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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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei53 – 531FAD1 Publication
Binding sitei119 – 1191FAD; via amide nitrogen and carbonyl oxygen1 Publication
Binding sitei142 – 1421FAD; via carbonyl oxygen1 Publication
Binding sitei182 – 1821FAD1 Publication
Binding sitei202 – 2021NAD1 Publication
Binding sitei236 – 2361NAD; via amide nitrogen1 Publication
Binding sitei306 – 3061FAD; via amide nitrogen1 Publication
Binding sitei312 – 3121NAD; via carbonyl oxygen1 Publication
Binding sitei314 – 3141FAD; via amide nitrogen1 Publication
Active sitei438 – 4381Proton acceptorBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi36 – 449FAD1 Publication
Nucleotide bindingi179 – 1835NAD1 Publication
Nucleotide bindingi264 – 2674NAD1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Glycolysis

Keywords - Ligandi

FAD, Flavoprotein, NAD

Enzyme and pathway databases

BioCyciRETL1328306-WGS:GSTH-6669-MONOMER.

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

DrugBankiDB03147. Flavin adenine dinucleotide.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 459459Dihydrolipoyl dehydrogenasePRO_0000068038Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
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

1
459
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi8 – 125Combined sources
Helixi16 – 2813Combined sources
Beta strandi32 – 354Combined sources
Helixi42 – 476Combined sources
Helixi49 – 6719Combined sources
Helixi85 – 10925Combined sources
Beta strandi113 – 1153Combined sources
Beta strandi119 – 1235Combined sources
Beta strandi126 – 1294Combined sources
Beta strandi132 – 1354Combined sources
Beta strandi137 – 1415Combined sources
Beta strandi145 – 1473Combined sources
Helixi162 – 1654Combined sources
Beta strandi173 – 1786Combined sources
Helixi182 – 19413Combined sources
Beta strandi197 – 2015Combined sources
Beta strandi203 – 2086Combined sources
Helixi213 – 22614Combined sources
Beta strandi229 – 2313Combined sources
Beta strandi235 – 2406Combined sources
Beta strandi243 – 2475Combined sources
Beta strandi249 – 2513Combined sources
Beta strandi261 – 2633Combined sources
Beta strandi267 – 2693Combined sources
Beta strandi272 – 2754Combined sources
Helixi276 – 2783Combined sources
Beta strandi301 – 3033Combined sources
Helixi305 – 3084Combined sources
Helixi314 – 32815Combined sources
Beta strandi342 – 3443Combined sources
Beta strandi346 – 3549Combined sources
Helixi357 – 3626Combined sources
Beta strandi367 – 3737Combined sources
Helixi374 – 3763Combined sources
Helixi378 – 3825Combined sources
Beta strandi389 – 3957Combined sources
Turni396 – 3983Combined sources
Beta strandi400 – 4089Combined sources
Helixi411 – 4133Combined sources
Helixi414 – 42411Combined sources
Helixi428 – 4325Combined sources
Helixi443 – 45210Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1LVLX-ray2.45A2-459[»]
ProteinModelPortaliP09063.
SMRiP09063. Positions 2-459.
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
EntryMethodResolution (Å)ChainPositionsPDBsum
1LVLX-ray2.45A2-459[»]
ProteinModelPortaliP09063.
SMRiP09063. Positions 2-459.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi160488.PP_4404.

Chemistry

DrugBankiDB03147. Flavin adenine dinucleotide.

Proteomic databases

PRIDEiP09063.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4107QN2. Bacteria.
COG1249. LUCA.

Enzyme and pathway databases

BioCyciRETL1328306-WGS:GSTH-6669-MONOMER.

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 11, 2015
This is version 137 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.