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Protein

Dihydrolipoyl dehydrogenase, mitochondrial

Gene

LPD

Organism
Pisum sativum (Garden pea)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Lipoamide dehydrogenase is a component of the glycine cleavage system as well as of the alpha-ketoacid dehydrogenase complexes. The pyruvate dehydrogenase complex contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase (E3).

Catalytic activityi

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

Cofactori

FADNote: Binds 1 FAD per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei85 – 851FADBy similarity
Binding sitei149 – 1491FAD; via amide nitrogen and carbonyl oxygen1 Publication
Binding sitei238 – 2381NADBy similarity
Binding sitei272 – 2721NAD; via amide nitrogen and carbonyl oxygenBy similarity
Binding sitei307 – 3071NAD; via amide nitrogenBy similarity
Binding sitei348 – 3481FAD1 Publication
Active sitei480 – 4801Proton acceptorBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi67 – 7610FAD1 Publication
Nucleotide bindingi178 – 1803FADBy similarity
Nucleotide bindingi215 – 2228NADBy similarity
Nucleotide bindingi354 – 3574FAD1 Publication

GO - Molecular functioni

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

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

FAD, Flavoprotein, NAD

Enzyme and pathway databases

SABIO-RKP31023.

Names & Taxonomyi

Protein namesi
Recommended name:
Dihydrolipoyl dehydrogenase, mitochondrial (EC:1.8.1.4)
Alternative name(s):
Dihydrolipoamide dehydrogenase
Glycine cleavage system L protein
Pyruvate dehydrogenase complex E3 subunit
Short name:
E3
Short name:
PDC-E3
Gene namesi
Name:LPD
OrganismiPisum sativum (Garden pea)
Taxonomic identifieri3888 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsfabidsFabalesFabaceaePapilionoideaeFabeaePisum

Subcellular locationi

GO - Cellular componenti

  • glycine cleavage complex Source: UniProtKB
  • mitochondrial matrix Source: UniProtKB-SubCell
  • mitochondrion Source: CACAO
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 3131Mitochondrion1 PublicationAdd
BLAST
Chaini32 – 501470Dihydrolipoyl dehydrogenase, mitochondrialPRO_0000030299Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi76 ↔ 81Redox-active1 Publication

Keywords - PTMi

Disulfide bond

Proteomic databases

PRIDEiP31023.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

IntActiP31023. 1 interaction.

Structurei

Secondary structure

1
501
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi40 – 434Combined sources
Helixi47 – 5812Combined sources
Beta strandi63 – 675Combined sources
Beta strandi69 – 724Combined sources
Helixi76 – 794Combined sources
Helixi81 – 9919Combined sources
Helixi102 – 1043Combined sources
Beta strandi106 – 1094Combined sources
Beta strandi111 – 1133Combined sources
Helixi115 – 14026Combined sources
Beta strandi143 – 1475Combined sources
Beta strandi149 – 1535Combined sources
Beta strandi156 – 1594Combined sources
Beta strandi162 – 1643Combined sources
Beta strandi167 – 1704Combined sources
Beta strandi172 – 1765Combined sources
Beta strandi180 – 1823Combined sources
Beta strandi192 – 1965Combined sources
Helixi198 – 2014Combined sources
Beta strandi209 – 2146Combined sources
Helixi218 – 23013Combined sources
Beta strandi233 – 2375Combined sources
Beta strandi239 – 2446Combined sources
Helixi249 – 26113Combined sources
Beta strandi269 – 2768Combined sources
Beta strandi278 – 29114Combined sources
Beta strandi295 – 3039Combined sources
Beta strandi308 – 3103Combined sources
Turni318 – 3214Combined sources
Beta strandi326 – 3283Combined sources
Beta strandi343 – 3453Combined sources
Beta strandi350 – 3523Combined sources
Helixi356 – 37015Combined sources
Beta strandi384 – 3863Combined sources
Beta strandi388 – 3969Combined sources
Helixi399 – 4046Combined sources
Beta strandi409 – 4157Combined sources
Helixi416 – 4183Combined sources
Helixi420 – 4256Combined sources
Beta strandi431 – 4377Combined sources
Turni438 – 4403Combined sources
Beta strandi442 – 4509Combined sources
Helixi453 – 46513Combined sources
Helixi470 – 4745Combined sources
Helixi485 – 49511Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DXLX-ray3.15A/B/C/D32-501[»]
ProteinModelPortaliP31023.
SMRiP31023. Positions 35-501.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP31023.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Redox-active center, Transit peptide

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]

Sequencei

Sequence statusi: Complete.

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

P31023-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAMANLARRK GYSLLSSETL RYSFSLRSRA FASGSDENDV VIIGGGPGGY
60 70 80 90 100
VAAIKAAQLG FKTTCIEKRG ALGGTCLNVG CIPSKALLHS SHMYHEAKHS
110 120 130 140 150
FANHGVKVSN VEIDLAAMMG QKDKAVSNLT RGIEGLFKKN KVTYVKGYGK
160 170 180 190 200
FVSPSEISVD TIEGENTVVK GKHIIIATGS DVKSLPGVTI DEKKIVSSTG
210 220 230 240 250
ALALSEIPKK LVVIGAGYIG LEMGSVWGRI GSEVTVVEFA SEIVPTMDAE
260 270 280 290 300
IRKQFQRSLE KQGMKFKLKT KVVGVDTSGD GVKLTVEPSA GGEQTIIEAD
310 320 330 340 350
VVLVSAGRTP FTSGLNLDKI GVETDKLGRI LVNERFSTNV SGVYAIGDVI
360 370 380 390 400
PGPMLAHKAE EDGVACVEYL AGKVGHVDYD KVPGVVYTNP EVASVGKTEE
410 420 430 440 450
QVKETGVEYR VGKFPFMANS RAKAIDNAEG LVKIIAEKET DKILGVHIMA
460 470 480 490 500
PNAGELIHEA AIALQYDASS EDIARVCHAH PTMSEAIKEA AMATYDKPIH

I
Length:501
Mass (Da):53,310
Last modified:July 11, 2001 - v2
Checksum:i639D2D6368589FCE
GO

Mass spectrometryi

Molecular mass is 49753±5 Da from positions 32 - 501. Determined by ESI. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X63464 mRNA. Translation: CAA45066.2.
X62995 mRNA. Translation: CAA44729.1.
PIRiS22384.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X63464 mRNA. Translation: CAA45066.2.
X62995 mRNA. Translation: CAA44729.1.
PIRiS22384.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DXLX-ray3.15A/B/C/D32-501[»]
ProteinModelPortaliP31023.
SMRiP31023. Positions 35-501.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP31023. 1 interaction.

Proteomic databases

PRIDEiP31023.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

SABIO-RKP31023.

Miscellaneous databases

EvolutionaryTraceiP31023.

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 nameiDLDH_PEA
AccessioniPrimary (citable) accession number: P31023
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: July 11, 2001
Last modified: September 7, 2016
This is version 119 of the entry and version 2 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.

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.