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Protein

Lipoyl synthase, mitochondrial

Gene

LIP1

Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

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: protein 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, chloroplastic (LIP1P-1), Lipoyl synthase, mitochondrial (LIP1), Lipoyl synthase 2, chloroplastic (LIP1P-2)
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 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

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, 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
Ordered Locus Names:Os04g0455800, LOC_Os04g38330
ORF Names:OsJ_15022, OSJNBa0006M15.16
OrganismiOryza sativa subsp. japonica (Rice)
Taxonomic identifieri39947 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBOP cladeOryzoideaeOryzeaeOryzinaeOryza
ProteomesiUP000000763 Componenti: Chromosome 4

Organism-specific databases

GrameneiQ7XRF1.

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
Transit peptidei1 – 3030MitochondrionUniRule annotationAdd
BLAST
Chaini31 – 382352Lipoyl synthase, mitochondrialPRO_0000398849Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi39947.LOC_Os04g38330.1.

Structurei

3D structure databases

ProteinModelPortaliQ7XRF1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

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

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiCOG0320.
InParanoidiQ7XRF1.
KOiK03644.
OMAiCAFCQVE.

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]
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.

Q7XRF1-1 [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 ETPDQVISTT
310 320 330 340 350
EKVRAAGVDV MTFGQYMRPS KRHMPVSEYV TPEAFERYRS LGVDMGFRYV
360 370 380
ASGPMVRSSY KAGEFYIKAM IEADRAKATT AI
Length:382
Mass (Da):41,652
Last modified:March 1, 2004 - v2
Checksum:iEC4A60D426171697
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL731584 Genomic DNA. Translation: CAE02573.2.
AP008210 Genomic DNA. Translation: BAF14878.1.
CM000141 Genomic DNA. Translation: EAZ30943.1.
AK120652 mRNA. Translation: BAH00110.1.
RefSeqiNP_001052964.1. NM_001059499.1.
UniGeneiOs.50311.

Genome annotation databases

EnsemblPlantsiOS04T0455800-01; OS04T0455800-01; OS04G0455800.
GeneIDi4336023.
KEGGiosa:4336023.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL731584 Genomic DNA. Translation: CAE02573.2.
AP008210 Genomic DNA. Translation: BAF14878.1.
CM000141 Genomic DNA. Translation: EAZ30943.1.
AK120652 mRNA. Translation: BAH00110.1.
RefSeqiNP_001052964.1. NM_001059499.1.
UniGeneiOs.50311.

3D structure databases

ProteinModelPortaliQ7XRF1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi39947.LOC_Os04g38330.1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiOS04T0455800-01; OS04T0455800-01; OS04G0455800.
GeneIDi4336023.
KEGGiosa:4336023.

Organism-specific databases

GrameneiQ7XRF1.

Phylogenomic databases

eggNOGiCOG0320.
InParanoidiQ7XRF1.
KOiK03644.
OMAiCAFCQVE.

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]
SMARTiSM00729. Elp3. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00510. lipA. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Nipponbare.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Nipponbare.
  3. "The rice annotation project database (RAP-DB): 2008 update."
    The rice annotation project (RAP)
    Nucleic Acids Res. 36:D1028-D1033(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENOME REANNOTATION.
    Strain: cv. Nipponbare.
  4. "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. Nipponbare.
  5. "Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice."
    The rice full-length cDNA consortium
    Science 301:376-379(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Nipponbare.

Entry informationi

Entry nameiLIAS_ORYSJ
AccessioniPrimary (citable) accession number: Q7XRF1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 5, 2010
Last sequence update: March 1, 2004
Last modified: June 24, 2015
This is version 83 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. Oryza sativa (rice)
    Index of Oryza sativa entries and their corresponding gene designations
  3. 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.