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Protein

Dihydrolipoyl dehydrogenase

Gene

lpd

Organism
Pseudomonas fluorescens
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

FADNote: Binds 1 FAD per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei58 – 581FAD1 Publication
Binding sitei122 – 1221FAD; via amide nitrogen and carbonyl oxygen1 Publication
Binding sitei211 – 2111NADBy similarity
Binding sitei245 – 2451NAD; via amide nitrogenBy similarity
Binding sitei319 – 3191FAD1 Publication
Binding sitei327 – 3271FAD; via amide nitrogen1 Publication
Active sitei451 – 4511Proton acceptorBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi34 – 4916FAD1 PublicationAdd
BLAST
Nucleotide bindingi188 – 1925NADBy similarity
Nucleotide bindingi276 – 2794NADBy similarity

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 2-oxoglutarate dehydrogenase complex
Gene namesi
Name:lpd
OrganismiPseudomonas fluorescens
Taxonomic identifieri294 [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
Initiator methionineiRemoved1 Publication
Chaini2 – 478477Dihydrolipoyl dehydrogenasePRO_0000068037Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi49 ↔ 54Redox-active1 Publication

Keywords - PTMi

Disulfide bond

Proteomic databases

PRIDEiP14218.

Interactioni

Subunit structurei

Homodimer.1 Publication

Structurei

Secondary structure

1
478
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 107Combined sources
Helixi14 – 2512Combined sources
Beta strandi30 – 345Combined sources
Beta strandi39 – 435Combined sources
Helixi47 – 526Combined sources
Helixi54 – 7219Combined sources
Helixi75 – 773Combined sources
Beta strandi79 – 868Combined sources
Helixi88 – 11326Combined sources
Beta strandi115 – 12410Combined sources
Helixi126 – 1283Combined sources
Beta strandi129 – 1346Combined sources
Beta strandi139 – 14911Combined sources
Beta strandi153 – 1553Combined sources
Turni165 – 1673Combined sources
Helixi171 – 1744Combined sources
Beta strandi182 – 1876Combined sources
Helixi191 – 20212Combined sources
Beta strandi206 – 2105Combined sources
Beta strandi212 – 2176Combined sources
Helixi222 – 23514Combined sources
Beta strandi238 – 2403Combined sources
Beta strandi244 – 2474Combined sources
Beta strandi254 – 2607Combined sources
Beta strandi265 – 2717Combined sources
Beta strandi273 – 2753Combined sources
Beta strandi279 – 2813Combined sources
Turni284 – 2863Combined sources
Beta strandi308 – 3114Combined sources
Beta strandi314 – 3163Combined sources
Helixi318 – 3203Combined sources
Beta strandi321 – 3233Combined sources
Helixi327 – 34115Combined sources
Helixi350 – 3523Combined sources
Beta strandi355 – 3573Combined sources
Beta strandi359 – 3679Combined sources
Helixi370 – 3756Combined sources
Beta strandi380 – 3867Combined sources
Helixi387 – 3893Combined sources
Helixi391 – 3966Combined sources
Beta strandi402 – 41110Combined sources
Beta strandi413 – 4219Combined sources
Helixi424 – 43613Combined sources
Helixi441 – 4455Combined sources
Helixi455 – 46511Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1LPFX-ray2.80A/B2-478[»]
ProteinModelPortaliP14218.
SMRiP14218. Positions 2-473.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP14218.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Redox-active center

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.

P14218-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSQKFDVVVI GAGPGGYVAA IRAAQLGLKT ACIEKYIGKE GKVALGGTCL
60 70 80 90 100
NVGCIPSKAL LDSSYKYHEA KEAFKVHGIE AKGVTIDVPA MVARKANIVK
110 120 130 140 150
NLTGGIATLF KANGVTSFEG HGKLLANKQV EVTGLDGKTQ VLEAENVIIA
160 170 180 190 200
SGSRPVEIPP APLSDDIIVD STGALEFQAV PKKLGVIGAG VIGLELGSVW
210 220 230 240 250
ARLGAEVTVL EALDKFLPAA DEQIAKEALK VLTKQGLNIR LGARVTASEV
260 270 280 290 300
KKKQVTVTFT DANGEQKETF DKLIVAVGRR PVTTDLLAAD SGVTLDERGF
310 320 330 340 350
IYVDDHCKTS VPGVFAIGDV VRGAMLAHKA SEEGVMVAER IAGHKAQMNY
360 370 380 390 400
DLIPSVIYTH PEIAWVGKTE QTLKAEGVEV NVGTFPFAAS GRAMAANDTT
410 420 430 440 450
GLVKVIADAK TDRVLGVHVI GPSAAELVQQ GAIGMEFGTS AEDLGMMVFS
460 470
HPTLSEALHE AALAVNGHAI HIANRKKR
Length:478
Mass (Da):50,151
Last modified:January 23, 2007 - v3
Checksum:iB23EB31268C69EC7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M28356 Genomic DNA. Translation: AAA99234.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M28356 Genomic DNA. Translation: AAA99234.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1LPFX-ray2.80A/B2-478[»]
ProteinModelPortaliP14218.
SMRiP14218. Positions 2-473.
ModBaseiSearch...
MobiDBiSearch...

Chemistry

DrugBankiDB03147. Flavin adenine dinucleotide.

Proteomic databases

PRIDEiP14218.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP14218.

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...

Publicationsi

  1. "Molecular cloning and sequence determination of the lpd gene encoding lipoamide dehydrogenase from Pseudomonas fluorescens."
    Benen J.A.E., van Berkel W.J.H., van Dongen W.M.A.M., Mueller F., de Kok A.
    J. Gen. Microbiol. 135:1787-1797(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-23.
  2. "Three-dimensional structure of lipoamide dehydrogenase from Pseudomonas fluorescens at 2.8-A resolution. Analysis of redox and thermostability properties."
    Mattevi A., Obmolova G., Kalk K.H., van Berkel W.J.H., Hol W.G.J.
    J. Mol. Biol. 230:1200-1215(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEX WITH FAD, SUBUNIT, DISULFIDE BOND.

Entry informationi

Entry nameiDLDH_PSEFL
AccessioniPrimary (citable) accession number: P14218
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: January 23, 2007
Last modified: November 11, 2015
This is version 123 of the entry and version 3 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.