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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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei78 – 781NADBy similarity
Binding sitei175 – 1751NADBy similarity
Binding sitei207 – 2071NAD; via carbonyl oxygenBy similarity
Active sitei236 – 2361By similarity
Binding sitei260 – 2601NADBy similarity
Active sitei265 – 2651By similarity
Active sitei283 – 2831Proton donorBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi155 – 1562NADBy similarity
Nucleotide bindingi234 – 2363NADBy similarity
Nucleotide bindingi283 – 2864NADBy similarity

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

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)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 533532D-3-phosphoglycerate dehydrogenasePRO_0000318300Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanineBy similarity
Modified residuei14 – 141PhosphoserineBy similarity
Modified residuei58 – 581N6-acetyllysineBy similarity
Modified residuei78 – 781PhosphothreonineBy similarity

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PaxDbiA5GFY8.
PRIDEiA5GFY8.

Expressioni

Gene expression databases

GenevisibleiA5GFY8. SS.

Interactioni

Subunit structurei

Homotetramer.By similarity

Protein-protein interaction databases

STRINGi9823.ENSSSCP00000007163.

Structurei

3D structure databases

ProteinModelPortaliA5GFY8.
SMRiA5GFY8. Positions 6-307.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG0068. Eukaryota.
COG0111. LUCA.
GeneTreeiENSGT00840000129939.
HOGENOMiHOG000136693.
HOVERGENiHBG054241.
InParanoidiA5GFY8.
KOiK00058.
OMAiDNTFAQC.
OrthoDBiEOG7JT6WT.
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.
SMRiA5GFY8. Positions 6-307.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9823.ENSSSCP00000007163.

Proteomic databases

PaxDbiA5GFY8.
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.
OrthoDBiEOG7JT6WT.
TreeFamiTF314548.

Enzyme and pathway databases

UniPathwayiUPA00135; UER00196.

Gene expression databases

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...

Publicationsi

  1. Porcine genome sequencing project
    Submitted (MAY-2007) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

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: June 8, 2016
This is version 74 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.