UniProtKB - O04130 (SERA2_ARATH)
Protein
D-3-phosphoglycerate dehydrogenase 2, chloroplastic
Gene
PGDH2
Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Functioni
Involved in the plastidial phosphorylated pathway of serine biosynthesis (PPSB).3 Publications
Catalytic activityi
- EC:1.1.1.952 Publications
Activity regulationi
Inhibited by 90 µM 3-phosphonooxypyruvate, but not by Ser, Thr, Val, Gly Trp, O-acetyl-L-Ser and Cys.2 Publications
Kineticsi
- KM=1.926 mM for 3-phospho-D-glycerate (at pH 7.2)2 Publications
- KM=0.899 mM for 3-phospho-D-glycerate (at pH 8.1)2 Publications
- KM=1.19 mM for 3-phospho-D-glycerate (at pH 9.0)2 Publications
- KM=0.271 mM for NAD+ (at pH 7.2)2 Publications
- KM=0.189 mM for NAD+ (at pH 8.1)2 Publications
- KM=0.01 mM for NAD+ (at pH 9.0)2 Publications
- KM=0.35 mM for 3-phosphonooxypyruvate (at pH 7.1)2 Publications
- KM=0.12 mM for NADH (at pH 7.1)2 Publications
- Vmax=133 µmol/min/mg enzyme (at pH 8.1)2 Publications
- Vmax=108 µmol/min/mg enzyme (at pH 7.2)2 Publications
: 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 | 251 | NADBy similarity | 1 | |
Active sitei | 312 | By similarity | 1 | |
Binding sitei | 336 | NADBy similarity | 1 | |
Active sitei | 341 | By similarity | 1 | |
Active sitei | 360 | Proton donorBy similarity | 1 |
Regions
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Nucleotide bindingi | 231 – 232 | NADBy similarity | 2 | |
Nucleotide bindingi | 310 – 312 | NADBy similarity | 3 | |
Nucleotide bindingi | 360 – 363 | NADBy similarity | 4 |
GO - Molecular functioni
- NAD binding Source: InterPro
- phosphoglycerate dehydrogenase activity Source: GO_Central
GO - Biological processi
- cellular amino acid metabolic process Source: GO_Central
- L-serine biosynthetic process Source: UniProtKB-KW
Keywordsi
Molecular function | Oxidoreductase |
Biological process | Amino-acid biosynthesis, Serine biosynthesis |
Ligand | NAD |
Enzyme and pathway databases
BioCyci | ARA:AT1G17745-MONOMER MetaCyc:AT1G17745-MONOMER |
Reactomei | R-ATH-977347 Serine biosynthesis |
SABIO-RKi | O04130 |
UniPathwayi | UPA00135;UER00196 |
Names & Taxonomyi
Protein namesi | Recommended name: D-3-phosphoglycerate dehydrogenase 2, chloroplastic (EC:1.1.1.952 Publications)Short name: PGDH |
Gene namesi | Name:PGDH2 Synonyms:3-PGDH, PGDH Ordered Locus Names:At1g17745 ORF Names:F11A6.8 |
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 | AT1G17745 |
TAIRi | locus:505006128 AT1G17745 |
Subcellular locationi
Chloroplast
- chloroplast 3 Publications
Chloroplast
- chloroplast Source: TAIR
- chloroplast stroma Source: TAIR
Cytosol
- cytosol Source: TAIR
Nucleus
- nucleus Source: TAIR
Keywords - Cellular componenti
Chloroplast, PlastidPathology & Biotechi
Disruption phenotypei
No visible phenotype.2 Publications
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Transit peptidei | 1 – 49 | ChloroplastSequence analysisAdd BLAST | 49 | |
ChainiPRO_0000007192 | 50 – 624 | D-3-phosphoglycerate dehydrogenase 2, chloroplasticAdd BLAST | 575 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Modified residuei | 71 | PhosphoserineCombined sources | 1 |
Keywords - PTMi
PhosphoproteinProteomic databases
PaxDbi | O04130 |
PRIDEi | O04130 |
PTM databases
iPTMneti | O04130 |
Expressioni
Tissue specificityi
Ubiquitous, but highly expressed in roots and in dark-grown leaf tissues. Expressed in the vasculature, stigma, anther filaments and shoot apical meristem. Not detected in the root meristem or in embryo.3 Publications
Inductioni
Not regulated by high CO2 levels. Up-regulated upon necrotrophic pathogen infection.1 Publication
Gene expression databases
ExpressionAtlasi | O04130 baseline and differential |
Genevisiblei | O04130 AT |
Interactioni
Protein-protein interaction databases
BioGridi | 23591, 1 interactor |
IntActi | O04130, 1 interactor |
STRINGi | 3702.AT1G17745.2 |
Structurei
3D structure databases
ProteinModelPortali | O04130 |
SMRi | O04130 |
ModBasei | Search... |
MobiDBi | Search... |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 552 – 624 | ACTPROSITE-ProRule annotationAdd BLAST | 73 |
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 | O04130 |
KOi | K00058 |
OMAi | PVTTKYK |
OrthoDBi | 911009at2759 |
PhylomeDBi | O04130 |
Family and domain databases
Gene3Di | 3.30.1330.90, 1 hit |
InterProi | View protein in InterPro IPR002912 ACT_dom 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 |
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 |
s (2)i Sequence
Sequence statusi: Complete.
: The displayed sequence is further processed into a mature form. Sequence processingi
This entry describes 2 produced by isoformsialternative splicing. AlignAdd to basketIsoform 1 (identifier: O04130-1) [UniParc]FASTAAdd to basket
This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
10 20 30 40 50
MAFSSSCSSV KAVNSRWTSP SPSPSSRFAV LPAFLHRRYA TSVKLTAISA
60 70 80 90 100
ALKTVEQTTL TEDNRFSTVG SDSDEYNPTL PKPRILVTEK LGEAGVNLLR
110 120 130 140 150
EFGDVDCSYD LSPEDLKKKV AESDALIVRS GTKVTREVFE AAKGRLKVVG
160 170 180 190 200
RAGVGIDNVD LQAATEHGCL VVNAPTANTV AAAEHGIALL ASMARNVAQA
210 220 230 240 250
DASIKAGKWE RSKYVGVSLV GKTLAVMGFG KVGTEVARRA KGLGMTVISH
260 270 280 290 300
DPYAPADRAR ALGVDLVSFD QAISTADFVS LHMPLTPATK KVFNDETFSK
310 320 330 340 350
MKKGVRLINV ARGGVIDEDA LVRALDAGIV AQAALDVFCE EPPSKDSRLI
360 370 380 390 400
QHENVTVTPH LGASTKEAQE GVAIEIAEAV AGALKGELSA TAVNAPMVAP
410 420 430 440 450
EVLSELTPYI VLAEKLGRLA VQLASGGKGV QSIRVVYRSA RDRDDLDTRL
460 470 480 490 500
LRAMITKGII EPISDSYVNL VNADFIAKQK GLRISEERMV VDSSPEYPVD
510 520 530 540 550
SIQVQILNVE SNFAGAVSDA GDISIEGKVK YGVPHLTCVG SFGVDVSLEG
560 570 580 590 600
NLILCRQVDQ PGMIGQVGNI LGEQNVNVNF MSVGRTVLRK QAIMAIGVDE
610 620
EPDNKTLERI GGVSAIEEFV FLKL
Alternative sequence
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Alternative sequenceiVSP_055873 | 208 – 210 | KWE → TLNYLFLVLLLRWNCRQSKH QYTIETETEK in isoform 2. Curated | 3 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AB003280 mRNA Translation: BAA20405.1 AB010407 Genomic DNA Translation: BAA24440.1 AC034257 Genomic DNA Translation: AAF99816.1 CP002684 Genomic DNA Translation: AEE29630.1 CP002684 Genomic DNA Translation: AEE29631.1 AY050399 mRNA Translation: AAK91415.1 AY098953 mRNA Translation: AAM19963.1 AY086001 mRNA Translation: AAM63210.1 |
PIRi | T52296 |
RefSeqi | NP_001031061.2, NM_001035984.2 [O04130-2] NP_564034.1, NM_101636.3 [O04130-1] |
UniGenei | At.21252 At.73011 |
Genome annotation databases
EnsemblPlantsi | AT1G17745.1; AT1G17745.1; AT1G17745 [O04130-1] AT1G17745.2; AT1G17745.2; AT1G17745 [O04130-2] |
GeneIDi | 838352 |
Gramenei | AT1G17745.1; AT1G17745.1; AT1G17745 [O04130-1] AT1G17745.2; AT1G17745.2; AT1G17745 [O04130-2] |
KEGGi | ath:AT1G17745 |
Keywords - Coding sequence diversityi
Alternative splicingSimilar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AB003280 mRNA Translation: BAA20405.1 AB010407 Genomic DNA Translation: BAA24440.1 AC034257 Genomic DNA Translation: AAF99816.1 CP002684 Genomic DNA Translation: AEE29630.1 CP002684 Genomic DNA Translation: AEE29631.1 AY050399 mRNA Translation: AAK91415.1 AY098953 mRNA Translation: AAM19963.1 AY086001 mRNA Translation: AAM63210.1 |
PIRi | T52296 |
RefSeqi | NP_001031061.2, NM_001035984.2 [O04130-2] NP_564034.1, NM_101636.3 [O04130-1] |
UniGenei | At.21252 At.73011 |
3D structure databases
ProteinModelPortali | O04130 |
SMRi | O04130 |
ModBasei | Search... |
MobiDBi | Search... |
Protein-protein interaction databases
BioGridi | 23591, 1 interactor |
IntActi | O04130, 1 interactor |
STRINGi | 3702.AT1G17745.2 |
PTM databases
iPTMneti | O04130 |
Proteomic databases
PaxDbi | O04130 |
PRIDEi | O04130 |
Protocols and materials databases
Structural Biology Knowledgebase | Search... |
Genome annotation databases
EnsemblPlantsi | AT1G17745.1; AT1G17745.1; AT1G17745 [O04130-1] AT1G17745.2; AT1G17745.2; AT1G17745 [O04130-2] |
GeneIDi | 838352 |
Gramenei | AT1G17745.1; AT1G17745.1; AT1G17745 [O04130-1] AT1G17745.2; AT1G17745.2; AT1G17745 [O04130-2] |
KEGGi | ath:AT1G17745 |
Organism-specific databases
Araporti | AT1G17745 |
TAIRi | locus:505006128 AT1G17745 |
Phylogenomic databases
eggNOGi | KOG0068 Eukaryota COG0111 LUCA |
HOGENOMi | HOG000136693 |
InParanoidi | O04130 |
KOi | K00058 |
OMAi | PVTTKYK |
OrthoDBi | 911009at2759 |
PhylomeDBi | O04130 |
Enzyme and pathway databases
UniPathwayi | UPA00135;UER00196 |
BioCyci | ARA:AT1G17745-MONOMER MetaCyc:AT1G17745-MONOMER |
Reactomei | R-ATH-977347 Serine biosynthesis |
SABIO-RKi | O04130 |
Miscellaneous databases
PROi | PR:O04130 |
Gene expression databases
ExpressionAtlasi | O04130 baseline and differential |
Genevisiblei | O04130 AT |
Family and domain databases
Gene3Di | 3.30.1330.90, 1 hit |
InterProi | View protein in InterPro IPR002912 ACT_dom 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 |
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 | SERA2_ARATH | |
Accessioni | O04130Primary (citable) accession number: O04130 Secondary accession number(s): F4I918 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | July 15, 1998 |
Last sequence update: | January 1, 1998 | |
Last modified: | January 16, 2019 | |
This is version 160 of the entry and version 2 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