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 NameCount
homocitrate synthase activity1
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
lysine biosynthetic process10
Annotation ExtensionEvidenceWith/FromReference
lysine biosynthetic process via aminoadipic acid8
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
cytosol2302
Annotation ExtensionEvidenceWith/FromReference
mitochondrion752
Annotation ExtensionEvidenceWith/FromReference
nucleus2691
Annotation ExtensionEvidenceWith/FromReference
FYPO Single-Allele Phenotypes
Gene Deletion Viability: Viable

Population Phenotype

Term NameGenotypesCount
growth auxotrophic for lysinelys4Δ8
lys4-95
viable vegetative cell populationlys4Δ3844

Cell Phenotype

Term NameGenotypesCount
viable vegetative cell with normal cell morphologylys4Δ3100
Target Of
OntologyRelationshipGeneProduct
FYPO affected by mutation in sod1 superoxide dismutase Sod1
GO regulated by phx1 stationary phase-specific homeobox transcription factor Phx1
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons3507472..3505708
mRNA3507472..3505708
5' UTR3507472..3507308AU007953
CDS3507307..3506051
3' UTR3506050..3505708PMID: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 35 294 3
PS50991 Prosite Profiles IPR000891 Pyruvate carboxyltransferase 35 288 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
PTHR10277:SF9 HMMPANTHER 1 396 1
PTHR10277 HMMPANTHER 1 396 2
3.20.20.70 Gene3D IPR013785 Aldolase-type TIM barrel 34 367 35
SSF51569 SuperFamily 33 310 9
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
Codon Adaptation Index 0.71
Isoelectric point 5.95
Molecular weight 46.29 kDa
Number of residues 418
Modifications

Protein Modifications

Term NameResidueCount
O-phospho-L-serine 1677
present during mitotic M phaseS360
Annotation ExtensionEvidenceResidueReference
present during mitotic M phase experimental evidence S360 PMID:21712547
O-phospho-L-threonine 701
present during cellular response to thiabendazoleT202
Annotation ExtensionEvidenceResidueReference
present during cellular response to thiabendazole IDA T202 PMID:18257517
phosphorylated residue 1932
Annotation ExtensionEvidenceResidueReference
IDA PMID:19547744
ubiquitinylated lysineK139 512
Annotation ExtensionEvidenceResidueReference
mass spectrometry evidence K139 PMID:26412298
IDA PMID:26412298
Sequence
Gene Expression

Qualitative Gene Expression

DescriptionLevelEvidenceReference
protein levelpresent during GO:0072690Western blot evidencePMID:16299000
decreased in presence of paraquat dichloride Western blot evidencePMID:16299000
RNA levelpresent during GO:0072690Northern assay evidencePMID:16299000
unchanged in presence of paraquat dichloride Northern assay evidencePMID:16299000

Quantitative Gene Expression

View graphical display of gene expression data for lys4 (SPBC1105.02c)

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
188843during GO:0000080PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
177812during GO:0000084PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
177742during GO:0000085PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
167151during GO:0000087PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
174121during GO:0072690PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
85763.45during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
26853.36during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
25during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
3.9during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
Taxonomic Conservation
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3092
conserved in fungi4606
conserved in eukaryotes4516
conserved in bacteria1002
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

Load genes that interact physically with SPBC1105.02c into the Query Builder
View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
affinity captured bytea1cell end marker Tea1 Affinity Capture-MSPMID:21652630
affinity captured byslm9hira protein Slm9 Affinity Capture-MSPMID:20976105
co-locates (via crystalisation or NMR) withlys4homocitrate synthase Co-crystal or NMR structurePMID:20089861
binds activation domain construct withlys4homocitrate synthase Two-hybridPMID:26771498
Genetic Interactions

Source: BioGRID

Load genes that interact genetically with SPBC1105.02c into the Query Builder
View these interactions in esyN

Gene Product Evidence Reference
negative genetic interaction withmak3histidine kinase Mak3 Negative GeneticPMID:22681890
negative genetic interaction withres1MBF transcription factor complex subunit Res1 Negative GeneticPMID:22681890
negative genetic interaction withsre1sterol regulatory element binding protein, transcription factor Sre1 Negative GeneticPMID:22681890
negative genetic interaction withdsc4Golgi Dsc E3 ligase complex subunit Dsc4 Negative GeneticPMID:22681890
negative genetic interaction withmlo3RNA binding protein Mlo3 Negative GeneticPMID:22681890
negative genetic interaction withtrt1telomerase reverse transcriptase 1 protein Trt1 Negative GeneticPMID:22681890
negative genetic interaction withapc10anaphase-promoting complex substrate recognition subunit Apc10 Negative GeneticPMID:22681890
negative genetic interaction withpof9F-box protein Pof9 Negative GeneticPMID:22681890
negative genetic interaction withsaf4splicing associated factor Saf4 Negative GeneticPMID:22681890
negative genetic interaction withcdc37Hsp90 co-chaperone Cdc37 Negative GeneticPMID:22681890
negative genetic interaction withptc1protein phosphatase 2C Ptc1 Negative GeneticPMID:22681890
negative genetic interaction withubp4ubiquitin C-terminal hydrolase Ubp4 Negative GeneticPMID:22681890
negative genetic interaction withgim6prefoldin subunit 1 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withhrp3ATP-dependent DNA helicase Hrp3 Negative GeneticPMID:22681890
negative genetic interaction withfar10SIP/FAR complex FHA domain subunit Far10/Csc1 Negative GeneticPMID:22681890
negative genetic interaction withSPAC1687.14cEF hand family protein, centrin-like Negative GeneticPMID:22681890
negative genetic interaction withpst2Clr6 histone deacetylase complex subunit Pst2 Negative GeneticPMID:22681890
negative genetic interaction withppk32serine/threonine protein kinase Ppk32 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withcph2Clr6 histone deacetylase associated PHD protein-2 Cph2 Negative GeneticPMID:22681890
negative genetic interaction withmcs2TFIIH complex cyclin Mcs2 Negative GeneticPMID:22681890
negative genetic interaction withvps5retromer complex subunit Vps5 Negative GeneticPMID:22681890
negative genetic interaction withuch1ubiquitin C-terminal hydrolase Uch1 Negative GeneticPMID:22681890
negative genetic interaction withvph2endoplasmic reticulum membrane protein involved in assembly of the V-ATPase (predicted) Negative GeneticPMID:22681890
negative genetic interaction withcph1Clr6 histone deacetylase associated PHD protein-1 Cph1 Negative GeneticPMID:22681890
negative genetic interaction withsap14U2 snRNP-associated protein SF3B14 Sap14 Negative GeneticPMID:22681890
negative genetic interaction withmkh1MEK kinase (MEKK) Mkh1 Negative GeneticPMID:22681890
negative genetic interaction withebs1EST1 family nonsense-mediated mRNA decay (NMD) pathway protein Ebs1 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withSPBC11B10.08WW domain containing conserved fungal protein Negative GeneticPMID:22681890
negative genetic interaction withtoe4transcription factor, zf-fungal binuclear cluster type(predicted) Negative GeneticPMID:22681890
negative genetic interaction withpab2poly(A) binding protein Pab2 Negative GeneticPMID:22681890
negative genetic interaction withswd2Set1C complex subunit Swd2.1 Negative GeneticPMID:22681890
negative genetic interaction withpyp1tyrosine phosphatase Pyp1 Negative GeneticPMID:22681890
negative genetic interaction withSPBC18H10.05WD repeat protein, human WDR44 family Negative GeneticPMID:22681890
negative genetic interaction withcdk11serine/threonine protein kinase cdk11 Negative GeneticPMID:22681890
negative genetic interaction withpub3HECT-type ubiquitin-protein ligase E3 Pub3 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withSPAC1952.06cspliceosomal complex subunit (predicted) Negative GeneticPMID:22681890
negative genetic interaction withprw1Clr6 histone deacetylase complex subunit Prw1 Negative GeneticPMID:22681890
positive genetic interaction withSPAC24B11.08cCOPII-coated vesicle component Erv46 (predicted) Positive GeneticPMID:22681890
positive genetic interaction withSPAC19B12.11czinc finger protein, human ZNF593 ortholog Positive GeneticPMID:22681890
positive genetic interaction withshg1Set1C complex subunit Shg1 Positive GeneticPMID:22681890
positive genetic interaction withrpl160160S ribosomal protein L13/L16 (predicted) Positive GeneticPMID:22681890
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)
GEO SPBC1105.02c GEO profiles
PInt SPBC1105.02c Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPBC1105.02c Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPBC1105.02c Fission yeast phenotypic data & analysis
Cyclebase SPBC1105.02c.1 Cell Cycle Data
SPD / RIKEN20/20A12Orfeome Localization Data
IntEnz2.3.3.14Integrated relational Enzyme database
Rhea2.3.3.14Annotated reactions database
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
PDB3IVSPDB
PDBsum3IVSPDBsum
ePDB3IVTThe European PDB
PDB3IVTPDB
PDBsum3IVTPDBsum
ePDB3IVUThe European PDB
PDB3IVUPDB
PDBsum3IVUPDBsum
ePDB3MI3The European PDB
PDB3MI3PDB
PDBsum3MI3PDBsum
European Nucleotide ArchiveCAB50965.1ENA Protein Mapping
MetaCycPWY-3081L-lysine biosynthesis V
MetaCycPWY-68713-methylbutanol biosynthesis
MetaCycPWY-7710FeMo cofactor biosynthesis
KEGG00290+2.3.3.13Valine, leucine and isoleucine biosynthesis
KEGG00300+2.3.3.14Lysine biosynthesis
KEGG00620+2.3.3.13Pyruvate metabolism
KEGG00620+2.3.3.14Pyruvate metabolism
UniParcUPI000006C25CUniProt Archive
UniPathwayUPA00048Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 2/4

Literature for lys4

Search: Europe PMC or PubMed

Release Version: PomBase:30_60 - 12 May 2016