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Protein

Lipoyl synthase

Gene

lipA

Organism
Nitrosococcus oceani (strain ATCC 19707 / NCIMB 11848)
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: 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. Octanoyltransferase (lipB)
  2. Lipoyl synthase (lipA)
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 bindingi71 – 711Iron-sulfur 1 (4Fe-4S)UniRule annotation
Metal bindingi76 – 761Iron-sulfur 1 (4Fe-4S)UniRule annotation
Metal bindingi82 – 821Iron-sulfur 1 (4Fe-4S)UniRule annotation
Metal bindingi97 – 971Iron-sulfur 2 (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi101 – 1011Iron-sulfur 2 (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi104 – 1041Iron-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

BioCyciNOCE323261:GCI3-2676-MONOMER.
UniPathwayiUPA00538; UER00593.

Names & Taxonomyi

Protein namesi
Recommended name:
Lipoyl synthaseUniRule annotation (EC:2.8.1.8UniRule annotation)
Alternative name(s):
Lip-synUniRule annotation
Short name:
LSUniRule annotation
Lipoate synthaseUniRule annotation
Lipoic acid synthaseUniRule annotation
Sulfur insertion protein LipAUniRule annotation
Gene namesi
Name:lipAUniRule annotation
Ordered Locus Names:Noc_2629
OrganismiNitrosococcus oceani (strain ATCC 19707 / NCIMB 11848)
Taxonomic identifieri323261 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaChromatialesChromatiaceaeNitrosococcus
ProteomesiUP000006838 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 324324Lipoyl synthasePRO_1000012246Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi323261.Noc_2629.

Structurei

3D structure databases

ProteinModelPortaliQ3J7W4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0320.
HOGENOMiHOG000235997.
KOiK03644.
OMAiEEYVTPE.
OrthoDBiEOG6038ZS.

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.

Q3J7W4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSQKTPSPPG ELKRDIRALK GASKVARIPV KVEPTTERQR KPHWIRAKAP
60 70 80 90 100
IGPEVLRLKG LLREHRLHTV CEEASCPNLG ECFGHGTATF LIMGNICTRR
110 120 130 140 150
CPFCDVAHGR PDPLDAEEPM HLAQAIGAMG LRHVVVTSVD RDDLRDGGAA
160 170 180 190 200
HFTHCIQAIR TQSPQTRIEV LVPDFRGRMD RALEALTAGP PDIFNHNLET
210 220 230 240 250
VPRLYKAVRP GADYLWSLRL LARFKEDHPT VPTKSGLMLG LGEELAEVEQ
260 270 280 290 300
VMKDLRDHGC DMLTLGQYLQ PSLYHLPVRR FVTPEEFDGL GDKAREMGFT
310 320
HVASGPMVRS SYHADRQAAG ESVV
Length:324
Mass (Da):36,030
Last modified:November 8, 2005 - v1
Checksum:iF4CB25CA76020502
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000127 Genomic DNA. Translation: ABA59082.1.
RefSeqiWP_002812480.1. NC_007484.1.
YP_344612.1. NC_007484.1.

Genome annotation databases

EnsemblBacteriaiABA59082; ABA59082; Noc_2629.
KEGGinoc:Noc_2629.
PATRICi22709720. VBINitOce57959_3062.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000127 Genomic DNA. Translation: ABA59082.1.
RefSeqiWP_002812480.1. NC_007484.1.
YP_344612.1. NC_007484.1.

3D structure databases

ProteinModelPortaliQ3J7W4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi323261.Noc_2629.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABA59082; ABA59082; Noc_2629.
KEGGinoc:Noc_2629.
PATRICi22709720. VBINitOce57959_3062.

Phylogenomic databases

eggNOGiCOG0320.
HOGENOMiHOG000235997.
KOiK03644.
OMAiEEYVTPE.
OrthoDBiEOG6038ZS.

Enzyme and pathway databases

UniPathwayiUPA00538; UER00593.
BioCyciNOCE323261:GCI3-2676-MONOMER.

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

  1. "Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707."
    Klotz M.G., Arp D.J., Chain P.S.G., El-Sheikh A.F., Hauser L.J., Hommes N.G., Larimer F.W., Malfatti S.A., Norton J.M., Poret-Peterson A.T., Vergez L.M., Ward B.B.
    Appl. Environ. Microbiol. 72:6299-6315(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 19707 / NCIMB 11848.

Entry informationi

Entry nameiLIPA_NITOC
AccessioniPrimary (citable) accession number: Q3J7W4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: November 8, 2005
Last modified: May 27, 2015
This is version 69 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic 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.