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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)DescriptionActionsGraphical viewLength
Binding sitei25ATP1
Binding sitei52ATP1
Binding sitei53ATP; via amide nitrogen1
Active sitei57Proton acceptor1
Active sitei82Proton acceptor1
Binding sitei119ATP1
Binding sitei133Substrate1
Metal bindingi208Magnesium1
Metal bindingi212Magnesium; via carbonyl oxygen1
Metal bindingi214Magnesium1

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 biosynthetic process Source: GO_Central
  • 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.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi82S → A: Loss of racemase activity. Reduces D-serine dehydratase activity by 99%. Slightly reduced L-serine dehydratase activity. 1 Publication1

Chemistry databases

ChEMBLiCHEMBL3097984.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001855881 – 323Serine racemaseAdd BLAST323

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei57Lysino-D-alanine (Lys); alternate1
Modified residuei57N6-(pyridoxal phosphate)lysine; alternate1

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.
PRIDEiO59791.

Interactioni

Subunit structurei

Homodimer.2 Publications

GO - Molecular functioni

  • protein homodimerization activity Source: UniProtKB

Protein-protein interaction databases

BioGridi275321. 5 interactors.

Chemistry databases

BindingDBiO59791.

Structurei

Secondary structure

1323
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi10 – 20Combined sources11
Turni21 – 23Combined sources3
Helixi33 – 39Combined sources7
Beta strandi41 – 47Combined sources7
Helixi48 – 50Combined sources3
Helixi52 – 54Combined sources3
Helixi57 – 65Combined sources9
Helixi70 – 75Combined sources6
Beta strandi77 – 79Combined sources3
Helixi84 – 95Combined sources12
Beta strandi100 – 105Combined sources6
Helixi110 – 118Combined sources9
Beta strandi122 – 126Combined sources5
Turni128 – 131Combined sources4
Helixi133 – 144Combined sources12
Beta strandi151 – 154Combined sources4
Helixi155 – 161Combined sources7
Helixi163 – 172Combined sources10
Beta strandi176 – 181Combined sources6
Beta strandi183 – 185Combined sources3
Helixi186 – 198Combined sources13
Beta strandi203 – 209Combined sources7
Helixi210 – 212Combined sources3
Helixi214 – 221Combined sources8
Helixi235 – 237Combined sources3
Helixi244 – 253Combined sources10
Beta strandi256 – 260Combined sources5
Helixi262 – 275Combined sources14
Helixi282 – 285Combined sources4
Helixi286 – 293Combined sources8
Helixi294 – 298Combined sources5
Beta strandi302 – 307Combined sources6
Helixi314 – 321Combined sources8

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiO59791.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni235 – 236Substrate binding2

Sequence similaritiesi

Phylogenomic databases

HOGENOMiHOG000046974.
InParanoidiO59791.
OMAiIAYWTQW.
OrthoDBiEOG092C3P3F.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1V71X-ray1.70A1-323[»]
1WTCX-ray1.90A1-323[»]
2ZPUX-ray1.70A1-323[»]
2ZR8X-ray2.20A1-323[»]
ProteinModelPortaliO59791.
SMRiO59791.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi275321. 5 interactors.

Chemistry databases

BindingDBiO59791.
ChEMBLiCHEMBL3097984.

Proteomic databases

MaxQBiO59791.
PRIDEiO59791.

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.
OMAiIAYWTQW.
OrthoDBiEOG092C3P3F.
PhylomeDBiO59791.

Enzyme and pathway databases

BRENDAi5.1.1.18. 5613.

Miscellaneous databases

EvolutionaryTraceiO59791.
PROiO59791.

Family and domain databases

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

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: November 2, 2016
This is version 121 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.