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Protein

D-3-phosphoglycerate dehydrogenase 1

Gene

SER3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

3-phospho-D-glycerate + NAD+ = 3-phosphonooxypyruvate + NADH.
2-hydroxyglutarate + NAD+ = 2-oxoglutarate + NADH.

Pathwayi: L-serine biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes L-serine from 3-phospho-D-glycerate.
Proteins known to be involved in the 3 steps of the subpathway in this organism are:
  1. D-3-phosphoglycerate dehydrogenase 1 (SER3), D-3-phosphoglycerate dehydrogenase 2 (SER33)
  2. Phosphoserine aminotransferase (SER1)
  3. Phosphoserine phosphatase (SER2)
This subpathway is part of the pathway L-serine biosynthesis, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-serine from 3-phospho-D-glycerate, the pathway L-serine biosynthesis and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei228 – 2281NADBy similarity
Active sitei287 – 2871By similarity
Binding sitei311 – 3111NADBy similarity
Active sitei316 – 3161By similarity
Active sitei347 – 3471Proton donorBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi208 – 2092NADBy similarity
Nucleotide bindingi285 – 2873NADBy similarity
Nucleotide bindingi347 – 3504NADBy similarity

GO - Molecular functioni

  • alpha-ketoglutarate reductase activity Source: SGD
  • amino acid binding Source: InterPro
  • identical protein binding Source: IntAct
  • NAD binding Source: InterPro
  • phosphoglycerate dehydrogenase activity Source: SGD

GO - Biological processi

  • L-serine biosynthetic process Source: UniProtKB-KW
  • serine family amino acid biosynthetic process Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Amino-acid biosynthesis, Serine biosynthesis

Keywords - Ligandi

NAD

Enzyme and pathway databases

BioCyciYEAST:YER081W-MONOMER.
ReactomeiR-SCE-977347. Serine biosynthesis.
UniPathwayiUPA00135; UER00196.

Names & Taxonomyi

Protein namesi
Recommended name:
D-3-phosphoglycerate dehydrogenase 1 (EC:1.1.1.95)
Short name:
3-PGDH 1
Gene namesi
Name:SER3
Ordered Locus Names:YER081W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome V

Organism-specific databases

EuPathDBiFungiDB:YER081W.
SGDiS000000883. SER3.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 469468D-3-phosphoglycerate dehydrogenase 1PRO_0000076018Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei22 – 221PhosphoserineCombined sources
Modified residuei29 – 291PhosphoserineBy similarity
Modified residuei33 – 331PhosphoserineBy similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP40054.
PRIDEiP40054.

PTM databases

iPTMnetiP40054.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
itself3EBI-16961,EBI-16961
SER33P405104EBI-16961,EBI-16821

GO - Molecular functioni

  • identical protein binding Source: IntAct

Protein-protein interaction databases

BioGridi36826. 37 interactions.
DIPiDIP-5336N.
IntActiP40054. 21 interactions.
MINTiMINT-404076.

Structurei

3D structure databases

ProteinModelPortaliP40054.
SMRiP40054. Positions 59-469.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini399 – 46971ACTPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 ACT domain.PROSITE-ProRule annotation

Phylogenomic databases

GeneTreeiENSGT00530000063021.
HOGENOMiHOG000136696.
InParanoidiP40054.
KOiK00058.
OMAiAIDEDHV.
OrthoDBiEOG092C2PBN.

Family and domain databases

Gene3Di3.40.50.720. 2 hits.
InterProiIPR002912. ACT_dom.
IPR006139. D-isomer_2_OHA_DH_cat_dom.
IPR029753. D-isomer_DH_CS.
IPR029752. D-isomer_DH_CS1.
IPR006140. D-isomer_DH_NAD-bd.
IPR016040. NAD(P)-bd_dom.
IPR029015. PGDH_2.
[Graphical view]
PANTHERiPTHR10996:SF165. PTHR10996:SF165. 1 hit.
PfamiPF00389. 2-Hacid_dh. 1 hit.
PF02826. 2-Hacid_dh_C. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.
PROSITEiPS51671. ACT. 1 hit.
PS00065. D_2_HYDROXYACID_DH_1. 1 hit.
PS00670. D_2_HYDROXYACID_DH_2. 1 hit.
PS00671. D_2_HYDROXYACID_DH_3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P40054-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTSIDINNLQ NTFQQAMNMS GSPGAVCTSP TQSFMNTVPQ RLNAVKHPKI
60 70 80 90 100
LKPFSTGDMK ILLLENVNQT AITIFEEQGY QVEFYKSSLP EEELIEKIKD
110 120 130 140 150
VHAIGIRSKT RLTSNVLQHA KNLVCIGCFC IGTNQVDLDY ATSRGIAVFN
160 170 180 190 200
SPFSNSRSVA ELVIAEIISL ARQLGDRSIE LHTGTWNKVA ARCWEVRGKT
210 220 230 240 250
LGIIGYGHIG SQLSVLAEAM GLHVLYYDIV TIMALGTARQ VSTLDELLNK
260 270 280 290 300
SDFVTLHVPA TPETEKMLSA PQFAAMKDGA YVINASRGTV VDIPSLIQAV
310 320 330 340 350
KANKIAGAAL DVYPHEPAKN GEGSFNDELN SWTSELVSLP NIILTPHIGG
360 370 380 390 400
STEEAQSSIG IEVATALSKY INEGNSVGSV NFPEVALKSL SYDQENTVRV
410 420 430 440 450
LYIHQNVPGV LKTVNDILSN HNIEKQFSDS NGEIAYLMAD ISSVDQSDIK
460
DIYEQLNQTS AKISIRLLY
Length:469
Mass (Da):51,193
Last modified:February 1, 1995 - v1
Checksum:iE1E69070BF41A87C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U18839 Genomic DNA. Translation: AAB64636.1.
BK006939 Genomic DNA. Translation: DAA07742.1.
PIRiS50584.
RefSeqiNP_011004.3. NM_001178972.3.

Genome annotation databases

EnsemblFungiiYER081W; YER081W; YER081W.
GeneIDi856814.
KEGGisce:YER081W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U18839 Genomic DNA. Translation: AAB64636.1.
BK006939 Genomic DNA. Translation: DAA07742.1.
PIRiS50584.
RefSeqiNP_011004.3. NM_001178972.3.

3D structure databases

ProteinModelPortaliP40054.
SMRiP40054. Positions 59-469.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36826. 37 interactions.
DIPiDIP-5336N.
IntActiP40054. 21 interactions.
MINTiMINT-404076.

PTM databases

iPTMnetiP40054.

Proteomic databases

MaxQBiP40054.
PRIDEiP40054.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYER081W; YER081W; YER081W.
GeneIDi856814.
KEGGisce:YER081W.

Organism-specific databases

EuPathDBiFungiDB:YER081W.
SGDiS000000883. SER3.

Phylogenomic databases

GeneTreeiENSGT00530000063021.
HOGENOMiHOG000136696.
InParanoidiP40054.
KOiK00058.
OMAiAIDEDHV.
OrthoDBiEOG092C2PBN.

Enzyme and pathway databases

UniPathwayiUPA00135; UER00196.
BioCyciYEAST:YER081W-MONOMER.
ReactomeiR-SCE-977347. Serine biosynthesis.

Miscellaneous databases

PROiP40054.

Family and domain databases

Gene3Di3.40.50.720. 2 hits.
InterProiIPR002912. ACT_dom.
IPR006139. D-isomer_2_OHA_DH_cat_dom.
IPR029753. D-isomer_DH_CS.
IPR029752. D-isomer_DH_CS1.
IPR006140. D-isomer_DH_NAD-bd.
IPR016040. NAD(P)-bd_dom.
IPR029015. PGDH_2.
[Graphical view]
PANTHERiPTHR10996:SF165. PTHR10996:SF165. 1 hit.
PfamiPF00389. 2-Hacid_dh. 1 hit.
PF02826. 2-Hacid_dh_C. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.
PROSITEiPS51671. ACT. 1 hit.
PS00065. D_2_HYDROXYACID_DH_1. 1 hit.
PS00670. D_2_HYDROXYACID_DH_2. 1 hit.
PS00671. D_2_HYDROXYACID_DH_3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSERA_YEAST
AccessioniPrimary (citable) accession number: P40054
Secondary accession number(s): D3DLY8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: September 7, 2016
This is version 159 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 7670 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome V
    Yeast (Saccharomyces cerevisiae) chromosome V: entries and gene names

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.