SRR_ORYSJ
ID SRR_ORYSJ Reviewed; 339 AA.
AC Q7XSN8; A0A0P0WDF8;
DT 28-NOV-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2004, sequence version 2.
DT 03-AUG-2022, entry version 115.
DE RecName: Full=Serine racemase {ECO:0000303|PubMed:19249065};
DE EC=5.1.1.18 {ECO:0000269|PubMed:19249065, ECO:0000269|PubMed:20564571};
DE AltName: Full=D-serine dehydratase {ECO:0000303|PubMed:19249065};
DE Short=D-serine ammonia-lyase;
DE EC=4.3.1.18 {ECO:0000269|PubMed:19249065, ECO:0000269|PubMed:20564571};
DE AltName: Full=L-serine dehydratase {ECO:0000303|PubMed:19249065};
DE Short=L-serine ammonia-lyase;
DE EC=4.3.1.17 {ECO:0000269|PubMed:19249065, ECO:0000269|PubMed:20564571};
GN Name=SERR {ECO:0000303|PubMed:19249065};
GN OrderedLocusNames=Os04g0555900, LOC_Os04g46930;
GN ORFNames=OsJ_15733 {ECO:0000312|EMBL:EAZ31592.1},
GN OSJNBb0012E24.7 {ECO:0000312|EMBL:CAE01865.2};
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, CATALYTIC ACTIVITY, ACTIVITY
RP REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RC STRAIN=cv. Nipponbare;
RX PubMed=19249065; DOI=10.1016/j.phytochem.2009.01.003;
RA Gogami Y., Ito K., Kamitani Y., Matsushima Y., Oikawa T.;
RT "Occurrence of D-serine in rice and characterization of rice serine
RT racemase.";
RL Phytochemistry 70:380-387(2009).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12447439; DOI=10.1038/nature01183;
RA Feng Q., Zhang Y., Hao P., Wang S., Fu G., Huang Y., Li Y., Zhu J., Liu Y.,
RA Hu X., Jia P., Zhang Y., Zhao Q., Ying K., Yu S., Tang Y., Weng Q.,
RA Zhang L., Lu Y., Mu J., Lu Y., Zhang L.S., Yu Z., Fan D., Liu X., Lu T.,
RA Li C., Wu Y., Sun T., Lei H., Li T., Hu H., Guan J., Wu M., Zhang R.,
RA Zhou B., Chen Z., Chen L., Jin Z., Wang R., Yin H., Cai Z., Ren S., Lv G.,
RA Gu W., Zhu G., Tu Y., Jia J., Zhang Y., Chen J., Kang H., Chen X., Shao C.,
RA Sun Y., Hu Q., Zhang X., Zhang W., Wang L., Ding C., Sheng H., Gu J.,
RA Chen S., Ni L., Zhu F., Chen W., Lan L., Lai Y., Cheng Z., Gu M., Jiang J.,
RA Li J., Hong G., Xue Y., Han B.;
RT "Sequence and analysis of rice chromosome 4.";
RL Nature 420:316-320(2002).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
RN [8]
RP MUTAGENESIS OF GLU-219 AND ASP-225, FUNCTION, BIOPHYSICOCHEMICAL
RP PROPERTIES, CATALYTIC ACTIVITY, AND ACTIVITY REGULATION.
RX PubMed=20564571; DOI=10.1002/cbdv.200900257;
RA Gogami Y., Kobayashi A., Ikeuchi T., Oikawa T.;
RT "Site-directed mutagenesis of rice serine racemase: evidence that Glu219
RT and Asp225 mediate the effects of Mg2+ on the activity.";
RL Chem. Biodivers. 7:1579-1590(2010).
CC -!- FUNCTION: Catalyzes the synthesis of D-serine from L-serine
CC (PubMed:19249065, PubMed:20564571). Has dehydratase activity towards
CC both L-serine and D-serine (PubMed:19249065, PubMed:20564571).
CC {ECO:0000269|PubMed:19249065, ECO:0000269|PubMed:20564571}.
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:19249065, ECO:0000269|PubMed:20564571};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:10981;
CC Evidence={ECO:0000269|PubMed:19249065, ECO:0000269|PubMed:20564571};
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:19249065, ECO:0000269|PubMed:20564571};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:19170;
CC Evidence={ECO:0000269|PubMed:19249065, ECO:0000269|PubMed:20564571};
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:19249065, ECO:0000269|PubMed:20564571};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:13978;
CC Evidence={ECO:0000269|PubMed:19249065, ECO:0000269|PubMed:20564571};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000250|UniProtKB:O59791};
CC -!- ACTIVITY REGULATION: Inhibited by semicarbazide, hydroxylamine,
CC aminooxyacetate, sodium borate or phenylhydrazine (PubMed:19249065).
CC Racemase activity is enhanced by Ca(2+), Mg(2+) and is decreased by
CC ATP, Cu(2+), Zn(2+) (PubMed:19249065, PubMed:20564571). Hydratase
CC activity is enhanced by ATP and is decreased by Ca(2+), Mg(2+), Co(2+),
CC Cu(2+), Ni(2+), Zn(2+) (PubMed:19249065, PubMed:20564571).
CC {ECO:0000269|PubMed:19249065, ECO:0000269|PubMed:20564571}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=18 mM for L-serine (racemase activity)
CC {ECO:0000269|PubMed:19249065, ECO:0000269|PubMed:20564571};
CC KM=20 mM for D-serine (racemase activity)
CC {ECO:0000269|PubMed:19249065, ECO:0000269|PubMed:20564571};
CC KM=28 mM for L-serine (dehydratase activity)
CC {ECO:0000269|PubMed:19249065, ECO:0000269|PubMed:20564571};
CC KM=19 mM for L-serine (dehydratase activity)
CC {ECO:0000269|PubMed:19249065, ECO:0000269|PubMed:20564571};
CC pH dependence:
CC Optimum pH is 9.5 for racemization and 9.0 for hydration.
CC {ECO:0000269|PubMed:19249065, ECO:0000269|PubMed:20564571};
CC Temperature dependence:
CC Optimum temperature is 35 degrees Celsius (racemase or dehydratase
CC activity). {ECO:0000269|PubMed:19249065,
CC ECO:0000269|PubMed:20564571};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:19249065}.
CC -!- SIMILARITY: Belongs to the serine/threonine dehydratase family.
CC {ECO:0000305}.
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DR EMBL; AB425957; BAH59439.1; -; mRNA.
DR EMBL; AL606647; CAE01865.2; -; Genomic_DNA.
DR EMBL; AP008210; BAF15435.1; -; Genomic_DNA.
DR EMBL; AP014960; BAS90428.1; -; Genomic_DNA.
DR EMBL; CM000141; EAZ31592.1; -; Genomic_DNA.
DR EMBL; AK063168; BAG88574.1; -; mRNA.
DR RefSeq; XP_015637224.1; XM_015781738.1.
DR RefSeq; XP_015637225.1; XM_015781739.1.
DR RefSeq; XP_015637226.1; XM_015781740.1.
DR RefSeq; XP_015637227.1; XM_015781741.1.
DR RefSeq; XP_015637228.1; XM_015781742.1.
DR AlphaFoldDB; Q7XSN8; -.
DR SMR; Q7XSN8; -.
DR STRING; 4530.OS04T0555900-01; -.
DR PaxDb; Q7XSN8; -.
DR PRIDE; Q7XSN8; -.
DR EnsemblPlants; Os04t0555900-01; Os04t0555900-01; Os04g0555900.
DR GeneID; 4336624; -.
DR Gramene; Os04t0555900-01; Os04t0555900-01; Os04g0555900.
DR KEGG; osa:4336624; -.
DR eggNOG; KOG1251; Eukaryota.
DR HOGENOM; CLU_021152_4_2_1; -.
DR InParanoid; Q7XSN8; -.
DR OMA; LIHPFDH; -.
DR OrthoDB; 943371at2759; -.
DR BRENDA; 5.1.1.18; 4460.
DR Proteomes; UP000000763; Chromosome 4.
DR Proteomes; UP000007752; Chromosome 4.
DR Proteomes; UP000059680; Chromosome 4.
DR Genevisible; Q7XSN8; OS.
DR GO; GO:0005524; F:ATP binding; IBA:GO_Central.
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; IBA:GO_Central.
DR GO; GO:0043621; F:protein self-association; IDA:UniProtKB.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IBA:GO_Central.
DR GO; GO:0030378; F:serine racemase activity; IBA:GO_Central.
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 Allosteric enzyme; ATP-binding; Isomerase; Lyase; Magnesium; Metal-binding;
KW Nucleotide-binding; Pyridoxal phosphate; Reference proteome;
KW S-nitrosylation.
FT CHAIN 1..339
FT /note="Serine racemase"
FT /id="PRO_0000420348"
FT ACT_SITE 68
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:O59791"
FT ACT_SITE 93
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:O59791"
FT BINDING 63
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O59791"
FT BINDING 130
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O59791"
FT BINDING 144
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O59791"
FT BINDING 219
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:O59791"
FT BINDING 223
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:O59791"
FT BINDING 225
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:O59791"
FT BINDING 246..247
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O59791"
FT MOD_RES 68
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000250|UniProtKB:O59791"
FT MOD_RES 122
FT /note="S-nitrosocysteine"
FT /evidence="ECO:0000250|UniProtKB:Q9QZX7"
FT MUTAGEN 219
FT /note="E->A: Reduces catalytic activity and abolishes the
FT regulatory effect of Mg(2+) addition; when associated with
FT A-225."
FT /evidence="ECO:0000269|PubMed:20564571"
FT MUTAGEN 225
FT /note="D->A: Reduces catalytic activity and abolishes the
FT regulatory effect of Mg(2+) addition; when associated with
FT A-219."
FT /evidence="ECO:0000269|PubMed:20564571"
SQ SEQUENCE 339 AA; 35597 MW; 71C28D4F16C23875 CRC64;
MGSRGGSGGD GAESHGYAAD IHSIREAQAR IAPYVHKTPV LSSTSIDAIV GKQLFFKCEC
FQKAGAFKIR GASNSIFALD DDEASKGVVT HSSGNHAAAV ALAAKLRGIP AYIVIPRNAP
ACKVDNVKRY GGHIIWSDVS IESRESVAKR VQEETGAILV HPFNNKNTIS GQGTVSLELL
EEVPEIDTII VPISGGGLIS GVALAAKAIN PSIRILAAEP KGADDSAQSK AAGKIITLPS
TNTIADGLRA FLGDLTWPVV RDLVDDIIVV DDNAIVDAMK MCYEMLKVAV EPSGAIGLAA
ALSDEFKQSS AWHESSKIGI IVSGGNVDLG VLWESLYKR
