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Protein

Lipoyl synthase 2, mitochondrial

Gene

PHATRDRAFT_28652

Organism
Phaeodactylum tricornutum (strain CCAP 1055/1)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes, thereby converting the octanoylated domains into lipoylated derivatives.UniRule annotation

Catalytic activityi

Protein N(6)-(octanoyl)lysine + 2 sulfur-(sulfur carrier) + 2 S-adenosyl-L-methionine + 2 reduced [2Fe-2S] ferredoxin = protein N(6)-(lipoyl)lysine + 2 (sulfur carrier) + 2 L-methionine + 2 5'-deoxyadenosine + 2 oxidized [2Fe-2S] ferredoxin.UniRule annotation

Cofactori

[4Fe-4S] clusterUniRule annotationNote: Binds 2 [4Fe-4S] clusters per subunit. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.UniRule annotation

Pathway:iprotein lipoylation via endogenous pathway

This protein is involved in step 2 of the subpathway that synthesizes protein N(6)-(lipoyl)lysine from octanoyl-[acyl-carrier-protein].UniRule annotation
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. no protein annotated in this organism
  2. Lipoyl synthase 1, mitochondrial (PHATRDRAFT_18029), Lipoyl synthase 2, mitochondrial (PHATRDRAFT_28652)
This subpathway is part of the pathway protein lipoylation via endogenous pathway, which is itself part of Protein modification.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes protein N(6)-(lipoyl)lysine from octanoyl-[acyl-carrier-protein], the pathway protein lipoylation via endogenous pathway and in Protein modification.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi46 – 461Iron-sulfur 1 (4Fe-4S)UniRule annotation
Metal bindingi51 – 511Iron-sulfur 1 (4Fe-4S)UniRule annotation
Metal bindingi57 – 571Iron-sulfur 1 (4Fe-4S)UniRule annotation
Metal bindingi72 – 721Iron-sulfur 2 (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi76 – 761Iron-sulfur 2 (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi79 – 791Iron-sulfur 2 (4Fe-4S-S-AdoMet)UniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Ligandi

4Fe-4S, Iron, Iron-sulfur, Metal-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

UniPathwayiUPA00538; UER00593.

Names & Taxonomyi

Protein namesi
Recommended name:
Lipoyl synthase 2, mitochondrial (EC:2.8.1.8UniRule annotation)
Alternative name(s):
Lipoate synthase 2UniRule annotation
Short name:
LS 2UniRule annotation
Short name:
Lip-syn 2UniRule annotation
Lipoic acid synthase 2UniRule annotation
Gene namesi
ORF Names:PHATRDRAFT_28652
OrganismiPhaeodactylum tricornutum (strain CCAP 1055/1)
Taxonomic identifieri556484 [NCBI]
Taxonomic lineageiEukaryotaStramenopilesBacillariophytaBacillariophyceaeBacillariophycidaeNaviculalesPhaeodactylaceaePhaeodactylum
ProteomesiUP000000759 Componentsi: Chromosome 13, Unassembled WGS sequence

Subcellular locationi

  • Mitochondrion UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini? – 314Lipoyl synthase 2, mitochondrialPRO_0000398244
Transit peptidei1 – ?MitochondrionUniRule annotation

Structurei

3D structure databases

ProteinModelPortaliB7G3Y9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the radical SAM superfamily. Lipoyl synthase family.UniRule annotation

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiCOG0320.
HOGENOMiHOG000235998.
InParanoidiB7G3Y9.
KOiK03644.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00206. Lipoyl_synth.
InterProiIPR013785. Aldolase_TIM.
IPR006638. Elp3/MiaB/NifB.
IPR003698. Lipoyl_synth.
IPR007197. rSAM.
[Graphical view]
PANTHERiPTHR10949. PTHR10949. 1 hit.
PfamiPF04055. Radical_SAM. 1 hit.
[Graphical view]
PIRSFiPIRSF005963. Lipoyl_synth. 1 hit.
SMARTiSM00729. Elp3. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00510. lipA. 1 hit.

Sequencei

Sequence statusi: Complete.

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

B7G3Y9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPKGRPSWFK VPAPSQGTQS TYSTASYSRY AQVKDSLQKL DLHTVCEEAQ
60 70 80 90 100
CPNIGECWNG GTGTIMLLGD TCTRGCMFCA VNTDSKPPPP DPFEPFKTAE
110 120 130 140 150
AVVAWGVDYI VLTSVDRDDI ADGGAQHFAQ TVQLLKQNKP NLLVECLVSD
160 170 180 190 200
FQGMLDSVET LALSGLDVYA HNVETVERLQ PFVRDARANY QQSLSTLQHA
210 220 230 240 250
KVVKPELYTK TSIMLGLGET EEEVTQTMTD LRAIGVDVVT FGQYLRPTEH
260 270 280 290 300
HLSVVEYVTP EKFDHYRQVG ENMGFKYVAS GPMVRSSYKA GEFYLEHMIK
310
KERTEAAIDI GENA
Length:314
Mass (Da):34,862
Last modified:February 10, 2009 - v1
Checksum:i70E379E29A535340
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CM000615 Genomic DNA. Translation: EEC46905.1.
RefSeqiXP_002181691.1. XM_002181655.1.
UniGeneiPtc.241.

Genome annotation databases

GeneIDi7202486.
KEGGipti:PHATRDRAFT_28652.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CM000615 Genomic DNA. Translation: EEC46905.1.
RefSeqiXP_002181691.1. XM_002181655.1.
UniGeneiPtc.241.

3D structure databases

ProteinModelPortaliB7G3Y9.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi7202486.
KEGGipti:PHATRDRAFT_28652.

Phylogenomic databases

eggNOGiCOG0320.
HOGENOMiHOG000235998.
InParanoidiB7G3Y9.
KOiK03644.

Enzyme and pathway databases

UniPathwayiUPA00538; UER00593.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00206. Lipoyl_synth.
InterProiIPR013785. Aldolase_TIM.
IPR006638. Elp3/MiaB/NifB.
IPR003698. Lipoyl_synth.
IPR007197. rSAM.
[Graphical view]
PANTHERiPTHR10949. PTHR10949. 1 hit.
PfamiPF04055. Radical_SAM. 1 hit.
[Graphical view]
PIRSFiPIRSF005963. Lipoyl_synth. 1 hit.
SMARTiSM00729. Elp3. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00510. lipA. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The Phaeodactylum genome reveals the evolutionary history of diatom genomes."
    Bowler C., Allen A.E., Badger J.H., Grimwood J., Jabbari K., Kuo A., Maheswari U., Martens C., Maumus F., Otillar R.P., Rayko E., Salamov A., Vandepoele K., Beszteri B., Gruber A., Heijde M., Katinka M., Mock T.
    , Valentin K., Verret F., Berges J.A., Brownlee C., Cadoret J.P., Chiovitti A., Choi C.J., Coesel S., De Martino A., Detter J.C., Durkin C., Falciatore A., Fournet J., Haruta M., Huysman M.J., Jenkins B.D., Jiroutova K., Jorgensen R.E., Joubert Y., Kaplan A., Kroger N., Kroth P.G., La Roche J., Lindquist E., Lommer M., Martin-Jezequel V., Lopez P.J., Lucas S., Mangogna M., McGinnis K., Medlin L.K., Montsant A., Oudot-Le Secq M.P., Napoli C., Obornik M., Parker M.S., Petit J.L., Porcel B.M., Poulsen N., Robison M., Rychlewski L., Rynearson T.A., Schmutz J., Shapiro H., Siaut M., Stanley M., Sussman M.R., Taylor A.R., Vardi A., von Dassow P., Vyverman W., Willis A., Wyrwicz L.S., Rokhsar D.S., Weissenbach J., Armbrust E.V., Green B.R., Van de Peer Y., Grigoriev I.V.
    Nature 456:239-244(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: CCAP 1055/1.
  2. Cited for: GENOME REANNOTATION.
    Strain: CCAP 1055/1.

Entry informationi

Entry nameiLIPA2_PHATC
AccessioniPrimary (citable) accession number: B7G3Y9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 5, 2010
Last sequence update: February 10, 2009
Last modified: July 22, 2015
This is version 41 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.