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Protein

Lipoyl synthase, mitochondrial

Gene

LIP1

Organism
Oryza sativa subsp. indica (Rice)
Status
Reviewed-Annotation score: Annotation score: 4 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

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi112 – 1121Iron-sulfur 1 (4Fe-4S)UniRule annotation
Metal bindingi117 – 1171Iron-sulfur 1 (4Fe-4S)UniRule annotation
Metal bindingi123 – 1231Iron-sulfur 1 (4Fe-4S)UniRule annotation
Metal bindingi143 – 1431Iron-sulfur 2 (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi147 – 1471Iron-sulfur 2 (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi150 – 1501Iron-sulfur 2 (4Fe-4S-S-AdoMet)UniRule annotation

GO - Molecular functioni

  1. 4 iron, 4 sulfur cluster binding Source: UniProtKB-HAMAP
  2. lipoate synthase activity Source: UniProtKB-HAMAP
  3. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. aromatic amino acid family biosynthetic process Source: EnsemblPlants/Gramene
  2. cell differentiation Source: EnsemblPlants/Gramene
  3. chlorophyll biosynthetic process Source: EnsemblPlants/Gramene
  4. cysteine biosynthetic process Source: EnsemblPlants/Gramene
  5. glycine catabolic process Source: EnsemblPlants/Gramene
  6. isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway Source: EnsemblPlants/Gramene
  7. jasmonic acid biosynthetic process Source: EnsemblPlants/Gramene
  8. leaf morphogenesis Source: EnsemblPlants/Gramene
  9. nucleotide metabolic process Source: EnsemblPlants/Gramene
  10. oxidoreduction coenzyme metabolic process Source: EnsemblPlants/Gramene
  11. positive regulation of transcription, DNA-templated Source: EnsemblPlants/Gramene
  12. protein lipoylation Source: UniProtKB-HAMAP
  13. secondary metabolic process Source: EnsemblPlants/Gramene
  14. unsaturated fatty acid biosynthetic process Source: EnsemblPlants/Gramene
  15. vitamin metabolic process Source: EnsemblPlants/Gramene
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, mitochondrialUniRule annotation (EC:2.8.1.8UniRule annotation)
Alternative name(s):
Lipoate synthaseUniRule annotation
Short name:
LSUniRule annotation
Short name:
Lip-synUniRule annotation
Lipoic acid synthaseUniRule annotation
Gene namesi
Name:LIP1UniRule annotation
ORF Names:H0523F07.4, OsI_16128
OrganismiOryza sativa subsp. indica (Rice)
Taxonomic identifieri39946 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBEP cladeEhrhartoideaeOryzeaeOryza
ProteomesiUP000007015: Chromosome 4

Organism-specific databases

GrameneiA2XU53.

Subcellular locationi

Mitochondrion UniRule annotation

GO - Cellular componenti

  1. mitochondrial matrix Source: EnsemblPlants/Gramene
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 3030MitochondrionUniRule annotationAdd
BLAST
Chaini31 – 382352Lipoyl synthase, mitochondrialPRO_0000398848Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi39947.LOC_Os04g38330.1.

Structurei

3D structure databases

ProteinModelPortaliA2XU53.
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.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00206. Lipoyl_synth.
MF_03128. Lipoyl_synth_plantM.
InterProiIPR013785. Aldolase_TIM.
IPR006638. Elp3/MiaB/NifB.
IPR003698. Lipoyl_synth.
IPR027527. Lipoyl_synth_mt.
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.

A2XU53-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MHGRRHLAAS LARALTYAPS RSISSTPSLL QTLDPSTPSP AAAPPTAGRL
60 70 80 90 100
AELRQRLQAD APSLGDFTYS VEVGTRKKPL PKPKWMKETI PGGAKYAGIK
110 120 130 140 150
AKLRELKLHT VCEEARCPNL GECWSGGETG TATATIMILG DTCTRGCRFC
160 170 180 190 200
NVKTSRTPPP PDPDEPSNVA QAIASWGLEY IVITSVDRDD LPDQGSGHFA
210 220 230 240 250
ETVQKLKVLK PEMLIEALVP DFRGDPACVE KVATSGLHVF AHNIETVEEL
260 270 280 290 300
QRNVRDHRAN FKQSIDVLKL AKEYAPAGTL TKTSIMLGCG ETPDQVISTM
310 320 330 340 350
EKVRAAGVDV MTFGQYMRPS KRHMPVSEYV TPEAFERYRS LGVDMGFRYV
360 370 380
ASGPMVRSSY KAGEFYIKAM IEADRAKATT AI
Length:382
Mass (Da):41,682
Last modified:October 5, 2010 - v2
Checksum:i754A727161F5B3D0
GO

Sequence cautioni

The sequence EAY94363.1 differs from that shown. Reason: Erroneous termination at position 361. Translated as Lys.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti32 – 343TLD → NLE in CAH67016 (PubMed:12447439).Curated
Sequence conflicti41 – 455AAAPP → EDDPT in CAH67016 (PubMed:12447439).Curated
Sequence conflicti50 – 501L → I in CAH67016 (PubMed:12447439).Curated
Sequence conflicti55 – 551Q → K in CAH67016 (PubMed:12447439).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CR855164 Genomic DNA. Translation: CAH67016.1.
CM000129 Genomic DNA. Translation: EAY94363.1. Sequence problems.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CR855164 Genomic DNA. Translation: CAH67016.1.
CM000129 Genomic DNA. Translation: EAY94363.1. Sequence problems.

3D structure databases

ProteinModelPortaliA2XU53.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi39947.LOC_Os04g38330.1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Organism-specific databases

GrameneiA2XU53.

Phylogenomic databases

eggNOGiCOG0320.
HOGENOMiHOG000235998.

Enzyme and pathway databases

UniPathwayiUPA00538; UER00593.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00206. Lipoyl_synth.
MF_03128. Lipoyl_synth_plantM.
InterProiIPR013785. Aldolase_TIM.
IPR006638. Elp3/MiaB/NifB.
IPR003698. Lipoyl_synth.
IPR027527. Lipoyl_synth_mt.
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

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Guang-Lu-Ai No.4.
  2. "The genomes of Oryza sativa: a history of duplications."
    Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S., Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.
    , Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J., Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X., Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y., Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L., Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H., Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z., Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L., Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F., Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q., Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J., Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M., McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.
    PLoS Biol. 3:266-281(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. 93-11.

Entry informationi

Entry nameiLIAS_ORYSI
AccessioniPrimary (citable) accession number: A2XU53
Secondary accession number(s): Q01JQ9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 5, 2010
Last sequence update: October 5, 2010
Last modified: March 4, 2015
This is version 54 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

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.