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Protein

Serine racemase

Gene

SR

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the synthesis of D-serine from L-serine. Has dehydratase activity towards both L-serine and D-serine. Displays high substrate specificity for L-serine, whereas L-alanine, L-arginine, and L-glutamine were poor substrates.1 Publication

Catalytic activityi

L-serine = D-serine.
L-serine = pyruvate + NH3.
D-serine = pyruvate + NH3.

Cofactori

Enzyme regulationi

Inhibited by hydroxylamine. Racemase activity is enhanced by Ca2+, Mg2+, Mn2+, and is decreased by Ni2+, Zn2+. Hydratase activity is enhanced by Ca2+, Mg2+, Mn2+, Cu2+, Fe2+, Ni2+.1 Publication

Kineticsi

  1. KM=2.5 mM for L-serine (racemase activity)1 Publication
  2. KM=0.77 mM for D-serine (racemase activity)1 Publication
  3. KM=20 mM for L-serine (dehydratase activity)1 Publication
  4. KM=5 mM for D-serine (dehydratase activity)1 Publication
  1. Vmax=5 nmol/min/mg enzyme toward L-serine (racemase activity)1 Publication
  2. Vmax=1.1 nmol/min/mg enzyme toward D-serine (racemase activity)1 Publication
  3. Vmax=250 nmol/min/mg enzyme toward L-serine (dehydratase activity)1 Publication
  4. Vmax=26 nmol/min/mg enzyme toward L-serine (dehydratase activity)1 Publication

pH dependencei

Optimum pH is 8.5 for racemization and 9.5 for dehydration.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei54 – 541ATPBy similarity
Active sitei59 – 591Proton acceptorBy similarity
Active sitei84 – 841Proton acceptorBy similarity
Binding sitei121 – 1211ATPBy similarity
Binding sitei135 – 1351SubstrateBy similarity
Metal bindingi210 – 2101MagnesiumBy similarity
Metal bindingi214 – 2141Magnesium; via carbonyl oxygenBy similarity
Metal bindingi216 – 2161MagnesiumBy similarity

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • D-serine ammonia-lyase activity Source: UniProtKB
  • L-serine ammonia-lyase activity Source: UniProtKB
  • metal ion binding Source: UniProtKB-KW
  • pyridoxal phosphate binding Source: GO_Central
  • serine racemase activity Source: TAIR

GO - Biological processi

  • D-serine biosynthetic process Source: GO_Central
  • D-serine metabolic process Source: UniProtKB
  • L-serine metabolic process Source: UniProtKB
  • serine family amino acid metabolic process Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Lyase

Keywords - Ligandi

ATP-binding, Magnesium, Metal-binding, Nucleotide-binding, Pyridoxal phosphate

Enzyme and pathway databases

BioCyciARA:AT4G11640-MONOMER.
MetaCyc:MONOMER-14684.
BRENDAi5.1.1.18. 399.

Names & Taxonomyi

Protein namesi
Recommended name:
Serine racemase (EC:4.3.1.17, EC:4.3.1.18, EC:5.1.1.18)
Short name:
AtSR
Alternative name(s):
D-serine ammonia-lyase
D-serine dehydratase
L-serine ammonia-lyase
L-serine dehydratase
Gene namesi
Name:SR
Synonyms:SR1
Ordered Locus Names:At4g11640
ORF Names:T5C23.70
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 4

Organism-specific databases

TAIRiAT4G11640.

Pathology & Biotechi

Disruption phenotypei

Deformations and branching of pollen tubes grown in pistils.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 331331Serine racemasePRO_0000420346Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei59 – 591N6-(pyridoxal phosphate)lysineBy similarity

Proteomic databases

PaxDbiQ2PGG3.
PRIDEiQ2PGG3.

Expressioni

Tissue specificityi

Expressed in the whole plant.1 Publication

Gene expression databases

GenevisibleiQ2PGG3. AT.

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi3702.AT4G11640.1.

Structurei

3D structure databases

ProteinModelPortaliQ2PGG3.
SMRiQ2PGG3. Positions 7-323.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni237 – 2382Substrate bindingBy similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG1251. Eukaryota.
COG1171. LUCA.
HOGENOMiHOG000046974.
InParanoidiQ2PGG3.
KOiK12235.
OMAiSNADDCY.
PhylomeDBiQ2PGG3.

Family and domain databases

InterProiIPR000634. Ser/Thr_deHydtase_PyrdxlP-BS.
IPR001926. TrpB-like_PLP-dep.
[Graphical view]
PfamiPF00291. PALP. 1 hit.
[Graphical view]
SUPFAMiSSF53686. SSF53686. 1 hit.
PROSITEiPS00165. DEHYDRATASE_SER_THR. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q2PGG3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEANREKYAA DILSIKEAHD RIKPYIHRTP VLTSESLNSI SGRSLFFKCE
60 70 80 90 100
CLQKGGAFKF RGACNAVLSL DAEQAAKGVV THSSGNHAAA LSLAAKIQGI
110 120 130 140 150
PAYIVVPKGA PKCKVDNVIR YGGKVIWSEA TMSSREEIAS KVLQETGSVL
160 170 180 190 200
IHPYNDGRII SGQGTIALEL LEQIQEIDAI VVPISGGGLI SGVALAAKSI
210 220 230 240 250
KPSIRIIAAE PKGADDAAQS KVAGKIITLP VTNTIADGLR ASLGDLTWPV
260 270 280 290 300
VRDLVDDVVT LEECEIIEAM KMCYEILKVS VEPSGAIGLA AVLSNSFRNN
310 320 330
PSCRDCKNIG IVLSGGNVDL GSLWDSFKSS K
Length:331
Mass (Da):35,068
Last modified:February 7, 2006 - v1
Checksum:iF4FC4EE39DD60A7A
GO

Sequence cautioni

The sequence CAB39935.1 differs from that shown. Reason: Erroneous gene model prediction. Curated
The sequence CAB78207.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB206823 mRNA. Translation: BAE72067.1.
AL049500 Genomic DNA. Translation: CAB39935.1. Sequence problems.
AL161532 Genomic DNA. Translation: CAB78207.1. Sequence problems.
CP002687 Genomic DNA. Translation: AEE83032.1.
PIRiT04211.
RefSeqiNP_192901.2. NM_117233.2.
UniGeneiAt.33551.

Genome annotation databases

EnsemblPlantsiAT4G11640.1; AT4G11640.1; AT4G11640.
GeneIDi826769.
GrameneiAT4G11640.1; AT4G11640.1; AT4G11640.
KEGGiath:AT4G11640.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB206823 mRNA. Translation: BAE72067.1.
AL049500 Genomic DNA. Translation: CAB39935.1. Sequence problems.
AL161532 Genomic DNA. Translation: CAB78207.1. Sequence problems.
CP002687 Genomic DNA. Translation: AEE83032.1.
PIRiT04211.
RefSeqiNP_192901.2. NM_117233.2.
UniGeneiAt.33551.

3D structure databases

ProteinModelPortaliQ2PGG3.
SMRiQ2PGG3. Positions 7-323.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi3702.AT4G11640.1.

Proteomic databases

PaxDbiQ2PGG3.
PRIDEiQ2PGG3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT4G11640.1; AT4G11640.1; AT4G11640.
GeneIDi826769.
GrameneiAT4G11640.1; AT4G11640.1; AT4G11640.
KEGGiath:AT4G11640.

Organism-specific databases

TAIRiAT4G11640.

Phylogenomic databases

eggNOGiKOG1251. Eukaryota.
COG1171. LUCA.
HOGENOMiHOG000046974.
InParanoidiQ2PGG3.
KOiK12235.
OMAiSNADDCY.
PhylomeDBiQ2PGG3.

Enzyme and pathway databases

BioCyciARA:AT4G11640-MONOMER.
MetaCyc:MONOMER-14684.
BRENDAi5.1.1.18. 399.

Miscellaneous databases

PROiQ2PGG3.

Gene expression databases

GenevisibleiQ2PGG3. AT.

Family and domain databases

InterProiIPR000634. Ser/Thr_deHydtase_PyrdxlP-BS.
IPR001926. TrpB-like_PLP-dep.
[Graphical view]
PfamiPF00291. PALP. 1 hit.
[Graphical view]
SUPFAMiSSF53686. SSF53686. 1 hit.
PROSITEiPS00165. DEHYDRATASE_SER_THR. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Molecular and biochemical characterization of a serine racemase from Arabidopsis thaliana."
    Fujitani Y., Nakajima N., Ishihara K., Oikawa T., Ito K., Sugimoto M.
    Phytochemistry 67:668-674(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, TISSUE SPECIFICITY.
    Strain: cv. Columbia.
  2. "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana."
    Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M., de Simone V., Obermaier B.
    , Mache R., Mueller M., Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B., Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K., Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W., Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A., Martienssen R., McCombie W.R.
    Nature 402:769-777(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Glutamate receptor-like genes form Ca2+ channels in pollen tubes and are regulated by pistil D-serine."
    Michard E., Lima P.T., Borges F., Silva A.C., Portes M.T., Carvalho J.E., Gilliham M., Liu L.H., Obermeyer G., Feijo J.A.
    Science 332:434-437(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: DISRUPTION PHENOTYPE.

Entry informationi

Entry nameiSRR_ARATH
AccessioniPrimary (citable) accession number: Q2PGG3
Secondary accession number(s): Q9T0D1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 28, 2012
Last sequence update: February 7, 2006
Last modified: February 17, 2016
This is version 73 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Allosteric enzyme, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.