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Protein

Serine racemase

Gene

SRR

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
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.1 Publication

Catalytic activityi

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

Cofactori

pyridoxal 5'-phosphate2 Publications

Enzyme regulationi

Allosterically activated by ATP, by magnesium, and possibly also by other divalent metal cations.2 Publications

Kineticsi

  1. KM=36 mM for serine1 Publication
  1. Vmax=870 nmol/min/mg enzyme1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei25 – 251ATP
Binding sitei52 – 521ATP
Binding sitei53 – 531ATP; via amide nitrogen
Active sitei57 – 571Proton acceptor
Active sitei82 – 821Proton acceptor
Binding sitei119 – 1191ATP
Binding sitei133 – 1331Substrate
Metal bindingi208 – 2081Magnesium
Metal bindingi212 – 2121Magnesium; via carbonyl oxygen
Metal bindingi214 – 2141Magnesium

GO - Molecular functioni

  • ATP binding Source: UniProtKB
  • D-serine ammonia-lyase activity Source: UniProtKB
  • L-serine ammonia-lyase activity Source: UniProtKB
  • magnesium ion binding Source: UniProtKB
  • protein homodimerization activity Source: UniProtKB
  • pyridoxal phosphate binding Source: UniProtKB
  • serine racemase activity Source: UniProtKB

GO - Biological processi

  • D-serine metabolic process Source: UniProtKB
  • L-serine metabolic process Source: UniProtKB
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. 5613.

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
ORF Names:SPCC320.14, SPCC330.15c
OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Taxonomic identifieri284812 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
Proteomesi
  • UP000002485 Componenti: Chromosome III

Organism-specific databases

EuPathDBiFungiDB:SPCC320.14.
PomBaseiSPCC320.14.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi82 – 821S → A: Loss of racemase activity. Reduces D-serine dehydratase activity by 99%. Slightly reduced L-serine dehydratase activity. 1 Publication

Chemistry

ChEMBLiCHEMBL3097984.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 323323Serine racemasePRO_0000185588Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei57 – 571Lysino-D-alanine (Lys); alternate
Modified residuei57 – 571N6-(pyridoxal phosphate)lysine; alternate

Post-translational modificationi

Modification of the active site Lys by its substrate Ser to lysino-D-alanine reduces but does not abolish enzyme activity.

Proteomic databases

MaxQBiO59791.

Interactioni

Subunit structurei

Homodimer.2 Publications

GO - Molecular functioni

  • protein homodimerization activity Source: UniProtKB

Protein-protein interaction databases

BioGridi275321. 5 interactions.

Chemistry

BindingDBiO59791.

Structurei

Secondary structure

1
323
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi10 – 2011Combined sources
Turni21 – 233Combined sources
Helixi33 – 397Combined sources
Beta strandi41 – 477Combined sources
Helixi48 – 503Combined sources
Helixi52 – 543Combined sources
Helixi57 – 659Combined sources
Helixi70 – 756Combined sources
Beta strandi77 – 793Combined sources
Helixi84 – 9512Combined sources
Beta strandi100 – 1056Combined sources
Helixi110 – 1189Combined sources
Beta strandi122 – 1265Combined sources
Turni128 – 1314Combined sources
Helixi133 – 14412Combined sources
Beta strandi151 – 1544Combined sources
Helixi155 – 1617Combined sources
Helixi163 – 17210Combined sources
Beta strandi176 – 1816Combined sources
Beta strandi183 – 1853Combined sources
Helixi186 – 19813Combined sources
Beta strandi203 – 2097Combined sources
Helixi210 – 2123Combined sources
Helixi214 – 2218Combined sources
Helixi235 – 2373Combined sources
Helixi244 – 25310Combined sources
Beta strandi256 – 2605Combined sources
Helixi262 – 27514Combined sources
Helixi282 – 2854Combined sources
Helixi286 – 2938Combined sources
Helixi294 – 2985Combined sources
Beta strandi302 – 3076Combined sources
Helixi314 – 3218Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1V71X-ray1.70A1-323[»]
1WTCX-ray1.90A1-323[»]
2ZPUX-ray1.70A1-323[»]
2ZR8X-ray2.20A1-323[»]
ProteinModelPortaliO59791.
SMRiO59791. Positions 6-323.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO59791.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni235 – 2362Substrate binding

Sequence similaritiesi

Phylogenomic databases

HOGENOMiHOG000046974.
InParanoidiO59791.
OMAiSNADDCY.
OrthoDBiEOG70GMQ9.
PhylomeDBiO59791.

Family and domain databases

InterProiIPR001926. TrpB-like_PLP-dep.
[Graphical view]
PfamiPF00291. PALP. 1 hit.
[Graphical view]
SUPFAMiSSF53686. SSF53686. 1 hit.

Sequencei

Sequence statusi: Complete.

O59791-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSDNLVLPTY DDVASASERI KKFANKTPVL TSSTVNKEFV AEVFFKCENF
60 70 80 90 100
QKMGAFKFRG ALNALSQLNE AQRKAGVLTF SSGNHAQAIA LSAKILGIPA
110 120 130 140 150
KIIMPLDAPE AKVAATKGYG GQVIMYDRYK DDREKMAKEI SEREGLTIIP
160 170 180 190 200
PYDHPHVLAG QGTAAKELFE EVGPLDALFV CLGGGGLLSG SALAARHFAP
210 220 230 240 250
NCEVYGVEPE AGNDGQQSFR KGSIVHIDTP KTIADGAQTQ HLGNYTFSII
260 270 280 290 300
KEKVDDILTV SDEELIDCLK FYAARMKIVV EPTGCLSFAA ARAMKEKLKN
310 320
KRIGIIISGG NVDIERYAHF LSQ
Length:323
Mass (Da):35,048
Last modified:August 1, 1998 - v1
Checksum:i21187E5A69FA5348
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU329672 Genomic DNA. Translation: CAA20920.1.
PIRiT41297.
RefSeqiNP_587715.1. NM_001022710.2.

Genome annotation databases

EnsemblFungiiSPCC320.14.1; SPCC320.14.1:pep; SPCC320.14.
GeneIDi2538738.
KEGGispo:SPCC320.14.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU329672 Genomic DNA. Translation: CAA20920.1.
PIRiT41297.
RefSeqiNP_587715.1. NM_001022710.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1V71X-ray1.70A1-323[»]
1WTCX-ray1.90A1-323[»]
2ZPUX-ray1.70A1-323[»]
2ZR8X-ray2.20A1-323[»]
ProteinModelPortaliO59791.
SMRiO59791. Positions 6-323.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi275321. 5 interactions.

Chemistry

BindingDBiO59791.
ChEMBLiCHEMBL3097984.

Proteomic databases

MaxQBiO59791.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiSPCC320.14.1; SPCC320.14.1:pep; SPCC320.14.
GeneIDi2538738.
KEGGispo:SPCC320.14.

Organism-specific databases

EuPathDBiFungiDB:SPCC320.14.
PomBaseiSPCC320.14.

Phylogenomic databases

HOGENOMiHOG000046974.
InParanoidiO59791.
OMAiSNADDCY.
OrthoDBiEOG70GMQ9.
PhylomeDBiO59791.

Enzyme and pathway databases

BRENDAi5.1.1.18. 5613.

Miscellaneous databases

EvolutionaryTraceiO59791.
NextBioi20799922.
PROiO59791.

Family and domain databases

InterProiIPR001926. TrpB-like_PLP-dep.
[Graphical view]
PfamiPF00291. PALP. 1 hit.
[Graphical view]
SUPFAMiSSF53686. SSF53686. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The genome sequence of Schizosaccharomyces pombe."
    Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A., Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S., Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.
    , Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S., Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S., Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D., Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P., Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K., O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M., Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N., Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A., Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R., Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A., Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A., Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H., Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C., Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A., Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M., del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S., Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R., Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G., Nurse P.
    Nature 415:871-880(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 972 / ATCC 24843.
  2. Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL PHOSPHATE AND MAGNESIUM IONS, COFACTOR, ENZYME REGULATION, ACTIVE SITE, PYRIDOXAL PHOSPHATE AT LYS-57, SUBUNIT, IDENTIFICATION BY MASS SPECTROMETRY, LYSINO-D-ALANINE AT LYS-57.
  3. "Crystal structure of a homolog of mammalian serine racemase from Schizosaccharomyces pombe."
    Goto M., Yamauchi T., Kamiya N., Miyahara I., Yoshimura T., Mihara H., Kurihara T., Hirotsu K., Esaki N.
    J. Biol. Chem. 284:25944-25952(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL PHOSPHATE; SERINE; ATP ANALOG AND MAGNESIUM IONS, CATALYTIC ACTIVITY, FUNCTION, COFACTOR, ACTIVE SITE, PYRIDOXAL PHOSPHATE AT LYS-57, LYSINO-D-ALANINE AT LYS-57, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, ENZYME REGULATION, MUTAGENESIS OF SER-82.

Entry informationi

Entry nameiSRR_SCHPO
AccessioniPrimary (citable) accession number: O59791
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 31, 2002
Last sequence update: August 1, 1998
Last modified: May 11, 2016
This is version 116 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal 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. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
  3. 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.