SRR_ARATH
ID SRR_ARATH Reviewed; 331 AA.
AC Q2PGG3; Q9T0D1;
DT 28-NOV-2012, integrated into UniProtKB/Swiss-Prot.
DT 07-FEB-2006, sequence version 1.
DT 03-AUG-2022, entry version 107.
DE RecName: Full=Serine racemase {ECO:0000303|PubMed:16483618};
DE Short=AtSR {ECO:0000303|PubMed:16483618};
DE EC=4.3.1.17 {ECO:0000269|PubMed:16483618};
DE EC=4.3.1.18 {ECO:0000269|PubMed:16483618};
DE EC=5.1.1.18 {ECO:0000269|PubMed:16483618};
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=SR; Synonyms=SR1; OrderedLocusNames=At4g11640; ORFNames=T5C23.70;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY REGULATION, COFACTOR, AND TISSUE
RP SPECIFICITY.
RC STRAIN=cv. Columbia;
RX PubMed=16483618; DOI=10.1016/j.phytochem.2006.01.003;
RA Fujitani Y., Nakajima N., Ishihara K., Oikawa T., Ito K., Sugimoto M.;
RT "Molecular and biochemical characterization of a serine racemase from
RT Arabidopsis thaliana.";
RL Phytochemistry 67:668-674(2006).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP DISRUPTION PHENOTYPE.
RX PubMed=21415319; DOI=10.1126/science.1201101;
RA Michard E., Lima P.T., Borges F., Silva A.C., Portes M.T., Carvalho J.E.,
RA Gilliham M., Liu L.H., Obermeyer G., Feijo J.A.;
RT "Glutamate receptor-like genes form Ca2+ channels in pollen tubes and are
RT regulated by pistil D-serine.";
RL Science 332:434-437(2011).
CC -!- FUNCTION: Catalyzes the synthesis of D-serine from L-serine. Has
CC dehydratase activity towards both L-serine and D-serine. Displays high
CC substrate specificity for L-serine, whereas L-alanine, L-arginine, and
CC L-glutamine were poor substrates. {ECO:0000269|PubMed:16483618}.
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:16483618};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:10981;
CC Evidence={ECO:0000269|PubMed:16483618};
CC PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:10982;
CC Evidence={ECO:0000269|PubMed:16483618};
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:16483618};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:19170;
CC Evidence={ECO:0000269|PubMed:16483618};
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:16483618};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:13978;
CC Evidence={ECO:0000269|PubMed:16483618};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000269|PubMed:16483618};
CC -!- ACTIVITY REGULATION: Inhibited by hydroxylamine. Racemase activity is
CC enhanced by Ca(2+), Mg(2+), Mn(2+), and is decreased by Ni(2+), Zn(2+).
CC Hydratase activity is enhanced by Ca(2+), Mg(2+), Mn(2+), Cu(2+),
CC Fe(2+), Ni(2+). {ECO:0000269|PubMed:16483618}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=2.5 mM for L-serine (racemase activity)
CC {ECO:0000269|PubMed:16483618};
CC KM=0.77 mM for D-serine (racemase activity)
CC {ECO:0000269|PubMed:16483618};
CC KM=20 mM for L-serine (dehydratase activity)
CC {ECO:0000269|PubMed:16483618};
CC KM=5 mM for D-serine (dehydratase activity)
CC {ECO:0000269|PubMed:16483618};
CC Vmax=5 nmol/min/mg enzyme toward L-serine (racemase activity)
CC {ECO:0000269|PubMed:16483618};
CC Vmax=1.1 nmol/min/mg enzyme toward D-serine (racemase activity)
CC {ECO:0000269|PubMed:16483618};
CC Vmax=250 nmol/min/mg enzyme toward L-serine (dehydratase activity)
CC {ECO:0000269|PubMed:16483618};
CC Vmax=26 nmol/min/mg enzyme toward L-serine (dehydratase activity)
CC {ECO:0000269|PubMed:16483618};
CC pH dependence:
CC Optimum pH is 8.5 for racemization and 9.5 for dehydration.
CC {ECO:0000269|PubMed:16483618};
CC -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC -!- TISSUE SPECIFICITY: Expressed in the whole plant.
CC {ECO:0000269|PubMed:16483618}.
CC -!- DISRUPTION PHENOTYPE: Deformations and branching of pollen tubes grown
CC in pistils. {ECO:0000269|PubMed:21415319}.
CC -!- SIMILARITY: Belongs to the serine/threonine dehydratase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB39935.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB78207.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AB206823; BAE72067.1; -; mRNA.
DR EMBL; AL049500; CAB39935.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161532; CAB78207.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE83032.1; -; Genomic_DNA.
DR PIR; T04211; T04211.
DR RefSeq; NP_192901.2; NM_117233.3.
DR AlphaFoldDB; Q2PGG3; -.
DR SMR; Q2PGG3; -.
DR STRING; 3702.AT4G11640.1; -.
DR PaxDb; Q2PGG3; -.
DR PRIDE; Q2PGG3; -.
DR ProteomicsDB; 226824; -.
DR EnsemblPlants; AT4G11640.1; AT4G11640.1; AT4G11640.
DR GeneID; 826769; -.
DR Gramene; AT4G11640.1; AT4G11640.1; AT4G11640.
DR KEGG; ath:AT4G11640; -.
DR Araport; AT4G11640; -.
DR TAIR; locus:2139767; AT4G11640.
DR eggNOG; KOG1251; Eukaryota.
DR HOGENOM; CLU_021152_4_2_1; -.
DR InParanoid; Q2PGG3; -.
DR OMA; LIHPFDH; -.
DR OrthoDB; 943371at2759; -.
DR PhylomeDB; Q2PGG3; -.
DR BioCyc; ARA:AT4G11640-MON; -.
DR BioCyc; MetaCyc:MON-14684; -.
DR BRENDA; 5.1.1.18; 399.
DR PRO; PR:Q2PGG3; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q2PGG3; baseline and differential.
DR Genevisible; Q2PGG3; AT.
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; IEA:EnsemblPlants.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IBA:GO_Central.
DR GO; GO:0030378; F:serine racemase activity; IDA:TAIR.
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 GO; GO:0009069; P:serine family amino acid metabolic process; IDA:TAIR.
DR Gene3D; 3.40.50.1100; -; 2.
DR InterPro; IPR001926; PLP-dep.
DR InterPro; IPR000634; Ser/Thr_deHydtase_PyrdxlP-BS.
DR InterPro; IPR036052; Trypto_synt_PLP_dependent.
DR Pfam; PF00291; PALP; 1.
DR SUPFAM; SSF53686; SSF53686; 1.
DR PROSITE; PS00165; DEHYDRATASE_SER_THR; 1.
PE 1: Evidence at protein level;
KW Allosteric enzyme; ATP-binding; Isomerase; Lyase; Magnesium; Metal-binding;
KW Nucleotide-binding; Pyridoxal phosphate; Reference proteome.
FT CHAIN 1..331
FT /note="Serine racemase"
FT /id="PRO_0000420346"
FT ACT_SITE 59
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 84
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 54
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 121
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 135
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 210
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 214
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 216
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 237..238
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT MOD_RES 59
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000250"
SQ SEQUENCE 331 AA; 35068 MW; F4FC4EE39DD60A7A CRC64;
MEANREKYAA DILSIKEAHD RIKPYIHRTP VLTSESLNSI SGRSLFFKCE CLQKGGAFKF
RGACNAVLSL DAEQAAKGVV THSSGNHAAA LSLAAKIQGI PAYIVVPKGA PKCKVDNVIR
YGGKVIWSEA TMSSREEIAS KVLQETGSVL IHPYNDGRII SGQGTIALEL LEQIQEIDAI
VVPISGGGLI SGVALAAKSI KPSIRIIAAE PKGADDAAQS KVAGKIITLP VTNTIADGLR
ASLGDLTWPV VRDLVDDVVT LEECEIIEAM KMCYEILKVS VEPSGAIGLA AVLSNSFRNN
PSCRDCKNIG IVLSGGNVDL GSLWDSFKSS K
