lcf1 (SPBC18H10.02)


Gene Standard Namelcf1 Characterisation Statuspublished
Systematic IDSPBC18H10.02 Feature Typeprotein coding
Synonyms Name DescriptionLong Chain Fatty acyl-CoA synthetase
Productlong-chain-fatty-acid-CoA ligase Lcf1 Product Size676aa, 75.97 kDa
Genomic Location Chromosome II, 1769946-1772629 (2684nt); CDS:1770093-1772249 (2157nt)

Ensembl Gene Location
GO Molecular Function
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0005524ATP bindingIEAUniProtKB-KW:KW-0067GO_REF:0000037558
GO:0090432myristoyl-CoA ligase activityIMPPMID:126848812
IMPPMID:18071249
GO:0090434oleoyl-CoA ligase activityIMPPMID:180712491
IMPPMID:12684881
GO:0090433palmitoyl-CoA ligase activityIMPPMID:126848811
IMPPMID:18071249
GO Biological Process
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0001676long-chain fatty acid metabolic processIMPPMID:180712495
redundant_withIGIlcf2PMID:18071249
GO:0035336long-chain fatty-acyl-CoA metabolic processIMPPMID:126848811
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0005737cytoplasmISOSGD:S000004860GO_REF:00000244205
GO:0005783endoplasmic reticulumIDAPMID:16823372594
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Viable

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0001309increased viability in stationary phaseCell growth assaylcf1+ (wild type)OverexpressionPECO:0000126, PECO:0000103PMID:1268488153
FYPO:0001387loss of viability at high temperatureCell growth assaylcf1ΔNullPECO:0000102, PECO:0000126PMID:1268488120
FYPO:0000245loss of viability in stationary phaseCell growth assaylcf1ΔNullPECO:0000126PMID:1807124941
Cell growth assayE4 (G310D)Not specifiedPECO:0000201, PECO:0000103PMID:12684881
Cell growth assayE4 (G310D)Not specifiedPECO:0000102PMID:12684881
Cell growth assayE4 (G310D)Not specifiedPECO:0000126, PECO:0000103PMID:12684881
Cell growth assayG490D (G490D)Not specifiedPMID:12684881
Cell growth assayW376 (W376->stop)Not specifiedPMID:12684881
Cell growth assayE464K (E464K)Not specifiedPMID:12684881
Cell growth assayG339D (G339D)Not specifiedPMID:12684881
Cell growth assayG457E (G457E)Not specifiedPMID:12684881
Cell growth assayG249D (G249D)Not specifiedPMID:12684881
Cell growth assayW344 (W344->stop)Not specifiedPMID:12684881
Cell growth assaylcf1ΔNullPECO:0000104PMID:18071249
Cell growth assaylcf1ΔNullPMID:12684881
FYPO:0001164normal growth on glucose carbon sourceCell growth assayE4 (G310D)Not specifiedPECO:0000126, PECO:0000103PMID:12684881176
Cell growth assaylcf1ΔNullPECO:0000103, PECO:0000126PMID:12684881
FYPO:0000961normal growth on sorbitolCell growth assaylcf1ΔNullPECO:0000102, PECO:0000126PMID:1268488115
FYPO:0001420normal vegetative cell population growth rateCell growth assayE4 (G310D)Not specifiedPECO:0000126, PECO:0000103PMID:1268488151
Cell growth assaylcf1ΔNullPECO:0000103, PECO:0000126PMID:12684881
FYPO:0001245sensitive to cobalt56
expressivity FYPO_EXT:0000001Cell growth assaylcf1ΔNullPECO:0000201, PECO:0000005PMID:22806344
FYPO:0003559sensitive to doxorubicin91
expressivity FYPO_EXT:0000002Cell growth assaylcf1ΔNullPECO:0000137PMID:23365689
FYPO:0000271sensitive to salt stressCell growth assaylcf1ΔNullPECO:0000207, PECO:0000126, PECO:0000102PMID:1268488184
FYPO:0002060viable vegetative cell populationMicroscopylcf1ΔNullPMID:204732893759
Microscopylcf1ΔNullPECO:0000005, PECO:0000137PMID:23697806

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0001304decreased myristoyl-CoA ligase activityEnzyme assay datalcf1ΔNullPMID:180712492
Enzyme assay datalcf1ΔNullPMID:12684881
FYPO:0001302decreased oleoyl-CoA ligase activityEnzyme assay datalcf1ΔNullPMID:126848811
Enzyme assay datalcf1ΔNullPMID:18071249
Enzyme assay datalcf1ΔNullPMID:18071249
FYPO:0001298decreased palmitoyl-CoA ligase activityEnzyme assay datalcf1ΔNullPMID:126848811
FYPO:0001308increased long-chain fatty acid-CoA ligase activityEnzyme assay datalcf1+ (wild type)OverexpressionPMID:126848811
FYPO:0002177viable vegetative cell with normal cell morphology3089
penetrance FYPO_EXT:0000001Microscopylcf1ΔNullPECO:0000005, PECO:0000137PMID:23697806
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
117699461770111
217702381772629

UTRs

Region Coordinates Reference
five_prime_UTR1769946..1770092PMID:21511999
Protein Features

Graphical View

Ensembl protein image with mapped locations of structural domains

Protein Families and Domains

Feature ID Database InterPro Description Start End Count
PF00501 Pfam IPR000873 AMP-dependent synthetase/ligase 92 540 9
PS00455 Prosite Patterns IPR020845 AMP-binding, conserved site 244 255 7
PTHR24096:SF46 HMMPANTHER 2 676 2
PTHR24096 HMMPANTHER 2 676 2
3.40.50.980 Gene3D 251 349 9
3.40.50.980 Gene3D 393 447 9
3.40.50.980 Gene3D 95 250 9
3.40.50.980 Gene3D 37 60 9
2.30.38.10 Gene3D 455 530 7
SSF56801 SuperFamily 19 60 9
SSF56801 SuperFamily 396 674 9
SSF56801 SuperFamily 89 354 9

View domain organization at Pfam

Protein Properties

Ave. residue weight 112.38 Da
Charge 14.00
Isoelectric point 8.33
Molecular weight 75.97 kDa
Number of residues 676
Sequence
Gene Expression

Qualitative Gene Expression

DescriptionLevelEvidenceReference
RNA levelpresent during GO:0072690Northern assay evidencePMID:12684881

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
55966during GO:0000080PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
62967during GO:0000084PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
57752during GO:0000085PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
56774during GO:0000087PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
58580during GO:0072690PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
33181.56during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
23445.64during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
19during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
3during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633
Disease Association
DescriptionQualifierReferenceCount
cancer142
Species Distribution
DescriptionQualifierReferenceCount
conserved in fungi4600
conserved in eukaryotes4514
conserved in bacteria1000
conserved in metazoa3425
conserved in vertebrates3400
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Genetic Interactions

Source: BioGRID

Gene Product Evidence Reference
lcf2long-chain-fatty-acid-CoA ligase Synthetic Growth DefectPMID:18071249
Phenotypic Enhancement
Physical Interactions

Source: BioGRID

Gene Product Evidence Reference
hhp1serine/threonine protein kinase Hhp1 Affinity Capture-MSPMID:24055157
hhp2serine/threonine protein kinase Hhp2 Affinity Capture-MSPMID:24055157
External References
Database Identifier Description
NBRP SPBC18H10.02 Fission yeast strain database, National BioResource Project (Japan)
YOGY SPBC18H10.02 Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPBC18H10.02 BioGRID Interaction Datasets
Expression Viewer SPBC18H10.02 Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPBC18H10.02 Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPBC18H10.02 Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPBC18H10.02 Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPBC18H10.02 Polyadenylation Viewer (Gullerova lab)
pombeTV SPBC18H10.02 Transcriptome Viewer (Bähler Lab)
Cyclebase SPBC18H10.02 Cell Cycle Data
GEO SPBC18H10.02 GEO profiles
PInt SPBC18H10.02 Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPBC18H10.02 Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPBC18H10.02 Fission yeast phenotypic data & analysis
IntEnz6.2.1.3Integrated relational Enzyme database
Rhea6.2.1.3Annotated reactions database
SPD / RIKEN37/37F06Orfeome Localization Data
UniProtKB/SwissProtO60135Long-chain-fatty-acid--CoA ligase 1
ModBaseO60135Database of comparative protein structure models
STRINGO60135Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_595726long-chain-fatty-acid-CoA ligase Lcf1
RefSeq mRNANM_001021624972h- long-chain-fatty-acid-CoA ligase Lcf1 (lcf1), mRNA
European Nucleotide ArchiveCAA18399.1ENA Protein Mapping
UniParcUPI000006C32FUniProt Archive

Literature for lcf1

Search: Europe PMC or PubMed

Release Version: PomBase:23_47 - 27 Oct 2014