Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Dihydrolipoyl dehydrogenase 1, chloroplastic

Gene

LPD1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

Functioni

Lipoamide dehydrogenase is a component of the plastidial pyruvate dehydrogenase complex (PDC).1 Publication

Catalytic activityi

Protein N(6)-(dihydrolipoyl)lysine + NAD+ = protein N(6)-(lipoyl)lysine + NADH.

Cofactori

FADBy similarityNote: Binds 1 FAD per subunit.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei133 – 1331FADBy similarity
Binding sitei199 – 1991FAD; via amide nitrogen and carbonyl oxygenBy similarity
Binding sitei284 – 2841NADBy similarity
Binding sitei357 – 3571NAD; via amide nitrogenBy similarity
Binding sitei403 – 4031FADBy similarity
Active sitei539 – 5391Proton acceptorBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi116 – 1249FADBy similarity
Nucleotide bindingi224 – 2263FADBy similarity
Nucleotide bindingi261 – 2688NADBy similarity
Nucleotide bindingi409 – 4124FADBy similarity

GO - Molecular functioni

  • dihydrolipoyl dehydrogenase activity Source: TAIR
  • flavin adenine dinucleotide binding Source: InterPro

GO - Biological processi

  • acetyl-CoA biosynthetic process from pyruvate Source: TAIR
  • cell redox homeostasis Source: InterPro
  • response to arsenic-containing substance Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

FAD, Flavoprotein, NAD

Names & Taxonomyi

Protein namesi
Recommended name:
Dihydrolipoyl dehydrogenase 1, chloroplastic (EC:1.8.1.4)
Short name:
ptLPD1
Alternative name(s):
Dihydrolipoamide dehydrogenase 1
Protein LIPOAMIDE DEHYDROGENASE 1
Pyruvate dehydrogenase complex E3 subunit 1
Short name:
E3-1
Short name:
PDC-E3 1
Gene namesi
Name:LPD1
Ordered Locus Names:At3g16950
ORF Names:K14A17.6
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 3

Organism-specific databases

TAIRiAT3G16950.

Subcellular locationi

  • Plastidchloroplast stroma 1 Publication

GO - Cellular componenti

  • chloroplast Source: TAIR
  • chloroplast envelope Source: TAIR
  • chloroplast stroma Source: TAIR
  • nucleolus Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Plastid

Pathology & Biotechi

Disruption phenotypei

Arsenate hypersensitivity.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 7070ChloroplastSequence analysisAdd
BLAST
Chaini71 – 623553Dihydrolipoyl dehydrogenase 1, chloroplasticPRO_0000423493Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi124 ↔ 129Redox-activeBy similarity

Keywords - PTMi

Disulfide bond

Proteomic databases

PaxDbiA8MS68.
PRIDEiA8MS68.

Expressioni

Tissue specificityi

Expressed mainly in flower buds and immature siliques, and to a lesser extend in flowers.1 Publication

Gene expression databases

GenevisibleiA8MS68. AT.

Interactioni

Subunit structurei

Homodimer (By similarity). Part of the plastidial pyruvate dehydrogenase complex (PDC) containing multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase (E3).By similarity

Protein-protein interaction databases

BioGridi6284. 2 interactions.
IntActiA8MS68. 1 interaction.
STRINGi3702.AT3G16950.2.

Structurei

3D structure databases

ProteinModelPortaliA8MS68.
SMRiA8MS68. Positions 87-552.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Redox-active center, Transit peptide

Phylogenomic databases

eggNOGiKOG1335. Eukaryota.
COG1249. LUCA.
HOGENOMiHOG000276708.
KOiK00382.
OMAiSIFRGMN.
OrthoDBiEOG093607YW.
PhylomeDBiA8MS68.

Family and domain databases

Gene3Di3.30.390.30. 1 hit.
3.50.50.60. 2 hits.
InterProiIPR023753. FAD/NAD-binding_dom.
IPR016156. FAD/NAD-linked_Rdtase_dimer.
IPR006258. Lipoamide_DH.
IPR004099. Pyr_nucl-diS_OxRdtase_dimer.
IPR012999. Pyr_OxRdtase_I_AS.
[Graphical view]
PfamiPF07992. Pyr_redox_2. 1 hit.
PF02852. Pyr_redox_dim. 1 hit.
[Graphical view]
SUPFAMiSSF51905. SSF51905. 1 hit.
SSF55424. SSF55424. 1 hit.
TIGRFAMsiTIGR01350. lipoamide_DH. 1 hit.
PROSITEiPS00076. PYRIDINE_REDOX_1. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

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

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: A8MS68-1) [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.

« Hide

        10         20         30         40         50
MQSAMALSFS QTSFTRPNHV LGSSGSVFST PRSLRFCGLR REAFGFSTSN
60 70 80 90 100
QLAIRSNRIQ FLSRKSFQVS ASASSNGNGA PPKSFDYDLI IIGAGVGGHG
110 120 130 140 150
AALHAVEKGL KTAIIEGDVV GGTCVNRGCV PSKALLAVSG RMRELQNEHH
160 170 180 190 200
MKSFGLQVSA AGYDRQGVAD HANNLATKIR NNLTNSMKAI GVDILTGFGS
210 220 230 240 250
VLGPQKVKYG KDNIITAKDI IIATGSVPFV PKGIEVDGKT VITSDHALKL
260 270 280 290 300
ESVPEWIAIV GSGYIGLEFS DVYTALGSEV TFIEALDQLM PGFDPEISKL
310 320 330 340 350
AQRVLINPRK IDYHTGVFAS KITPARDGKP VLIELIDAKT KEPKDTLEVD
360 370 380 390 400
AALIATGRAP FTNGLGLENV NVVTQRGFIP VDERMRVIDG KGTLVPNLYC
410 420 430 440 450
IGDANGKLML AHAASAQGIS VVEQVSGRDH VLNHLSIPAA CFTHPEISMV
460 470 480 490 500
GLTEPQAKEK GEKEGFKVSV VKTSFKANTK ALAENEGEGI AKMIYRPDNG
510 520 530 540 550
EILGVHIFGL HAADLIHEAS NAIALGTRIQ DIKLAVHAHP TLSEVLDELF
560 570 580 590 600
KAAKVESHAT TRTGDAKIKL NTNQEDRKGR RRGGDDEKQP SVSKDLKDIS
610 620
TRPSSFFENI SVGVLSLLSL IFV
Length:623
Mass (Da):66,661
Last modified:December 4, 2007 - v1
Checksum:i6747C79E1D2DE365
GO
Isoform 2 (identifier: A8MS68-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     564-570: GDAKIKL → VSEKVVV
     571-623: Missing.

Show »
Length:570
Mass (Da):60,757
Checksum:i55E9206F67E849B9
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti14 – 141F → L in BAH19701 (PubMed:19423640).Curated
Sequence conflicti222 – 2221I → T in BAH19701 (PubMed:19423640).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei564 – 5707GDAKIKL → VSEKVVV in isoform 2. 2 PublicationsVSP_047927
Alternative sequencei571 – 62353Missing in isoform 2. 2 PublicationsVSP_047928Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF228637 mRNA. Translation: AAF37698.1.
AB026636 Genomic DNA. No translation available.
CP002686 Genomic DNA. Translation: AEE75887.1.
CP002686 Genomic DNA. Translation: AEE75888.1.
AY050376 mRNA. Translation: AAK91394.1.
AY120695 mRNA. Translation: AAM52238.1.
AK317007 mRNA. Translation: BAH19701.1.
RefSeqiNP_001078165.1. NM_001084696.1. [A8MS68-1]
NP_566562.1. NM_112571.2. [A8MS68-2]
UniGeneiAt.16905.

Genome annotation databases

EnsemblPlantsiAT3G16950.2; AT3G16950.2; AT3G16950. [A8MS68-1]
GeneIDi820951.
KEGGiath:AT3G16950.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF228637 mRNA. Translation: AAF37698.1.
AB026636 Genomic DNA. No translation available.
CP002686 Genomic DNA. Translation: AEE75887.1.
CP002686 Genomic DNA. Translation: AEE75888.1.
AY050376 mRNA. Translation: AAK91394.1.
AY120695 mRNA. Translation: AAM52238.1.
AK317007 mRNA. Translation: BAH19701.1.
RefSeqiNP_001078165.1. NM_001084696.1. [A8MS68-1]
NP_566562.1. NM_112571.2. [A8MS68-2]
UniGeneiAt.16905.

3D structure databases

ProteinModelPortaliA8MS68.
SMRiA8MS68. Positions 87-552.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi6284. 2 interactions.
IntActiA8MS68. 1 interaction.
STRINGi3702.AT3G16950.2.

Proteomic databases

PaxDbiA8MS68.
PRIDEiA8MS68.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT3G16950.2; AT3G16950.2; AT3G16950. [A8MS68-1]
GeneIDi820951.
KEGGiath:AT3G16950.

Organism-specific databases

TAIRiAT3G16950.

Phylogenomic databases

eggNOGiKOG1335. Eukaryota.
COG1249. LUCA.
HOGENOMiHOG000276708.
KOiK00382.
OMAiSIFRGMN.
OrthoDBiEOG093607YW.
PhylomeDBiA8MS68.

Miscellaneous databases

PROiA8MS68.

Gene expression databases

GenevisibleiA8MS68. AT.

Family and domain databases

Gene3Di3.30.390.30. 1 hit.
3.50.50.60. 2 hits.
InterProiIPR023753. FAD/NAD-binding_dom.
IPR016156. FAD/NAD-linked_Rdtase_dimer.
IPR006258. Lipoamide_DH.
IPR004099. Pyr_nucl-diS_OxRdtase_dimer.
IPR012999. Pyr_OxRdtase_I_AS.
[Graphical view]
PfamiPF07992. Pyr_redox_2. 1 hit.
PF02852. Pyr_redox_dim. 1 hit.
[Graphical view]
SUPFAMiSSF51905. SSF51905. 1 hit.
SSF55424. SSF55424. 1 hit.
TIGRFAMsiTIGR01350. lipoamide_DH. 1 hit.
PROSITEiPS00076. PYRIDINE_REDOX_1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPLPD1_ARATH
AccessioniPrimary (citable) accession number: A8MS68
Secondary accession number(s): B9DG34, Q9M5K5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 18, 2013
Last sequence update: December 4, 2007
Last modified: September 7, 2016
This is version 69 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

The active site is a redox-active disulfide bond.By similarity

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  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.