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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)DescriptionActionsGraphical viewLength
Binding sitei85FADBy similarity1
Binding sitei149FAD; via amide nitrogen and carbonyl oxygen1 Publication1
Binding sitei238NADBy similarity1
Binding sitei272NAD; via amide nitrogen and carbonyl oxygenBy similarity1
Binding sitei307NAD; via amide nitrogenBy similarity1
Binding sitei348FAD1 Publication1
Active sitei480Proton acceptorBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi67 – 76FAD1 Publication10
Nucleotide bindingi178 – 180FADBy similarity3
Nucleotide bindingi215 – 222NADBy similarity8
Nucleotide bindingi354 – 357FAD1 Publication4

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)DescriptionActionsGraphical viewLength
Transit peptidei1 – 31Mitochondrion1 PublicationAdd BLAST31
ChainiPRO_000003029932 – 501Dihydrolipoyl dehydrogenase, mitochondrialAdd BLAST470

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi76 ↔ 81Redox-active1 Publication

Keywords - PTMi

Disulfide bond

Proteomic databases

PRIDEiP31023.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

IntActiP31023. 1 interactor.

Structurei

Secondary structure

1501
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi40 – 43Combined sources4
Helixi47 – 58Combined sources12
Beta strandi63 – 67Combined sources5
Beta strandi69 – 72Combined sources4
Helixi76 – 79Combined sources4
Helixi81 – 99Combined sources19
Helixi102 – 104Combined sources3
Beta strandi106 – 109Combined sources4
Beta strandi111 – 113Combined sources3
Helixi115 – 140Combined sources26
Beta strandi143 – 147Combined sources5
Beta strandi149 – 153Combined sources5
Beta strandi156 – 159Combined sources4
Beta strandi162 – 164Combined sources3
Beta strandi167 – 170Combined sources4
Beta strandi172 – 176Combined sources5
Beta strandi180 – 182Combined sources3
Beta strandi192 – 196Combined sources5
Helixi198 – 201Combined sources4
Beta strandi209 – 214Combined sources6
Helixi218 – 230Combined sources13
Beta strandi233 – 237Combined sources5
Beta strandi239 – 244Combined sources6
Helixi249 – 261Combined sources13
Beta strandi269 – 276Combined sources8
Beta strandi278 – 291Combined sources14
Beta strandi295 – 303Combined sources9
Beta strandi308 – 310Combined sources3
Turni318 – 321Combined sources4
Beta strandi326 – 328Combined sources3
Beta strandi343 – 345Combined sources3
Beta strandi350 – 352Combined sources3
Helixi356 – 370Combined sources15
Beta strandi384 – 386Combined sources3
Beta strandi388 – 396Combined sources9
Helixi399 – 404Combined sources6
Beta strandi409 – 415Combined sources7
Helixi416 – 418Combined sources3
Helixi420 – 425Combined sources6
Beta strandi431 – 437Combined sources7
Turni438 – 440Combined sources3
Beta strandi442 – 450Combined sources9
Helixi453 – 465Combined sources13
Helixi470 – 474Combined sources5
Helixi485 – 495Combined sources11

3D structure databases

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

Protein-protein interaction databases

IntActiP31023. 1 interactor.

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: November 2, 2016
This is version 121 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.