cut3 (SPBC146.03c)


Gene Standard Namecut3 Characterisation Statuspublished
Systematic IDSPBC146.03c Feature Typeprotein coding
Synonymssmc4 Name Description
Productcondensin complex SMC subunit Smc4 Product Size1324aa, 150.65 kDa
Genomic Location Chromosome II, 1006688-1002263 (4426nt); CDS:1006463-1002489 (3975nt)

Ensembl Gene Location
GO Molecular Function
Term NameCount
ATP binding557
Annotation ExtensionEvidenceWith/FromReference
ATPase activity238
Annotation ExtensionEvidenceWith/FromReference
DNA/DNA annealing activity3
Annotation ExtensionEvidenceWith/FromReference
involved in mitotic chromosome condensation
double-stranded DNA binding161
Annotation ExtensionEvidenceWith/FromReference
single-stranded DNA binding37
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
DNA strand renaturation2
Annotation ExtensionEvidenceWith/FromReference
mitotic chromosome condensation19
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
FYPO Single-Allele Phenotypes
Gene Deletion Viability: Inviable

Population Phenotype

Term NameGenotypesCount
inviable vegetative cell populationATT (T19A)1455
AAT (T19A, T51A)
cut3Δ
ATA (T19A, T86A)
cut3-477 (S1147P)
AAA (T19A, T51A, T86A)
cut3::ura4+
loss of viability at high temperaturecut3-477 (S1147P)59
normal viability following cellular response to UVcut3-477 (S1147P)7
viable vegetative cell populationTTA (T86A)3850
TAT (T51A)
cut3-477 (S1147P)
TAA (T51A, T86A)

Cell Phenotype

Term NameGenotypesCount
abnormal cell cycle arrest in mitotic anaphasecut3-477 (S1147P)3
abnormal mitotic cell cyclecut3Δ894
abnormal mitotic chromosome condensationcut3-477 (S1147P)19
AAA (T19A, T51A, T86A)
ATT (T19A)
abnormal mitotic sister chromatid arm separationcut3-477 (S1147P)1
abnormal mitotic sister chromatid segregationcut3-477 (S1147P)281
abolished protein localization to nucleus during mitosis6
affects localization of cut3ATT (T19A)
affects localization of cut14cut3-T19A (T19A)
affects localization of cut14ATT (T19A)
affects localization of cnd2cut3Δ
cutcut3-477 (S1147P)128
cut cell with decreased poly(A)+ mRNA export from nucleuscut3-12
decreased mitotic chromosome condensationcut3-477 (S1147P)12
cut3-m26 (L289F)
cut3-l23 (S1116P)
decreased protein kinase activity56
affecting cds1cut3Δ
decreased protein localization to chromatin during vegetative growth55
affects localization of cut14cut3-477 (S1147P)
affects localization of cnd2cut3-477 (S1147P)
decreased protein localization to chromosome during vegetative growth90
affects localization of cnd1cut3-477 (S1147P)
gene expression regulation phenotypecut3-477 (S1147P)220
incomplete mitotic sister chromatid segregation, with chromatin bridgecut3-477 (S1147P)6
incomplete, unequal mitotic sister chromatid segregation, with smeared DNAcut3-477 (S1147P)4
inviable after spore germination with elongated germ tubecut3Δ164
inviable after spore germination, without cell division, elongated cell with abnormal nuclear morphologycut3::ura4+1
inviable sporecut3Δ476
normal protein localization to centromere38
affecting csm1cut3-477 (S1147P)
normal protein localization to chromatin41
affecting mde4cut3-477 (S1147P)
normal protein localization to nucleus during mitosis1-528 (529-1324)2
normal protein phosphorylation103
affecting cut3cut3ΔNΔC
affecting cut3cut3ΔC
affecting cut3cut3ΔN

FYPO Multi-allele Phenotypes

Population Phenotype

Term NameGenotypes
decreased vegetative cell population growthcut3-477 (S1147P), cut14+
top1+, cut3-477 (S1147P)
inviable vegetative cell populationcut14-G35N (G35N), cut3+
cut3-5E-phosphomimic (T774E, S783E, T785E, T787E, T791E), cut3-477 (S1147P)
top1Δ, cut3-477 (S1147P)
top2-250, cut3-477 (S1147P)
slow vegetative cell population growthcsm1Δ, cut3-477 (S1147P)
viable vegetative cell populationtop1Δ, cut3-477 (S1147P)
cut3-5A (T774A, S783A, T785A, T787A, T791A), cut3-477 (S1147P)
cut3-477 (S1147P), sfc3-1

Cell Phenotype

Term NameGenotypes
abnormal mitotic chromosome condensationcut14-G35N (G35N), cut3+
abolished protein phosphorylation
affecting cut3cut3-K38T (K38T), cut14-K38T (K38T)
affecting cut14cut3-K38T (K38T), cut14-K38T (K38T)
cutcut3-477 (S1147P), cut14-208 (S861P)
decreased DNA/DNA annealing activity
affecting activity of GO:0000797cut3-477 (S1147P), cut14-208 (S861P)
decreased mitotic chromosome condensationcut3-477 (S1147P), sfc3-1
mitotic catastrophe with cutcut14-G35N (G35N), cut3+
normal DNA/DNA annealing activitycut3-K161I (K161I), cut14-K38T (K38T)
protein mislocalized to nucleus during mitotic interphase
affects localization of cut31-528 (529-1324), crm1-809 (E430K)
viable elongated vegetative cell, elongated upon mitotic entrycut3+, cut14+
Target Of
OntologyRelationshipGeneProduct
FYPO affected by mutation in cut14 condensin complex SMC subunit Smc2
FYPO affected by mutation in cut3 condensin complex SMC subunit Smc4
FYPO localization affected by mutation in crm1 importin family nuclear export receptor Crm1
FYPO localization affected by mutation in cut3 condensin complex SMC subunit Smc4
GO substrate of cdc2 cyclin-dependent protein kinase Cdk1/Cdc2
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons1006688..1002263
mRNA1006688..1002263
5' UTR1006688..1006464PMID:21511999
CDS1006463..1002489
3' UTR1002488..1002263AU009580
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
PF06470 Pfam IPR010935 SMCs flexible hinge 651 764 4
PF02463 Pfam IPR003395 RecF/RecN/SMC, N-terminal 126 1312 5
SM00968 SMART IPR010935 SMCs flexible hinge 651 764 4
PTHR18937:SF231 HMMPANTHER 830 1321 1
PTHR18937:SF231 HMMPANTHER 106 790 1
PTHR18937 HMMPANTHER 830 1321 6
PTHR18937 HMMPANTHER 106 790 6
3.40.50.300 Gene3D IPR027417 P-loop containing nucleoside triphosphate hydrolase 1040 1041 288
3.40.50.300 Gene3D IPR027417 P-loop containing nucleoside triphosphate hydrolase 1185 1322 288
3.40.50.300 Gene3D IPR027417 P-loop containing nucleoside triphosphate hydrolase 128 294 288
SSF52540 SuperFamily IPR027417 P-loop containing nucleoside triphosphate hydrolase 127 290 294
SSF52540 SuperFamily IPR027417 P-loop containing nucleoside triphosphate hydrolase 1205 1309 294
SSF52540 SuperFamily IPR027417 P-loop containing nucleoside triphosphate hydrolase 426 457 294
0038317 SuperFamily IPR010935 SMCs flexible hinge 616 798 4
Coil ncoils Predicted coiled-coil protein (DUF2205) 976 1017 1055
Coil ncoils Predicted coiled-coil protein (DUF2205) 379 420 1055
Coil ncoils Predicted coiled-coil protein (DUF2205) 477 504 1055
Coil ncoils Predicted coiled-coil protein (DUF2205) 586 606 1055
Coil ncoils Predicted coiled-coil protein (DUF2205) 530 550 1055
Coil ncoils Predicted coiled-coil protein (DUF2205) 428 448 1055
Coil ncoils Predicted coiled-coil protein (DUF2205) 825 852 1055
Coil ncoils Predicted coiled-coil protein (DUF2205) 867 925 1055
Coil ncoils Predicted coiled-coil protein (DUF2205) 1032 1066 1055
PIRSF005719 PIRSF IPR024704 Structural maintenance of chromosomes protein 123 1323 4

View domain organization at Pfam

Term IDTerm NameReferenceCount
PBO:0000849SMC familyTemporary processing gif - replaced by AJAX with count of genes annotated with the term PBO:0000849

Term IDTerm NameReferenceCount
SO:0001531nuclear_export_signal7

Protein Properties

Ave. residue weight 113.79 Da
Charge -1.00
Codon Adaptation Index 0.40
Isoelectric point 6.46
Molecular weight 150.65 kDa
Number of residues 1324
Modifications

Protein Modifications

Term NameResidueCount
O-phospho-L-serine 2289
present during mitotic M phaseS68
present during mitotic M phaseS32
present during mitotic M phaseS38
present during mitotic M phaseS36
present during mitotic M phaseS899
S10, S11, S36, S38, S68, S88
Annotation ExtensionEvidenceResidueReference
present during mitotic M phase experimental evidence S68 PMID:21712547
present during mitotic M phase experimental evidence S32 PMID:21712547
present during mitotic M phase experimental evidence S38 PMID:21712547
present during mitotic M phase experimental evidence S36 PMID:21712547
present during mitotic M phase experimental evidence S899 PMID:21712547
IDA S36 PMID:25720772
experimental evidence S38 PMID:24763107
IDA S68 PMID:21540296
IDA S88 PMID:21540296
IDA S10 PMID:21540296
IDA S36 PMID:21540296
IDA S11 PMID:25720772
O-phospho-L-threonine 1085
added by cdc2, added during mitotic metaphaseT19
present during mitotic M phaseT51
present during mitotic M phaseT917
present during mitotic M phaseT19
S460, S630, S633, S783, S804, S807, S1109, T9, T19, T785, T787, T791, T803, T813, T1323
Annotation ExtensionEvidenceResidueReference
added by cdc2
added during mitotic metaphase
IDA T19 PMID:10485849
present during mitotic M phase experimental evidence T51 PMID:21712547
present during mitotic M phase experimental evidence T917 PMID:21712547
present during mitotic M phase experimental evidence T19 PMID:21712547
IDA S1109 PMID:25520186
IDA S630 PMID:25520186
IDA S807 PMID:25520186
IDA S804 PMID:25520186
IDA T9 PMID:25720772
IDA S460 PMID:25520186
IDA T791 PMID:25520186
IDA T785 PMID:25520186
IDA T813 PMID:25520186
IDA S783 PMID:25520186
IDA T803 PMID:25520186
IDA T787 PMID:25520186
IDA T19 PMID:21540296
IDA T1323 PMID:25720772
IDA S633 PMID:25520186
O-phosphorylated residueS10,S14, S11,S14, S11,T12, T9,S14, T9,T12 2457
Annotation ExtensionEvidenceResidueReference
IDA S10,S14 PMID:25720772
IDA T9,S14 PMID:25720772
IDA S11,T12 PMID:25720772
IDA S11,S14 PMID:25720772
IDA T9,T12 PMID:25720772
Sequence
Gene Expression

Qualitative Gene Expression

DescriptionLevelEvidenceReference
protein levelunchanged during GO:0000278Western blot evidencePMID:7957061

Quantitative Gene Expression

View graphical display of gene expression data for cut3 (SPBC146.03c)

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
4353during GO:0000080PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
5178during GO:0000084PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
3677during GO:0000085PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
4807during GO:0000087PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
4969during GO:0072690PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
1019.97during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
437.27during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
1.8during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
0.53during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
Misc
DescriptionQualifierReferenceCount
thiophosphorylated Cut3 residues are located along the interface with Cut14 PMID:255201861
Taxonomic Conservation
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3093
conserved in fungi4607
conserved in eukaryotes4517
conserved in bacteria1005
conserved in metazoa3427
conserved in vertebrates3402
conserved in archaea242
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

Load genes that interact physically with SPBC146.03c into the Query Builder
View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
binds DNA-binding domain construct withcti1C1D family exosome subunit Cti1 Two-hybridPMID:15148393
binds DNA-binding domain construct withcsm1microtubule-site clamp monopolin complex subunit Csm1/Pcs1 Two-hybridPMID:21633354
affinity captured bycbf11CBF1/Su(H)/LAG-1 family transcription factor Cbf11 Affinity Capture-MSPMID:22540037
affinity captured bycut14condensin complex SMC subunit Smc2 Affinity Capture-WesternPMID:9285594
affinity captured byepe1Jmjc domain chromatin associated protein Epe1 Affinity Capture-MSPMID:24013502
affinity captured bycnd2condensin complex non-SMC subunit Cnd2 Affinity Capture-WesternPMID:21633354
affinity captured byccq1telomere maintenance protein Ccq1 Affinity Capture-MSPMID:20709788
affinity captured byrpc25DNA-directed RNA polymerase III complex subunit Rpc25 Affinity Capture-WesternPMID:19910488
affinity capturespku80Ku domain protein Pku80 Affinity Capture-WesternPMID:23084836
affinity capturescnd1condensin complex non-SMC subunit Cnd1 Affinity Capture-MSPMID:10485849
affinity capturescnd2condensin complex non-SMC subunit Cnd2 Affinity Capture-MSPMID:10485849
affinity capturescnd3condensin complex non-SMC subunit Cnd3 Affinity Capture-MSPMID:10485849
affinity capturescut14condensin complex SMC subunit Smc2 Affinity Capture-MSPMID:10485849
modified bycdc2cyclin-dependent protein kinase Cdk1/Cdc2 Biochemical ActivityPMID:10485849
Genetic Interactions

Source: BioGRID

Load genes that interact genetically with SPBC146.03c into the Query Builder
View these interactions in esyN

Gene Product Evidence Reference
synthetically rescued bysen1ATP-dependent 5' to 3' DNA/RNA helicase Sen1 Synthetic RescuePMID:25392932
synthetically rescued byswd22mRNA cleavage and polyadenylation specificity factor complex subunit, WD repeat protein Swd22 Synthetic RescuePMID:25392932
synthetically rescued byppn1mRNA cleavage and polyadenylation specificity factor complex associated protein Synthetic RescuePMID:24945319
synthetically rescued bypin1peptidyl-prolyl cis-trans isomerase Pin1 Synthetic RescuePMID:24945319
synthetically rescued byypa1protein phosphatase type 2A regulator, PTPA family Ypa1 Synthetic RescuePMID:24945319
synthetically rescued bytfs1transcription elongation factor TFIIS Synthetic RescuePMID:24945319
synthetically rescued bydis2serine/threonine protein phosphatase PP1, Dis2 Synthetic RescuePMID:24945319
synthetically rescued bymms19Dos2 silencing complex subunit Mms19 Synthetic RescuePMID:24945319
synthetically rescued byssu72phosphoric ester hydrolase Ssu72 (predicted) Synthetic RescuePMID:24945319
synthetically rescued bytop1DNA topoisomerase I Synthetic RescuePMID:24945319
synthetically rescued bycid14poly(A) polymerase Cid14 Synthetic RescuePMID:24945319
synthetically rescued bysfc3transcription factor TFIIIC complex B box binding subunit Sfc3 Synthetic RescuePMID:21633354
synthetically rescued bynut2mediator complex subunit Med10 Synthetic RescuePMID:24362309
positive genetic interaction witharp6actin-like protein Arp6 Positive GeneticPMID:22681890
positive genetic interaction withmrf1mitochondrial peptide chain release factor (predicted) Positive GeneticPMID:22681890
positive genetic interaction withrtt109RTT109 family histone lysine acetyltransferase Positive GeneticPMID:22681890
positive genetic interaction withsil1nucleotide exchange factor for the ER lumenal Hsp70 chaperone, Sil1 (predicted) Positive GeneticPMID:22681890
positive genetic interaction withsno1glutamine aminotransferase subunit Sno1 (predicted) Positive GeneticPMID:22681890
negative genetic interaction withraf2Rik1-associated factor Raf2 Negative GeneticPMID:22681890
negative genetic interaction withulp2SUMO deconjugating cysteine peptidase Ulp2 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withsey1GTP binding protein Sey1 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withSPBC15C4.04camino acid transmembrane transporter (predicted) Negative GeneticPMID:22681890
negative genetic interaction withnup124nucleoporin Nup124 Negative GeneticPMID:22681890
negative genetic interaction withsgf29SAGA complex subunit Sgf29 Negative GeneticPMID:22681890
negative genetic interaction withase1antiparallel microtubule cross-linking factor Ase1 Negative GeneticPMID:22681890
negative genetic interaction withlam2human LAMTOR2 ortholog Lam2 Negative GeneticPMID:22681890
negative genetic interaction withtls1splicing factor Tls1 Negative GeneticPMID:22681890
negative genetic interaction withcph1Clr6 histone deacetylase associated PHD protein-1 Cph1 Negative GeneticPMID:22681890
negative genetic interaction withclr4histone H3 lysine methyltransferase Clr4 Negative GeneticPMID:22681890
negative genetic interaction withsat1Golgi membrane exchange factor subunit Sat1 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withnic1NiCoT heavy metal ion transmembrane transporter Nic1 Negative GeneticPMID:22681890
negative genetic interaction withSPCC16C4.106-phosphogluconolactonase (predicted) Negative GeneticPMID:22681890
negative genetic interaction withSPBC9B6.11cCCR4/nocturin family endoribonuclease (predicted) Negative GeneticPMID:22681890
negative genetic interaction withhrk1haspin related kinase Hrk1 Negative GeneticPMID:22681890
negative genetic interaction withred1RNA elimination defective protein Red1 Negative GeneticPMID:22681890
negative genetic interaction withSPBC32H8.01cconserved fungal protein, involved in endocytic trafficking (predicted) Negative GeneticPMID:22681890
negative genetic interaction withfkbp39FKBP-type peptidyl-prolyl cis-trans isomerase (predicted) Negative GeneticPMID:22681890
negative genetic interaction withsnf5SWI/SNF complex subunit Snf5 Negative GeneticPMID:22681890
negative genetic interaction witharp42SWI/SNF and RSC complex subunit Arp42 Negative GeneticPMID:22681890
negative genetic interaction withccq1telomere maintenance protein Ccq1 Negative GeneticPMID:22681890
negative genetic interaction withapq12nuclear membrane organization protein Apq12 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withliz1pantothenate transmembrane transporter Liz1 Negative GeneticPMID:22681890
negative genetic interaction withpab2poly(A) binding protein Pab2 Negative GeneticPMID:22681890
negative genetic interaction withraf1CLRC ubiquitin E3 ligase complex specificiy factor Raf1/Dos1 Negative GeneticPMID:22681890
negative genetic interaction withgcn5SAGA complex histone acetyltransferase catalytic subunit Gcn5 Negative GeneticPMID:22681890
overexpression rescuescdc18MCM loader Dosage RescuePMID:15507118
overexpression rescuescut14condensin complex SMC subunit Smc2 Dosage RescuePMID:15507118
overexpression rescuesorc5origin recognition complex subunit Orc5 Dosage RescuePMID:15507118
phenotype enhanced bysfc3transcription factor TFIIIC complex B box binding subunit Sfc3 Phenotypic EnhancementPMID:19910488
rescuesccq1telomere maintenance protein Ccq1 Phenotypic SuppressionPMID:20709788
synthetic lethal withtop2DNA topoisomerase II Synthetic LethalityPMID:24362309
synthetic lethal withcut14condensin complex SMC subunit Smc2 Synthetic LethalityPMID:24362309
synthetic lethal withcnd1condensin complex non-SMC subunit Cnd1 Synthetic LethalityPMID:24362309
synthetic lethal withcnd3condensin complex non-SMC subunit Cnd3 Synthetic LethalityPMID:24362309
synthetic lethal withcsm1microtubule-site clamp monopolin complex subunit Csm1/Pcs1 Synthetic LethalityPMID:21633354
synthetic lethal withcph2Clr6 histone deacetylase associated PHD protein Cph2 Synthetic LethalityPMID:24362309
synthetic lethal withsnf21ATP-dependent DNA helicase Snf21 Synthetic LethalityPMID:24362309
synthetic lethal withulp2SUMO deconjugating cysteine peptidase Ulp2 (predicted) Synthetic LethalityPMID:24362309
synthetic lethal witharp9SWI/SNF and RSC complex subunit Arp9 Synthetic LethalityPMID:24362309
synthetic lethal withark1aurora-B kinase Ark1 Synthetic LethalityPMID:24362309
External References
Database Identifier Description
NBRP SPBC146.03c Fission yeast strain database, National BioResource Project (Japan)
YOGY SPBC146.03c Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPBC146.03c BioGRID Interaction Datasets
Expression Viewer SPBC146.03c Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPBC146.03c Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPBC146.03c Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPBC146.03c Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPBC146.03c Polyadenylation Viewer (Gullerova lab)
pombeTV SPBC146.03c Transcriptome Viewer (Bähler Lab)
GEO SPBC146.03c GEO profiles
PInt SPBC146.03c Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPBC146.03c Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPBC146.03c Fission yeast phenotypic data & analysis
Cyclebase SPBC146.03c.1 Cell Cycle Data
SPD / RIKEN34/34A12Orfeome Localization Data
UniProtKB/SwissProtP41004Structural maintenance of chromosomes protein 4
ModBaseP41004Database of comparative protein structure models
STRINGP41004Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_595392condensin complex subunit Cut3
RefSeq mRNANM_001021299972h- condensin complex subunit Cut3 (cut3), mRNA
European Nucleotide ArchiveBAA06454.1ENA Protein Mapping
European Nucleotide ArchiveBAA87263.1ENA Protein Mapping
European Nucleotide ArchiveCAB46756.1ENA Protein Mapping
UniParcUPI000012870DUniProt Archive

Literature for cut3

Search: Europe PMC or PubMed

Release Version: PomBase:30_61 - 12 Sep 2016