320.14; -.
DR PomBase; SPCC320.14; -.
DR VEuPathDB; FungiDB:SPCC320.14; -.
DR eggNOG; KOG1251; Eukaryota.
DR HOGENOM; CLU_021152_4_2_1; -.
DR InParanoid; O59791; -.
DR OMA; LIHPFDH; -.
DR PhylomeDB; O59791; -.
DR BRENDA; 5.1.1.18; 5613.
DR Reactome; R-SPO-977347; Serine biosynthesis.
DR SABIO-RK; O59791; -.
DR EvolutionaryTrace; O59791; -.
DR PRO; PR:O59791; -.
DR Proteomes; UP000002485; Chromosome III.
DR GO; GO:0005524; F:ATP binding; IDA:UniProtKB.
DR GO; GO:0008721; F:D-serine ammonia-lyase activity; IDA:UniProtKB.
DR GO; GO:0003941; F:L-serine ammonia-lyase activity; IDA:UniProtKB.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0042803; F:protein homodimerization activity; IPI:UniProtKB.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IDA:UniProtKB.
DR GO; GO:0030378; F:serine racemase activity; IDA:UniProtKB.
DR GO; GO:0018114; F:threonine racemase activity; IBA:GO_Central.
DR GO; GO:0070179; P:D-serine biosynthetic process; IBA:GO_Central.
DR GO; GO:0070178; P:D-serine metabolic process; IDA:UniProtKB.
DR GO; GO:0006563; P:L-serine metabolic process; IDA:UniProtKB.
DR GO; GO:0042866; P:pyruvate biosynthetic process; IBA:GO_Central.
DR Gene3D; 3.40.50.1100; -; 2.
DR InterPro; IPR001926; PLP-dep.
DR InterPro; IPR036052; Trypto_synt_PLP_dependent.
DR Pfam; PF00291; PALP; 1.
DR SUPFAM; SSF53686; SSF53686; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Allosteric enzyme; ATP-binding; Isomerase; Lyase; Magnesium;
KW Metal-binding; Nucleotide-binding; Pyridoxal phosphate; Reference proteome.
FT CHAIN 1..323
FT /note="Serine racemase"
FT /id="PRO_0000185588"
FT ACT_SITE 57
FT /note="Proton acceptor"
FT ACT_SITE 82
FT /note="Proton acceptor"
FT BINDING 25
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 52
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 53
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 119
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 133
FT /ligand="substrate"
FT BINDING 208
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 212
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 214
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 235..236
FT /ligand="substrate"
FT MOD_RES 57
FT /note="Lysino-D-alanine (Lys); alternate"
FT MOD_RES 57
FT /note="N6-(pyridoxal phosphate)lysine; alternate"
FT MUTAGEN 82
FT /note="S->A: Loss of racemase activity. Reduces D-serine
FT dehydratase activity by 99%. Slightly reduced L-serine
FT dehydratase activity."
FT /evidence="ECO:0000269|PubMed:19640845"
FT HELIX 10..20
FT /evidence="ECO:0007829|PDB:1V71"
FT TURN 21..23
FT /evidence="ECO:0007829|PDB:1V71"
FT HELIX 33..39
FT /evidence="ECO:0007829|PDB:1V71"
FT STRAND 41..47
FT /evidence="ECO:0007829|PDB:1V71"
FT HELIX 48..50
FT /evidence="ECO:0007829|PDB:1V71"
FT HELIX 52..54
FT /evidence="ECO:0007829|PDB:1V71"
FT HELIX 57..65
FT /evidence="ECO:0007829|PDB:1V71"
FT HELIX 70..75
FT /evidence="ECO:0007829|PDB:1V71"
FT STRAND 77..79
FT /evidence="ECO:0007829|PDB:1V71"
FT HELIX 84..95
FT /evidence="ECO:0007829|PDB:1V71"
FT STRAND 100..105
FT /evidence="ECO:0007829|PDB:1V71"
FT HELIX 110..118
FT /evidence="ECO:0007829|PDB:1V71"
FT STRAND 122..126
FT /evidence="ECO:0007829|PDB:1V71"
FT TURN 128..131
FT /evidence="ECO:0007829|PDB:1V71"
FT HELIX 133..144
FT /evidence="ECO:0007829|PDB:1V71"
FT STRAND 151..154
FT /evidence="ECO:0007829|PDB:1V71"
FT HELIX 155..161
FT /evidence="ECO:0007829|PDB:1V71"
FT HELIX 163..172
FT /evidence="ECO:0007829|PDB:1V71"
FT STRAND 176..181
FT /evidence="ECO:0007829|PDB:1V71"
FT STRAND 183..185
FT /evidence="ECO:0007829|PDB:1V71"
FT HELIX 186..198
FT /evidence="ECO:0007829|PDB:1V71"
FT STRAND 203..209
FT /evidence="ECO:0007829|PDB:1V71"
FT HELIX 210..212
FT /evidence="ECO:0007829|PDB:1V71"
FT HELIX 214..221
FT /evidence="ECO:0007829|PDB:1V71"
FT HELIX 235..237
FT /evidence="ECO:0007829|PDB:1WTC"
FT HELIX 244..253
FT /evidence="ECO:0007829|PDB:1V71"
FT STRAND 256..260
FT /evidence="ECO:0007829|PDB:1V71"
FT HELIX 262..275
FT /evidence="ECO:0007829|PDB:1V71"
FT HELIX 282..285
FT /evidence="ECO:0007829|PDB:1V71"
FT HELIX 286..293
FT /evidence="ECO:0007829|PDB:1V71"
FT HELIX 294..298
FT /evidence="ECO:0007829|PDB:1V71"
FT STRAND 302..307
FT /evidence="ECO:0007829|PDB:1V71"
FT HELIX 314..321
FT /evidence="ECO:0007829|PDB:1V71"
SQ SEQUENCE 323 AA; 35048 MW; 21187E5A69FA5348 CRC64;
MSDNLVLPTY DDVASASERI KKFANKTPVL TSSTVNKEFV AEVFFKCENF QKMGAFKFRG
ALNALSQLNE AQRKAGVLTF SSGNHAQAIA LSAKILGIPA KIIMPLDAPE AKVAATKGYG
GQVIMYDRYK DDREKMAKEI SEREGLTIIP PYDHPHVLAG QGTAAKELFE EVGPLDALFV
CLGGGGLLSG SALAARHFAP NCEVYGVEPE AGNDGQQSFR KGSIVHIDTP KTIADGAQTQ
HLGNYTFSII KEKVDDILTV SDEELIDCLK FYAARMKIVV EPTGCLSFAA ARAMKEKLKN
KRIGIIISGG NVDIERYAHF LSQ
