lys4 (SPBC1105.02c)


Gene Standard Namelys4 Characterisation Statuspublished
Systematic IDSPBC1105.02c Feature Typeprotein coding
Synonyms Name Description
Producthomocitrate synthase Product Size418aa, 46.29 kDa
Genomic Location Chromosome II, 3507472-3505708 (1765nt); CDS:3507307-3506051 (1257nt)

Ensembl Gene Location
GO Molecular Function
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0004410homocitrate synthase activityIMPPMID:162990001
GO Biological Process
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0006091generation of precursor metabolites and energyNASGO_REF:0000051115
GO:0009085lysine biosynthetic processIMPPMID:1762253310
GO:0019878lysine biosynthetic process via aminoadipic acidIMPPMID:162990007
IMPPMID:3142867
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0005829cytosolIDAPMID:168233722317
GO:0005739mitochondrionISOSGD:S000002341GO_REF:0000024756
GO:0005634nucleusISOSGD:S000002289GO_REF:00000242730
Fission Yeast Phenotype Ontology

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0000039growth auxotrophic for lysineCell growth assaylys4 unnamed mutantNot specifiedPECO:0000126, PECO:0000005, PECO:0000102PMID:176225337
Cell growth assaylys4-95EndogenousPMID:3142867
FYPO:0002060viable vegetative cell populationMicroscopylys4ΔNullPECO:0000005, PECO:0000137PMID:236978063755
Microscopylys4ΔNullPMID:20473289

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002177viable vegetative cell with normal cell morphologyMicroscopylys4ΔNullPECO:0000005, PECO:0000137PMID:236978063078
penetrance FYPO_EXT:0000001
Target Of
RelationshipGeneProductReference
regulated by phx1 homeobox transcription factor Phx1 PMID:16299000
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
135074723505708

UTRs

Region Start End Reference
three_prime_UTR35060503505708PMID: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
PF00682 Pfam IPR000891 Pyruvate carboxyltransferase 43 273 3
PS00816 Prosite Patterns IPR002034 Alpha-isopropylmalate/homocitrate synthase, conserved site 221 234 2
PS00815 Prosite Patterns IPR002034 Alpha-isopropylmalate/homocitrate synthase, conserved site 42 58 2
PS50991 Prosite Profiles IPR000891 Pyruvate carboxyltransferase 35 288 3
PTHR10277 HMMPANTHER 1 408 2
PTHR10277:SF21 HMMPANTHER IPR011872 1 408 1
G3DSA:3.20.20.70 Gene3D IPR013785 34 367 35
SSF51569 SuperFamily 33 310 9
Low complexity (SEG) seg 14 25
Low complexity (SEG) seg 118 125
TIGR02146 tigrfam IPR011872 Homocitrate synthase, fungi/archaea 37 383 1

View domain organization at Pfam

Protein Properties

Ave. residue weight 110.75 Da
Charge -4.00
Isoelectric point 5.95
Molecular weight 46.29 kDa
Number of residues 418
Modifications

Protein Modifications

Term IDTerm NameEvidenceResidueReferenceCount
MOD:00696phosphorylated residuePMID:182575171192
PMID:19547744
Sequence
Gene Expression

Qualitative Gene Expression

DescriptionLevelEvidenceReference
protein leveldecreased,
in presence of paraquat dichloride
Western blot evidencePMID:16299000
presentWestern blot evidencePMID:16299000
during GO:0072690
RNA levelunchanged,
in presence of paraquat dichloride
Northern assay evidencePMID:16299000
presentNorthern assay evidencePMID:16299000
during GO:0072690

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)DuringConditionScaleEvidenceReference
26853.36during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633
85763.45during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)DuringConditionScaleEvidenceReference
3.9during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633
25during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
Species Distribution
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3080
conserved in fungi4564
conserved in eukaryotes4482
conserved in bacteria1001
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Genetic Interactions

Source: BioGRID

Gene Product Evidence Reference
swd2Set1C complex subunit Swd2.1 Negative GeneticPMID:22681890
shg1Set1C complex subunit Shg1 Positive GeneticPMID:22681890
pab2poly(A) binding protein Pab2 Negative GeneticPMID:22681890
pyp1tyrosine phosphatase Pyp1 Negative GeneticPMID:22681890
saf4splicing associated factor Saf4 Negative GeneticPMID:22681890
sap14U2 snRNP-associated protein SF3B14 Sap14 Negative GeneticPMID:22681890
pof9F-box protein Pof9 Negative GeneticPMID:22681890
apc10anaphase-promoting complex subunit Apc10 Negative GeneticPMID:22681890
SPBC11B10.08WW domain containing conserved fungal protein Negative GeneticPMID:22681890
vph2endoplasmic reticulum membrane protein involved in assembly of the V-ATPase (predicted) Negative GeneticPMID:22681890
ubp4ubiquitin C-terminal hydrolase Ubp4 Negative GeneticPMID:22681890
far10SIP/FAR complex FHA domain subunit Far10/Csc1 Negative GeneticPMID:22681890
cdk11serine/threonine protein kinase cdk11 Negative GeneticPMID:22681890
pst2Clr6 histone deacetylase complex subunit Pst2 Negative GeneticPMID:22681890
pfd1prefoldin subunit 1 (predicted) Negative GeneticPMID:22681890
cph1Clr6 histone deacetylase associated PHD protein-1 Cph1 Negative GeneticPMID:22681890
mlo3RNA binding protein Mlo3 Negative GeneticPMID:22681890
SPAC1687.14cEF hand family protein, unknown role Negative GeneticPMID:22681890
SPAC24B11.08cCOPII-coated vesicle component Erv46 (predicted) Positive GeneticPMID:22681890
ptc1protein phosphatase 2C Ptc1 Negative GeneticPMID:22681890
uch1ubiquitin C-terminal hydrolase Uch1 Negative GeneticPMID:22681890
rpl160160S ribosomal protein L13/L16 (predicted) Positive GeneticPMID:22681890
cph2Clr6 histone deacetylase associated PHD protein-2 Cph2 Negative GeneticPMID:22681890
mak3histidine kinase Mak3 Negative GeneticPMID:22681890
pub3HECT-type ubiquitin-protein ligase Pub3 (predicted) Negative GeneticPMID:22681890
SPAC1952.06cspliceosomal complex subunit (predicted) Negative GeneticPMID:22681890
hrp3ATP-dependent DNA helicase Hrp3 Negative GeneticPMID:22681890
trt1telomerase reverse transcriptase 1 protein Trt1 Negative GeneticPMID:22681890
cdc37Hsp90 co-chaperone Cdc37 Negative GeneticPMID:22681890
res1MBF transcription factor complex subunit Res1 Negative GeneticPMID:22681890
sre1sterol regulatory element binding protein, transcription factor Sre1 Negative GeneticPMID:21504829
Negative GeneticPMID:22681890
mcs2TFIIH complex cyclin Mcs2 Negative GeneticPMID:22681890
ebs1EST1 family nonsense-mediated mRNA decay (NMD) pathway protein Ebs1 (predicted) Negative GeneticPMID:22681890
dsc4Golgi Dsc E3 ligase complex subunit Dsc3 Negative GeneticPMID:21504829
Negative GeneticPMID:22681890
prw1Clr6 histone deacetylase complex subunit Prw1 Negative GeneticPMID:22681890
toe4transcription factor, zf-fungal binuclear cluster type(predicted) Negative GeneticPMID:22681890
vps5retromer complex subunit Vps5 Negative GeneticPMID:22681890
mkh1MEK kinase (MEKK) Mkh1 Negative GeneticPMID:22681890
SPBC18H10.05WD repeat protein, human WDR44 family Negative GeneticPMID:22681890
SPAC19B12.11czinc finger protein, human ZNF593 ortholog Positive GeneticPMID:22681890
ppk32serine/threonine protein kinase Ppk32 (predicted) Negative GeneticPMID:22681890
Physical Interactions

Source: BioGRID

Gene Product Evidence Reference
bdf2BET family double bromodomain protein Bdf2 Affinity Capture-MSPMID:24013502
hhp1serine/threonine protein kinase Hhp1 Affinity Capture-MSPMID:24055157
tea1cell end marker Tea1 Affinity Capture-MSPMID:21652630
hhp2serine/threonine protein kinase Hhp2 Affinity Capture-MSPMID:24055157
slm9hira protein Slm9 Affinity Capture-MSPMID:20976105
External References
Database Identifier Description
NBRP SPBC1105.02c Fission yeast strain database, National BioResource Project (Japan)
YOGY SPBC1105.02c Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPBC1105.02c BioGRID Interaction Datasets
Expression Viewer SPBC1105.02c Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPBC1105.02c Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPBC1105.02c Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPBC1105.02c Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPBC1105.02c Polyadenylation Viewer (Gullerova lab)
pombeTV SPBC1105.02c Transcriptome Viewer (Bähler Lab)
Cyclebase SPBC1105.02c Cell Cycle Data
GEO SPBC1105.02c GEO profiles
PInt SPBC1105.02c Protein-Protein Interaction Predictor (Bähler Lab)
IntEnz2.3.3.14Integrated relational Enzyme database
Rhea2.3.3.14Annotated reactions database
EntrezGene2539815homocitrate synthase (predicted)
WikiGene2539815homocitrate synthase (predicted)
SPD / RIKEN20/20A12Orfeome Localization Data
UniProtKB/SwissProtQ9Y823Homocitrate synthase, mitochondrial
ModBaseQ9Y823Database of comparative protein structure models
StringQ9Y823Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_596458homocitrate synthase (predicted)
RefSeq mRNANM_001022377972h- homocitrate synthase (predicted) (lys4), mRNA
ePDB3IVSThe European PDB
PDBsum3IVSPDBsum
ePDB3IVTThe European PDB
PDBsum3IVTPDBsum
ePDB3IVUThe European PDB
PDBsum3IVUPDBsum
ePDB3MI3The European PDB
PDBsum3MI3PDBsum
European Nucleotide ArchiveCAB50965ENA Protein Mapping
UniParcUPI000006C25CUniProt Archive

Literature for lys4

Search: Europe PMC or PubMed

Release Version: PomBase:21_41 - 24 Feb 2014