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Protein

Dihydrolipoyl dehydrogenase

Gene

lpdV

Organism
Pseudomonas putida (Arthrobacter siderocapsulatus)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

The branched-chain alpha-keto dehydrogenase complex catalyzes the overall conversion of alpha-keto acids to acyl-CoA and CO2. It contains multiple copies of 3 enzymatic components: branched-chain alpha-keto acid decarboxylase (E1), lipoamide acyltransferase (E2) and lipoamide dehydrogenase (E3).

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)DescriptionActionsGraphical viewLength
Binding sitei53FAD1 Publication1
Binding sitei119FAD; via amide nitrogen and carbonyl oxygen1 Publication1
Binding sitei142FAD; via carbonyl oxygen1 Publication1
Binding sitei182FAD1 Publication1
Binding sitei202NAD1 Publication1
Binding sitei236NAD; via amide nitrogen1 Publication1
Binding sitei306FAD; via amide nitrogen1 Publication1
Binding sitei312NAD; via carbonyl oxygen1 Publication1
Binding sitei314FAD; via amide nitrogen1 Publication1
Active sitei438Proton acceptorBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi36 – 44FAD1 Publication9
Nucleotide bindingi179 – 183NAD1 Publication5
Nucleotide bindingi264 – 267NAD1 Publication4

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Glycolysis

Keywords - Ligandi

FAD, Flavoprotein, NAD

Names & Taxonomyi

Protein namesi
Recommended name:
Dihydrolipoyl dehydrogenase (EC:1.8.1.4)
Alternative name(s):
Dihydrolipoamide dehydrogenase
E3 component of branched-chain alpha-keto acid dehydrogenase complex
LPD-Val
Gene namesi
Name:lpdV
OrganismiPseudomonas putida (Arthrobacter siderocapsulatus)
Taxonomic identifieri303 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Chemistry databases

DrugBankiDB03147. Flavin adenine dinucleotide.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000680381 – 459Dihydrolipoyl dehydrogenaseAdd BLAST459

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi44 ↔ 49Redox-active1 Publication

Keywords - PTMi

Disulfide bond

Proteomic databases

PRIDEiP09063.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi160488.PP_4404.

Structurei

Secondary structure

1459
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi8 – 12Combined sources5
Helixi16 – 28Combined sources13
Beta strandi32 – 35Combined sources4
Helixi42 – 47Combined sources6
Helixi49 – 67Combined sources19
Helixi85 – 109Combined sources25
Beta strandi113 – 115Combined sources3
Beta strandi119 – 123Combined sources5
Beta strandi126 – 129Combined sources4
Beta strandi132 – 135Combined sources4
Beta strandi137 – 141Combined sources5
Beta strandi145 – 147Combined sources3
Helixi162 – 165Combined sources4
Beta strandi173 – 178Combined sources6
Helixi182 – 194Combined sources13
Beta strandi197 – 201Combined sources5
Beta strandi203 – 208Combined sources6
Helixi213 – 226Combined sources14
Beta strandi229 – 231Combined sources3
Beta strandi235 – 240Combined sources6
Beta strandi243 – 247Combined sources5
Beta strandi249 – 251Combined sources3
Beta strandi261 – 263Combined sources3
Beta strandi267 – 269Combined sources3
Beta strandi272 – 275Combined sources4
Helixi276 – 278Combined sources3
Beta strandi301 – 303Combined sources3
Helixi305 – 308Combined sources4
Helixi314 – 328Combined sources15
Beta strandi342 – 344Combined sources3
Beta strandi346 – 354Combined sources9
Helixi357 – 362Combined sources6
Beta strandi367 – 373Combined sources7
Helixi374 – 376Combined sources3
Helixi378 – 382Combined sources5
Beta strandi389 – 395Combined sources7
Turni396 – 398Combined sources3
Beta strandi400 – 408Combined sources9
Helixi411 – 413Combined sources3
Helixi414 – 424Combined sources11
Helixi428 – 432Combined sources5
Helixi443 – 452Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1LVLX-ray2.45A2-459[»]
ProteinModelPortaliP09063.
SMRiP09063.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP09063.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Redox-active center

Phylogenomic databases

eggNOGiENOG4107QN2. Bacteria.
COG1249. LUCA.

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.

P09063-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQQTIQTTLL IIGGGPGGYV AAIRAGQLGI PTVLVEGQAL GGTCLNIGCI
60 70 80 90 100
PSKALIHVAE QFHQASRFTE PSPLGISVAS PRLDIGQSVA WKDGIVDRLT
110 120 130 140 150
TGVAALLKKH GVKVVHGWAK VLDGKQVEVD GQRIQCEHLL LATGSSSVEL
160 170 180 190 200
PMLPLGGPVI SSTEALAPKA LPQHLVVVGG GYIGLELGIA YRKLGAQVSV
210 220 230 240 250
VEARERILPT YDSELTAPVA ESLKKLGIAL HLGHSVEGYE NGCLLANDGK
260 270 280 290 300
GGQLRLEADR VLVAVGRRPR TKGFNLECLD LKMNGAAIAI DERCQTSMHN
310 320 330 340 350
VWAIGDVAGE PMLAHRAMAQ GEMVAEIIAG KARRFEPAAI AAVCFTDPEV
360 370 380 390 400
VVVGKTPEQA SQQGLDCIVA QFPFAANGRA MSLESKSGFV RVVARRDNHL
410 420 430 440 450
ILGWQAVGVA VSELSTAFAQ SLEMGACLED VAGTIHAHPT LGEAVQEAAL

RALGHALHI
Length:459
Mass (Da):48,159
Last modified:November 1, 1988 - v1
Checksum:i3D60A7DE167D0586
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M57613 Genomic DNA. Translation: AAA65618.1.
PIRiS02139. DEPSLP.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M57613 Genomic DNA. Translation: AAA65618.1.
PIRiS02139. DEPSLP.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1LVLX-ray2.45A2-459[»]
ProteinModelPortaliP09063.
SMRiP09063.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi160488.PP_4404.

Chemistry databases

DrugBankiDB03147. Flavin adenine dinucleotide.

Proteomic databases

PRIDEiP09063.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4107QN2. Bacteria.
COG1249. LUCA.

Miscellaneous databases

EvolutionaryTraceiP09063.

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 nameiDLDH1_PSEPU
AccessioniPrimary (citable) accession number: P09063
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1988
Last sequence update: November 1, 1988
Last modified: November 2, 2016
This is version 139 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic 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.