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Protein

Serine racemase

Gene

Srr

Organism
Rattus norvegicus (Rat)
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. D-serine is a key coagonist with glutamate at NMDA receptors. Has dehydratase activity towards both L-serine and D-serine.2 Publications

Catalytic activityi

L-serine = D-serine.1 Publication
L-serine = pyruvate + NH3.1 Publication
D-serine = pyruvate + NH3.1 Publication

Cofactori

pyridoxal 5'-phosphate1 Publication

Enzyme regulationi

Allosterically activated by magnesium, and possibly also other divalent metal cations. Allosterically activated by ATP, ADP or GTP (By similarity). Competitively inhibited by malonate.By similarity1 Publication

Kineticsi

  1. KM=3.7 mM for L-serine1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei51 – 511ATPBy similarity
Active sitei56 – 561Proton acceptorBy similarity
Active sitei84 – 841Proton acceptorBy similarity
Binding sitei121 – 1211ATPBy similarity
Binding sitei135 – 1351SubstrateCurated
Metal bindingi210 – 2101MagnesiumBy similarity
Metal bindingi214 – 2141Magnesium; via carbonyl oxygen
Metal bindingi216 – 2161MagnesiumBy similarity

GO - Molecular functioni

  1. ATP binding Source: UniProtKB
  2. calcium ion binding Source: Ensembl
  3. D-serine ammonia-lyase activity Source: GO_Central
  4. glycine binding Source: Ensembl
  5. L-serine ammonia-lyase activity Source: GO_Central
  6. magnesium ion binding Source: UniProtKB
  7. protein homodimerization activity Source: UniProtKB
  8. pyridoxal phosphate binding Source: UniProtKB
  9. serine racemase activity Source: UniProtKB
  10. threonine racemase activity Source: Ensembl

GO - Biological processi

  1. aging Source: RGD
  2. brain development Source: RGD
  3. D-serine biosynthetic process Source: GO_Central
  4. D-serine metabolic process Source: UniProtKB
  5. L-serine metabolic process Source: UniProtKB
  6. protein homotetramerization Source: Ensembl
  7. pyruvate biosynthetic process Source: Ensembl
  8. response to drug Source: RGD
  9. response to lipopolysaccharide Source: Ensembl
  10. response to morphine Source: RGD
  11. response to organic cyclic compound Source: RGD
Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Lyase

Keywords - Ligandi

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

Enzyme and pathway databases

BRENDAi5.1.1.18. 5301.

Names & Taxonomyi

Protein namesi
Recommended name:
Serine racemase (EC:4.3.1.17, EC:4.3.1.18, EC:5.1.1.18)
Alternative name(s):
D-serine ammonia-lyase
D-serine dehydratase
L-serine ammonia-lyase
L-serine dehydratase
Gene namesi
Name:Srr
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
ProteomesiUP000002494: Chromosome 10

Organism-specific databases

RGDi735094. Srr.

Subcellular locationi

GO - Cellular componenti

  1. apical part of cell Source: RGD
  2. cytoplasm Source: RGD
  3. neuronal cell body Source: GO_Central
  4. plasma membrane Source: RGD
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 333333Serine racemasePRO_0000286173Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei56 – 561N6-(pyridoxal phosphate)lysine
Modified residuei113 – 1131S-nitrosocysteineBy similarity

Post-translational modificationi

S-nitrosylated, leading to decrease the enzyme activity.By similarity

Keywords - PTMi

S-nitrosylation

Proteomic databases

PaxDbiQ76EQ0.
PRIDEiQ76EQ0.

PTM databases

PhosphoSiteiQ76EQ0.

Expressioni

Gene expression databases

GenevestigatoriQ76EQ0.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

BioGridi257487. 1 interaction.
STRINGi10116.ENSRNOP00000050774.

Structurei

Secondary structure

1
333
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi9 – 1911Combined sources
Turni20 – 223Combined sources
Helixi32 – 387Combined sources
Beta strandi40 – 467Combined sources
Helixi47 – 493Combined sources
Helixi51 – 533Combined sources
Helixi57 – 6610Combined sources
Beta strandi70 – 734Combined sources
Beta strandi79 – 824Combined sources
Helixi86 – 9712Combined sources
Beta strandi102 – 1076Combined sources
Helixi112 – 1209Combined sources
Beta strandi124 – 1285Combined sources
Helixi134 – 14613Combined sources
Beta strandi153 – 1553Combined sources
Helixi157 – 1637Combined sources
Helixi165 – 1739Combined sources
Beta strandi179 – 1835Combined sources
Beta strandi185 – 1873Combined sources
Helixi188 – 20013Combined sources
Beta strandi204 – 2118Combined sources
Helixi212 – 2143Combined sources
Helixi216 – 2238Combined sources
Helixi238 – 2403Combined sources
Turni246 – 2483Combined sources
Helixi249 – 2557Combined sources
Beta strandi258 – 2625Combined sources
Helixi264 – 27815Combined sources
Helixi284 – 29411Combined sources
Helixi296 – 3005Combined sources
Beta strandi307 – 3126Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3HMKX-ray2.10A/B1-333[»]
3L6CX-ray2.20A/B1-333[»]
ProteinModelPortaliQ76EQ0.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ76EQ0.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni238 – 2392Substrate bindingBy similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG1171.
GeneTreeiENSGT00550000075026.
HOGENOMiHOG000046974.
HOVERGENiHBG023167.
InParanoidiQ76EQ0.
KOiK12235.
OMAiWKEEYLT.
OrthoDBiEOG7HB5B2.
PhylomeDBiQ76EQ0.
TreeFamiTF313346.

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.

Q76EQ0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MCAQYCISFA DVEKAHLNIQ DSVHLTPVLT SSILNQIAGR NLFFKCELFQ
60 70 80 90 100
KTGSFKIRGA LNAIRGLIPD TLEGKPKAVV THSSGNHGQA LTYAAKLEGI
110 120 130 140 150
PAYIVVPQTA PNCKKLAIQA YGASIVYSEP SDESRENVAQ RIIQETEGIL
160 170 180 190 200
VHPNQEPAVI AGQGTIALEV LNQVPLVDAL VVPVGGGGMV AGIAITIKTL
210 220 230 240 250
KPSVKVYAAE PSNADDCYQS KLKGELTPNL HPPETIADGV KSSIGLNTWP
260 270 280 290 300
IIRDLVDDVF TVTEDEIKYA TQLVWERMKL LIEPTAGVGL AAVLSQHFQT
310 320 330
VSPEVKNICI VLSGGNVDLT SLSWVKQAER PAP
Length:333
Mass (Da):35,693
Last modified:July 5, 2004 - v1
Checksum:iB0DDD8B7B5A8116C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB106282 mRNA. Translation: BAC84968.1.
BC082014 mRNA. Translation: AAH82014.1.
RefSeqiNP_942052.1. NM_198757.2.
XP_008766232.1. XM_008768010.1.
XP_008766233.1. XM_008768011.1.
XP_008766234.1. XM_008768012.1.
XP_008766235.1. XM_008768013.1.
XP_008766236.1. XM_008768014.1.
XP_008766237.1. XM_008768015.1.
UniGeneiRn.220332.

Genome annotation databases

EnsembliENSRNOT00000046110; ENSRNOP00000050774; ENSRNOG00000002991.
GeneIDi303306.
KEGGirno:303306.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB106282 mRNA. Translation: BAC84968.1.
BC082014 mRNA. Translation: AAH82014.1.
RefSeqiNP_942052.1. NM_198757.2.
XP_008766232.1. XM_008768010.1.
XP_008766233.1. XM_008768011.1.
XP_008766234.1. XM_008768012.1.
XP_008766235.1. XM_008768013.1.
XP_008766236.1. XM_008768014.1.
XP_008766237.1. XM_008768015.1.
UniGeneiRn.220332.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3HMKX-ray2.10A/B1-333[»]
3L6CX-ray2.20A/B1-333[»]
ProteinModelPortaliQ76EQ0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi257487. 1 interaction.
STRINGi10116.ENSRNOP00000050774.

PTM databases

PhosphoSiteiQ76EQ0.

Proteomic databases

PaxDbiQ76EQ0.
PRIDEiQ76EQ0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000046110; ENSRNOP00000050774; ENSRNOG00000002991.
GeneIDi303306.
KEGGirno:303306.

Organism-specific databases

CTDi63826.
RGDi735094. Srr.

Phylogenomic databases

eggNOGiCOG1171.
GeneTreeiENSGT00550000075026.
HOGENOMiHOG000046974.
HOVERGENiHBG023167.
InParanoidiQ76EQ0.
KOiK12235.
OMAiWKEEYLT.
OrthoDBiEOG7HB5B2.
PhylomeDBiQ76EQ0.
TreeFamiTF313346.

Enzyme and pathway databases

BRENDAi5.1.1.18. 5301.

Miscellaneous databases

EvolutionaryTraceiQ76EQ0.
NextBioi651104.
PROiQ76EQ0.

Gene expression databases

GenevestigatoriQ76EQ0.

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. "Rat cerebral serine racemase: amino acid deletion and truncation at carboxy terminus."
    Konno R.
    Neurosci. Lett. 349:111-114(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: Sprague-Dawley.
  2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Testis.
  3. "Glia-derived D-serine controls NMDA receptor activity and synaptic memory."
    Panatier A., Theodosis D.T., Mothet J.P., Touquet B., Pollegioni L., Poulain D.A., Oliet S.H.
    Cell 125:775-784(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  4. "The structure of mammalian serine racemase: evidence for conformational changes upon inhibitor binding."
    Smith M.A., Mack V., Ebneth A., Moraes I., Felicetti B., Wood M., Schonfeld D., Mather O., Cesura A., Barker J.
    J. Biol. Chem. 285:12873-12881(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 3-333 IN COMPLEX WITH MANGANESE IONS; MALONATE AND PYRIDOXAL PHOSPHATE, COFACTOR, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, SUBUNIT.

Entry informationi

Entry nameiSRR_RAT
AccessioniPrimary (citable) accession number: Q76EQ0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 2007
Last sequence update: July 5, 2004
Last modified: March 4, 2015
This is version 83 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Allosteric enzyme, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.