UniProtKB - O49485 (SERA1_ARATH)
Protein
D-3-phosphoglycerate dehydrogenase 1, chloroplastic
Gene
PGDH1
Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Functioni
Involved in the plastidial phosphorylated pathway of serine biosynthesis (PPSB). Required for mature pollen development.2 Publications
Catalytic activityi
- EC:1.1.1.951 Publication
Activity regulationi
Partially inhibited by 5 mM serine.1 Publication
Kineticsi
- KM=1.308 mM for 3-phospho-D-glycerate (at pH 8.1)1 Publication
- KM=0.39 mM for NAD+ (at pH 8.1)1 Publication
- KM=2.11 mM for 3-phospho-D-glycerate (at pH 7.2)1 Publication
- KM=0.377 mM for NAD+ (at pH 7.2)1 Publication
- Vmax=165 µmol/min/mg enzyme (at pH 8.1)1 Publication
- Vmax=109.1 µmol/min/mg enzyme (at pH 7.2)1 Publication
: L-serine biosynthesis Pathwayi
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:
- D-3-phosphoglycerate dehydrogenase 1, chloroplastic (PGDH1), D-3-phosphoglycerate dehydrogenase 2, chloroplastic (PGDH2), D-3-phosphoglycerate dehydrogenase 3, chloroplastic (PGDH3), D-3-phosphoglycerate dehydrogenase (AXX17_At1g18640), D-3-phosphoglycerate dehydrogenase (AXX17_At4g39120), D-3-phosphoglycerate dehydrogenase (AXX17_At3g20680)
- Phosphoserine aminotransferase 1, chloroplastic (PSAT1), Phosphoserine aminotransferase 2, chloroplastic (PSAT2), Phosphoserine aminotransferase (AXX17_At2g12910), Phosphoserine aminotransferase (AXX17_At4g40680)
- Phosphoserine phosphatase, chloroplastic (PSP)
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 key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Binding sitei | 230 | NADBy similarity | 1 | |
Active sitei | 291 | By similarity | 1 | |
Binding sitei | 315 | NADBy similarity | 1 | |
Active sitei | 320 | By similarity | 1 | |
Active sitei | 339 | Proton donorBy similarity | 1 |
Regions
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Nucleotide bindingi | 210 – 211 | NADBy similarity | 2 | |
Nucleotide bindingi | 289 – 291 | NADBy similarity | 3 | |
Nucleotide bindingi | 339 – 342 | NADBy similarity | 4 |
GO - Molecular functioni
- ATP binding Source: TAIR
- NAD binding Source: InterPro
- phosphoglycerate dehydrogenase activity Source: GO_Central
GO - Biological processi
- cellular amino acid metabolic process Source: GO_Central
- embryo development ending in seed dormancy Source: TAIR
- L-serine biosynthetic process Source: InterPro
- megagametogenesis Source: TAIR
- pollen development Source: TAIR
Keywordsi
Molecular function | Oxidoreductase |
Ligand | NAD |
Enzyme and pathway databases
BioCyci | ARA:AT4G34200-MONOMER |
Reactomei | R-ATH-977347 Serine biosynthesis |
UniPathwayi | UPA00135;UER00196 |
Names & Taxonomyi
Protein namesi | Recommended name: D-3-phosphoglycerate dehydrogenase 1, chloroplastic (EC:1.1.1.951 Publication)Alternative name(s): Protein EMBRYO SAC DEVELOPMENT ARREST 9 |
Gene namesi | Name:PGDH1 Synonyms:EDA9 Ordered Locus Names:At4g34200 ORF Names:F10M10.7 |
Organismi | Arabidopsis thaliana (Mouse-ear cress) |
Taxonomic identifieri | 3702 [NCBI] |
Taxonomic lineagei | Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › Gunneridae › Pentapetalae › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis |
Proteomesi |
|
Organism-specific databases
Araporti | AT4G34200 |
TAIRi | locus:2124266 AT4G34200 |
Subcellular locationi
Chloroplast
- chloroplast 2 Publications
Chloroplast
- chloroplast Source: TAIR
- chloroplast stroma Source: TAIR
Mitochondrion
- mitochondrion Source: TAIR
Other locations
Keywords - Cellular componenti
Chloroplast, PlastidPathology & Biotechi
Disruption phenotypei
Embryo lethal when homozygous.2 Publications
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Transit peptidei | 1 – 54 | ChloroplastCuratedAdd BLAST | 54 | |
ChainiPRO_0000430236 | 55 – 603 | D-3-phosphoglycerate dehydrogenase 1, chloroplasticAdd BLAST | 549 |
Proteomic databases
PaxDbi | O49485 |
PRIDEi | O49485 |
ProMEXi | O49485 |
PTM databases
SwissPalmi | O49485 |
Expressioni
Tissue specificityi
Ubiquitous, but highly expressed in roots. Expressed in vasculature, root and shoot meristems, distal part of cotyledons and leaves, anther, stigma and pollen grains. Detected at the tip of the cotyledons in late embryos.2 Publications
Inductioni
Up-regulated in the aerial parts by dark treatment, high CO2 levels and necrotrophic pathogen infection.2 Publications
Gene expression databases
ExpressionAtlasi | O49485 baseline and differential |
Genevisiblei | O49485 AT |
Interactioni
Protein-protein interaction databases
BioGridi | 14850, 1 interactor |
IntActi | O49485, 1 interactor |
STRINGi | 3702.AT4G34200.1 |
Structurei
3D structure databases
ProteinModelPortali | O49485 |
SMRi | O49485 |
ModBasei | Search... |
MobiDBi | Search... |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 531 – 603 | ACTPROSITE-ProRule annotationAdd BLAST | 73 |
Compositional bias
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Compositional biasi | 153 – 185 | Ala-richAdd BLAST | 33 |
Sequence similaritiesi
Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family.Curated
Keywords - Domaini
Transit peptidePhylogenomic databases
eggNOGi | KOG0068 Eukaryota COG0111 LUCA |
HOGENOMi | HOG000136693 |
InParanoidi | O49485 |
KOi | K00058 |
OMAi | NIAGMQV |
OrthoDBi | 911009at2759 |
PhylomeDBi | O49485 |
Family and domain databases
Gene3Di | 3.30.1330.90, 1 hit |
InterProi | View protein in InterPro IPR002912 ACT_dom IPR015878 Ado_hCys_hydrolase_NAD-bd IPR029009 ASB_dom_sf IPR006139 D-isomer_2_OHA_DH_cat_dom IPR029753 D-isomer_DH_CS IPR029752 D-isomer_DH_CS1 IPR006140 D-isomer_DH_NAD-bd IPR036291 NAD(P)-bd_dom_sf IPR006236 PGDH |
Pfami | View protein in Pfam PF00389 2-Hacid_dh, 1 hit PF02826 2-Hacid_dh_C, 1 hit PF01842 ACT, 1 hit |
SMARTi | View protein in SMART SM00997 AdoHcyase_NAD, 1 hit |
SUPFAMi | SSF143548 SSF143548, 1 hit SSF51735 SSF51735, 1 hit |
TIGRFAMsi | TIGR01327 PGDH, 1 hit |
PROSITEi | View protein in PROSITE PS51671 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 |
i Sequence
Sequence statusi: Complete.
: The displayed sequence is further processed into a mature form. Sequence processingi
O49485-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MSATAAASSS IAVATNSLRN VTLSSRSPLP SAISVAFPSR GRNTLQRRLV
60 70 80 90 100
LVSCSTGDGS KPTILVAEKL GDAGIKLLED VANVDCSYNM TPEELNIKIS
110 120 130 140 150
LCDALIVRSG TKVGREVFES SHGRLKVVGR AGVGIDNVDL SAATEFGCLV
160 170 180 190 200
VNAPTANTIA AAEHGIALMA AMARNVAQAD ASVKAGEWKR NKYVGVSLVG
210 220 230 240 250
KTLAVLGFGK VGTEVARRAK GLGMRVIAHD PYAPADRAHA IGVDLVSFDE
260 270 280 290 300
ALATADFISL HMPLTPTTSK ILNDETFAKM KKGVRIVNVA RGGVIDEDAL
310 320 330 340 350
VRALDAGIVA QAALDVFTKE PPAKDSKLVQ HERVTVTPHL GASTMEAQEG
360 370 380 390 400
VAIEIAEAVV GALNGELAAT AVNAPMVSAE VLTELKPYVV LAEKLGRLAV
410 420 430 440 450
QLVAGGSGVK NAKITYASAR ATDDLDTRLL RAMITKGIIE PISDVYVNLV
460 470 480 490 500
NADFTAKQRG LRLSEERVLL DGSPESPLET ITVQLSNVES KFASSLSESG
510 520 530 540 550
EVKVEGKVKD GVPHLTKVGS FEVDVTLEGS IILCRQVDQP GMIGTVGSIL
560 570 580 590 600
GESNVNVNFM SVGRIAPRKQ AIMAIGVDDI PSKETLKKIG EIPAVEEFVF
LKL
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 279 | K → N in AAM60833 (Ref. 4) Curated | 1 | |
Sequence conflicti | 354 | E → K in AAM60833 (Ref. 4) Curated | 1 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AL021961 Genomic DNA Translation: CAA17552.1 AL161585 Genomic DNA Translation: CAB80137.1 CP002687 Genomic DNA Translation: AEE86339.1 AY063810 mRNA Translation: AAL36166.1 AY150462 mRNA Translation: AAN12903.1 AY084236 mRNA Translation: AAM60833.1 |
PIRi | T05416 |
RefSeqi | NP_195146.1, NM_119583.4 |
UniGenei | At.21335 At.74573 |
Genome annotation databases
EnsemblPlantsi | AT4G34200.1; AT4G34200.1; AT4G34200 |
GeneIDi | 829568 |
Gramenei | AT4G34200.1; AT4G34200.1; AT4G34200 |
KEGGi | ath:AT4G34200 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AL021961 Genomic DNA Translation: CAA17552.1 AL161585 Genomic DNA Translation: CAB80137.1 CP002687 Genomic DNA Translation: AEE86339.1 AY063810 mRNA Translation: AAL36166.1 AY150462 mRNA Translation: AAN12903.1 AY084236 mRNA Translation: AAM60833.1 |
PIRi | T05416 |
RefSeqi | NP_195146.1, NM_119583.4 |
UniGenei | At.21335 At.74573 |
3D structure databases
ProteinModelPortali | O49485 |
SMRi | O49485 |
ModBasei | Search... |
MobiDBi | Search... |
Protein-protein interaction databases
BioGridi | 14850, 1 interactor |
IntActi | O49485, 1 interactor |
STRINGi | 3702.AT4G34200.1 |
PTM databases
SwissPalmi | O49485 |
Proteomic databases
PaxDbi | O49485 |
PRIDEi | O49485 |
ProMEXi | O49485 |
Protocols and materials databases
Structural Biology Knowledgebase | Search... |
Genome annotation databases
EnsemblPlantsi | AT4G34200.1; AT4G34200.1; AT4G34200 |
GeneIDi | 829568 |
Gramenei | AT4G34200.1; AT4G34200.1; AT4G34200 |
KEGGi | ath:AT4G34200 |
Organism-specific databases
Araporti | AT4G34200 |
TAIRi | locus:2124266 AT4G34200 |
Phylogenomic databases
eggNOGi | KOG0068 Eukaryota COG0111 LUCA |
HOGENOMi | HOG000136693 |
InParanoidi | O49485 |
KOi | K00058 |
OMAi | NIAGMQV |
OrthoDBi | 911009at2759 |
PhylomeDBi | O49485 |
Enzyme and pathway databases
UniPathwayi | UPA00135;UER00196 |
BioCyci | ARA:AT4G34200-MONOMER |
Reactomei | R-ATH-977347 Serine biosynthesis |
Miscellaneous databases
PROi | PR:O49485 |
Gene expression databases
ExpressionAtlasi | O49485 baseline and differential |
Genevisiblei | O49485 AT |
Family and domain databases
Gene3Di | 3.30.1330.90, 1 hit |
InterProi | View protein in InterPro IPR002912 ACT_dom IPR015878 Ado_hCys_hydrolase_NAD-bd IPR029009 ASB_dom_sf IPR006139 D-isomer_2_OHA_DH_cat_dom IPR029753 D-isomer_DH_CS IPR029752 D-isomer_DH_CS1 IPR006140 D-isomer_DH_NAD-bd IPR036291 NAD(P)-bd_dom_sf IPR006236 PGDH |
Pfami | View protein in Pfam PF00389 2-Hacid_dh, 1 hit PF02826 2-Hacid_dh_C, 1 hit PF01842 ACT, 1 hit |
SMARTi | View protein in SMART SM00997 AdoHcyase_NAD, 1 hit |
SUPFAMi | SSF143548 SSF143548, 1 hit SSF51735 SSF51735, 1 hit |
TIGRFAMsi | TIGR01327 PGDH, 1 hit |
PROSITEi | View protein in PROSITE PS51671 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 |
ProtoNeti | Search... |
Entry informationi
Entry namei | SERA1_ARATH | |
Accessioni | O49485Primary (citable) accession number: O49485 Secondary accession number(s): Q8LGJ6 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | September 3, 2014 |
Last sequence update: | June 1, 1998 | |
Last modified: | January 16, 2019 | |
This is version 146 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Plant Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
Complete proteome, Reference proteomeDocuments
- SIMILARITY comments
Index of protein domains and families - Arabidopsis thaliana
Arabidopsis thaliana: entries and gene names - PATHWAY comments
Index of metabolic and biosynthesis pathways