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Protein

D-3-phosphoglycerate dehydrogenase

Gene

PHGDH

Organism
Sus scrofa (Pig)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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 (PHGDH)
  2. no protein annotated in this organism
  3. no protein annotated in this organism
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)DescriptionActionsGraphical viewLength
Binding sitei78NADBy similarity1
Binding sitei175NADBy similarity1
Binding sitei207NAD; via carbonyl oxygenBy similarity1
Active sitei236By similarity1
Binding sitei260NADBy similarity1
Active sitei265By similarity1
Active sitei283Proton donorBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi155 – 156NADBy similarity2
Nucleotide bindingi234 – 236NADBy similarity3
Nucleotide bindingi283 – 286NADBy similarity4

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Amino-acid biosynthesis, Serine biosynthesis

Keywords - Ligandi

NAD

Enzyme and pathway databases

ReactomeiR-SSC-977347. Serine biosynthesis.
UniPathwayiUPA00135; UER00196.

Names & Taxonomyi

Protein namesi
Recommended name:
D-3-phosphoglycerate dehydrogenase (EC:1.1.1.95)
Short name:
3-PGDH
Gene namesi
Name:PHGDH
OrganismiSus scrofa (Pig)
Taxonomic identifieri9823 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaLaurasiatheriaCetartiodactylaSuinaSuidaeSus
Proteomesi
  • UP000008227 Componenti: Chromosome 4

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00003183002 – 533D-3-phosphoglycerate dehydrogenaseAdd BLAST532

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanineBy similarity1
Modified residuei14PhosphoserineBy similarity1
Modified residuei58N6-acetyllysineBy similarity1
Modified residuei78PhosphothreonineBy similarity1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PaxDbiA5GFY8.
PeptideAtlasiA5GFY8.
PRIDEiA5GFY8.

Expressioni

Gene expression databases

BgeeiENSSSCG00000006717.
GenevisibleiA5GFY8. SS.

Interactioni

Subunit structurei

Homotetramer.By similarity

Protein-protein interaction databases

STRINGi9823.ENSSSCP00000007163.

Structurei

3D structure databases

ProteinModelPortaliA5GFY8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG0068. Eukaryota.
COG0111. LUCA.
GeneTreeiENSGT00840000129939.
HOGENOMiHOG000136693.
HOVERGENiHBG054241.
InParanoidiA5GFY8.
KOiK00058.
OMAiDNTFAQC.
OrthoDBiEOG091G0C5D.
TreeFamiTF314548.

Family and domain databases

Gene3Di3.30.1330.90. 1 hit.
3.40.50.720. 2 hits.
InterProiIPR029009. ASB_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.
IPR006236. PGDH.
[Graphical view]
PfamiPF00389. 2-Hacid_dh. 1 hit.
PF02826. 2-Hacid_dh_C. 1 hit.
[Graphical view]
SUPFAMiSSF143548. SSF143548. 1 hit.
SSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR01327. PGDH. 1 hit.
PROSITEiPS00065. 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.

A5GFY8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAFANLRKVL ISDSLDPCCR EILQDGGLQV VEKQNLSKEE LIAELQDCEG
60 70 80 90 100
LIVRSATKVT SDVINAAKKL QVVGRAGTGV DNVDLEAATR KGILVMNTPN
110 120 130 140 150
GNSLSAAELT CGMILCLARQ IPQATASMKD GKWERKKFMG TELNGKVLGI
160 170 180 190 200
LGLGRIGREV ATRMQSFGMK TIGYDPIIAP EVSASFGVQQ LPLEEIWPLC
210 220 230 240 250
DFITVHTPLL PSTTGLLNDS TFALCKKGVR VVNCARGGIV DEGALLRALQ
260 270 280 290 300
SGQCAGAALD VFTEEPPRDR ALVDHEKVIS CPHLGASTRE AQSRCGEEIA
310 320 330 340 350
IQFVDMVKGR SLAGVVNAQA LTSAFSPHTK PWIGLAEALG ALMQAWAGSP
360 370 380 390 400
KGTIQVVTQG TSLKNSGTCL SPAVIVGLLK EASHRADVNL VNAKLLEKEA
410 420 430 440 450
GLHVTTSHNP AAPEEQGGAE CFLTVALAGA PYQAVGLVQG TAPMLHALNG
460 470 480 490 500
AVFRPEVPLR RGLPLLLFRA QPSNPTMLPT MIGLLAEARV QLLSYQTSVV
510 520 530
SDGETWHVMA ISSLLPSLEP WKQHVTEAFQ FHF
Length:533
Mass (Da):56,810
Last modified:June 12, 2007 - v1
Checksum:i2D80F1809E1579BE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CR956647 Genomic DNA. Translation: CAN13230.1.
RefSeqiNP_001116634.1. NM_001123162.1.
UniGeneiSsc.21431.

Genome annotation databases

EnsembliENSSSCT00000007358; ENSSSCP00000007163; ENSSSCG00000006717.
GeneIDi100144529.
KEGGissc:100144529.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CR956647 Genomic DNA. Translation: CAN13230.1.
RefSeqiNP_001116634.1. NM_001123162.1.
UniGeneiSsc.21431.

3D structure databases

ProteinModelPortaliA5GFY8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9823.ENSSSCP00000007163.

Proteomic databases

PaxDbiA5GFY8.
PeptideAtlasiA5GFY8.
PRIDEiA5GFY8.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSSSCT00000007358; ENSSSCP00000007163; ENSSSCG00000006717.
GeneIDi100144529.
KEGGissc:100144529.

Organism-specific databases

CTDi26227.

Phylogenomic databases

eggNOGiKOG0068. Eukaryota.
COG0111. LUCA.
GeneTreeiENSGT00840000129939.
HOGENOMiHOG000136693.
HOVERGENiHBG054241.
InParanoidiA5GFY8.
KOiK00058.
OMAiDNTFAQC.
OrthoDBiEOG091G0C5D.
TreeFamiTF314548.

Enzyme and pathway databases

UniPathwayiUPA00135; UER00196.
ReactomeiR-SSC-977347. Serine biosynthesis.

Gene expression databases

BgeeiENSSSCG00000006717.
GenevisibleiA5GFY8. SS.

Family and domain databases

Gene3Di3.30.1330.90. 1 hit.
3.40.50.720. 2 hits.
InterProiIPR029009. ASB_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.
IPR006236. PGDH.
[Graphical view]
PfamiPF00389. 2-Hacid_dh. 1 hit.
PF02826. 2-Hacid_dh_C. 1 hit.
[Graphical view]
SUPFAMiSSF143548. SSF143548. 1 hit.
SSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR01327. PGDH. 1 hit.
PROSITEiPS00065. 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_PIG
AccessioniPrimary (citable) accession number: A5GFY8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 5, 2008
Last sequence update: June 12, 2007
Last modified: October 5, 2016
This is version 77 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

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  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.