smc6 (SPCC5E4.06)


Gene Standard Namesmc6 Characterisation Statuspublished
Systematic IDSPCC5E4.06 Feature Typeprotein coding
Synonymsrad18 Name Description
ProductSmc5-6 complex SMC subunit Smc6 Product Size1140aa, 130.93 kDa
Genomic Location Chromosome III, 652648-656420 (3773nt); CDS:652783-656311 (3529nt)

Ensembl Gene Location
GO Molecular Function
Term NameCount
ATP binding558
Annotation ExtensionEvidenceWith/FromReference
double-stranded DNA-dependent ATPase activity1
Annotation ExtensionEvidenceWith/FromReference
protein binding859
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
double-strand break repair via homologous recombination36
Annotation ExtensionEvidenceWith/FromReference
meiotic cell cycle418
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
nucleus2696
Annotation ExtensionEvidenceWith/FromReference
Smc5-Smc6 complex8
Annotation ExtensionEvidenceWith/FromReference
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Inviable

Population Phenotype

Term NameAlleleExpressionCount
inviable vegetative cell populationsmc6ΔNull1438
normal growth on JM216rad18-XNot specified10
normal growth on tetraplatinrad18-XNot specified14
sensitive to cisplatinrad18-XNot specified29
sensitive to hydroxyureasmc6-XNot specified534
sensitive to ionizing radiationrad18-XNot specified60
sensitive to JM335rad18-XNot specified14
sensitive to oxaliplatinrad18-XNot specified16
sensitive to triplatin tetranitraterad18-XNot specified7
sensitive to UV during vegetative growthrad18 mutantNot specified142
rad18-XNot specified
smc6-XNot specified

Cell Phenotype

Term NameAlleleExpressionCount
abnormal mitotic cell cyclesmc6ΔNull834
decreased UV-damage excision repairrad18-XNot specified3
inviable after spore germination, single or double cell division, elongated cellsmc6ΔNull12
inviable elongated mononucleate aseptate cellrad18-XNot specified34
inviable elongated vegetative cellsmc6ΔNull401
inviable vegetative cell, abnormal cell shape, normal cell sizesmc6ΔNull199
viable elongated vegetative cellrad18-XNot specified301
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons652648..652893, 653000..656420
mRNA652648..656420
5' UTR652648..652782PMID:21511999
CDS652783..652893, 653000..656311
3' UTR656312..656420PMID: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
PF02463 Pfam IPR003395 RecF/RecN/SMC, N-terminal 97 1108 6
PTHR19306:SF2 HMMPANTHER IPR027132 Structural maintenance of chromosomes protein 6 6 1127 1
PTHR19306 HMMPANTHER 6 1127 2
3.40.50.300 Gene3D IPR027417 P-loop containing nucleoside triphosphate hydrolase 97 260 288
3.40.50.300 Gene3D IPR027417 P-loop containing nucleoside triphosphate hydrolase 962 1109 288
SSF52540 SuperFamily IPR027417 P-loop containing nucleoside triphosphate hydrolase 97 304 294
SSF52540 SuperFamily IPR027417 P-loop containing nucleoside triphosphate hydrolase 926 1108 294
Coil ncoils Rabaptin coiled-coil domain 451 486 968
Coil ncoils Rabaptin coiled-coil domain 951 979 968
Coil ncoils Rabaptin coiled-coil domain 715 750 968
Coil ncoils Rabaptin coiled-coil domain 787 822 968
Coil ncoils Rabaptin coiled-coil domain 757 778 968
Coil ncoils Rabaptin coiled-coil domain 829 885 968
Coil ncoils Rabaptin coiled-coil domain 331 366 968
Coil ncoils Rabaptin coiled-coil domain 264 285 968
Coil ncoils Rabaptin coiled-coil domain 912 933 968

View domain organization at Pfam

Manually Curated Family or Sub-families

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

Sequence Ontology

Term IDTerm NameReferenceCount
SO:0001528nuclear_localization_signal21

Protein Properties

Ave. residue weight 114.85 Da
Charge 10.50
Isoelectric point 7.59
Molecular weight 130.93 kDa
Number of residues 1140
Modifications

Protein Modifications

Term NameResidueCount
O-phospho-L-serine 1672
present during mitotic M phaseS27
present during cellular response to thiabendazoleS64
S27
Annotation ExtensionEvidenceResidueReference
experimental evidence S27 PMID:24763107
present during mitotic M phase experimental evidence S27 PMID:21712547
present during cellular response to thiabendazole IDA S64 PMID:18257517
sumoylated lysine 8
Annotation ExtensionEvidenceResidueReference
NAS PMID:15601841
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
4576during GO:0000080PECO:0000126,
PECO:0000005
single cellmass spectrometry evidencePMID:24763107
4858during GO:0000084PECO:0000126,
PECO:0000005
single cellmass spectrometry evidencePMID:24763107
4474during GO:0000085PECO:0000126,
PECO:0000005
single cellmass spectrometry evidencePMID:24763107
5945during GO:0000087PECO:0000126,
PECO:0000005
single cellmass spectrometry evidencePMID:24763107
34.71during GO:0072690PECO:0000005,
PECO:0000014
population wideexperimental evidencePMID:23101633
4373during GO:0072690PECO:0000126,
PECO:0000005
single cellmass spectrometry evidencePMID:24763107

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
1.9during GO:0072690PECO:0000005,
PECO:0000014
population wideexperimental evidencePMID:23101633
0.73during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population wideexperimental evidencePMID:23101633
Subunit Composition
DescriptionQualifierReferenceCount
heteromeric(2) PMID:1074703641
Species Distribution
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3092
conserved in fungi4603
conserved in eukaryotes4514
conserved in bacteria1001
conserved in metazoa3424
conserved in vertebrates3399
conserved in archaea238
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
affinity captured bynse1Smc5-6 complex ubiquitin-protein ligase E3 subunit 1 Affinity Capture-WesternPMID:14701739
affinity capturesnse1Smc5-6 complex ubiquitin-protein ligase E3 subunit 1 Affinity Capture-MSPMID:15601840
modifiesnse2Smc5-6 complex non-SMC subunit 2, SUMO ligase Biochemical ActivityPMID:15601841
affinity capturesnse2Smc5-6 complex non-SMC subunit 2, SUMO ligase Affinity Capture-MSPMID:15601840
modified bynse2Smc5-6 complex non-SMC subunit 2, SUMO ligase Biochemical ActivityPMID:18031226
affinity capturesnse3Smc5-6 complex non-SMC subunit Nse3 Affinity Capture-MSPMID:15601840
forms complex withnse3Smc5-6 complex non-SMC subunit Nse3 Reconstituted ComplexPMID:17005570
affinity captured bynse4Smc5-6 complex non-SMC subunit Nse4 Affinity Capture-WesternPMID:15485909
affinity capturesnse4Smc5-6 complex non-SMC subunit Nse4 Affinity Capture-MSPMID:15601840
affinity captured bynse4Smc5-6 complex non-SMC subunit Nse4 Affinity Capture-MSPMID:16478984
forms complex withnse4Smc5-6 complex non-SMC subunit Nse4 Reconstituted ComplexPMID:17005570
forms complex withnse5Smc5-6 complex non-SMC subunit Nse5 Reconstituted ComplexPMID:16478984
affinity captured bynse5Smc5-6 complex non-SMC subunit Nse5 Affinity Capture-MSPMID:16478984
forms complex withnse5Smc5-6 complex non-SMC subunit Nse5 Reconstituted ComplexPMID:17005570
forms complex withnse6Smc5-6 complex non-SMC subunit Nse6 Reconstituted ComplexPMID:16478984
affinity captured bynse6Smc5-6 complex non-SMC subunit Nse6 Affinity Capture-WesternPMID:16478984
affinity captured bynse6Smc5-6 complex non-SMC subunit Nse6 Affinity Capture-MSPMID:16478984
forms complex withnse6Smc5-6 complex non-SMC subunit Nse6 Reconstituted ComplexPMID:17005570
modified bypli1SUMO E3 ligase Pli1 Biochemical ActivityPMID:18031226
affinity captured bysmc5Smc5-6 complex SMC subunit Smc5 Affinity Capture-MSPMID:15331764
affinity captured bysmc5Smc5-6 complex SMC subunit Smc5 Affinity Capture-MSPMID:16478984
forms complex withsmc5Smc5-6 complex SMC subunit Smc5 Reconstituted ComplexPMID:16478984
co-purifies withsmc5Smc5-6 complex SMC subunit Smc5 Co-purificationPMID:10747036
affinity captured bysmc5Smc5-6 complex SMC subunit Smc5 Affinity Capture-WesternPMID:10747036
forms complex withsmc5Smc5-6 complex SMC subunit Smc5 Reconstituted ComplexPMID:15601840
affinity capturessmc5Smc5-6 complex SMC subunit Smc5 Affinity Capture-MSPMID:15601840
Genetic Interactions

Source: BioGRID

View these interactions in esyN

Gene Product Evidence Reference
synthetic lethal withapn2AP-endonuclease Apn2 Synthetic LethalityPMID:17277362
rescued byarp8actin-like protein, Ino80 complex subunit Arp8 Phenotypic SuppressionPMID:24687850
synthetically rescued byarp8actin-like protein, Ino80 complex subunit Arp8 Synthetic RescuePMID:24687850
rescued by overexpression ofbrc1BRCT domain protein Brc1 Dosage RescuePMID:10473635
synthetic lethal withbrc1BRCT domain protein Brc1 Synthetic LethalityPMID:10473635
rescued by overexpression ofbrc1BRCT domain protein Brc1 Dosage RescuePMID:17277362
rescued by overexpression ofbrc1BRCT domain protein Brc1 Dosage RescuePMID:19528228
rescued by overexpression ofbrc1BRCT domain protein Brc1 Dosage RescuePMID:15972456
rescued by overexpression ofbrc1BRCT domain protein Brc1 Dosage RescuePMID:22366461
phenotype enhanced bybrc1BRCT domain protein Brc1 Phenotypic EnhancementPMID:22366461
synthetic lethal withbrc1BRCT domain protein Brc1 Synthetic LethalityPMID:15485909
overexpression rescuesbrc1BRCT domain protein Brc1 Dosage RescuePMID:15485909
rescued by overexpression ofcut1separase/separin Dosage RescuePMID:19528228
phenotype enhanced byfin1serine/threonine protein kinase, NIMA related Fin1 Phenotypic EnhancementPMID:10473635
phenotype enhanced byhht2histone H3 h3.2 Phenotypic EnhancementPMID:24687850
synthetically rescued byhht2histone H3 h3.2 Synthetic RescuePMID:24687850
rescued byhht2histone H3 h3.2 Phenotypic SuppressionPMID:24687850
synthetic growth defect withhht2histone H3 h3.2 Synthetic Growth DefectPMID:24687850
synthetically rescued byhst4Sirtuin family histone deacetylase Hst4 Synthetic RescuePMID:24687850
rescued byhst4Sirtuin family histone deacetylase Hst4 Phenotypic SuppressionPMID:24687850
synthetic lethal withnse4Smc5-6 complex non-SMC subunit Nse4 Synthetic LethalityPMID:15485909
rescued bypht1histone H2A variant H2A.Z, Pht1 Phenotypic SuppressionPMID:24687850
synthetically rescued bypht1histone H2A variant H2A.Z, Pht1 Synthetic RescuePMID:24687850
phenotype enhanced bypht1histone H2A variant H2A.Z, Pht1 Phenotypic EnhancementPMID:24687850
enhances phenotype ofrad13DNA repair nuclease Rad13 Phenotypic EnhancementPMID:8524274
synthetic lethal withrad60DNA repair protein Rad60 Synthetic LethalityPMID:15485909
overexpression rescuesrad60DNA repair protein Rad60 Dosage RescuePMID:15485909
rescued by overexpression ofrad60DNA repair protein Rad60 Dosage RescuePMID:20885950
enhances phenotype ofrad60DNA repair protein Rad60 Phenotypic EnhancementPMID:19755492
synthetic growth defect withrad8ubiquitin-protein ligase E3 Rad8 Synthetic Growth DefectPMID:8290359
synthetic growth defect withrhp14XP-A family homolog Rhp14 Synthetic Growth DefectPMID:17277362
synthetic growth defect withrhp41DNA repair protein Rhp41 Synthetic Growth DefectPMID:17277362
phenotype enhanced byrtt109RTT109 family histone lysine acetyltransferase Phenotypic EnhancementPMID:24687850
synthetic growth defect withrtt109RTT109 family histone lysine acetyltransferase Synthetic Growth DefectPMID:24687850
synthetic lethal withslx1structure-specific endonuclease catalytic subunit Slx1 Synthetic LethalityPMID:15972456
synthetic growth defect withswi10DNA repair endonuclease non-catalytic subunit Swi10 Synthetic Growth DefectPMID:17277362
synthetically rescued byswr1SNF2 family ATP-dependent DNA helicase Swr1 Synthetic RescuePMID:24687850
rescued byswr1SNF2 family ATP-dependent DNA helicase Swr1 Phenotypic SuppressionPMID:24687850
synthetic lethal withtop2DNA topoisomerase II Synthetic LethalityPMID:19528228
synthetic lethal withtop2DNA topoisomerase II Synthetic LethalityPMID:20495382
synthetic lethal withtop2DNA topoisomerase II Synthetic LethalityPMID:10473635
phenotype enhanced bytop2DNA topoisomerase II Phenotypic EnhancementPMID:10473635
External References
Database Identifier Description
NBRP SPCC5E4.06 Fission yeast strain database, National BioResource Project (Japan)
YOGY SPCC5E4.06 Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPCC5E4.06 BioGRID Interaction Datasets
Expression Viewer SPCC5E4.06 Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPCC5E4.06 Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPCC5E4.06 Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPCC5E4.06 Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPCC5E4.06 Polyadenylation Viewer (Gullerova lab)
pombeTV SPCC5E4.06 Transcriptome Viewer (Bähler Lab)
GEO SPCC5E4.06 GEO profiles
PInt SPCC5E4.06 Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPCC5E4.06 Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPCC5E4.06 Fission yeast phenotypic data & analysis
Cyclebase SPCC5E4.06.1 Cell Cycle Data
SPD / RIKEN48/48D06Orfeome Localization Data
UniProtKB/SwissProtP53692Structural maintenance of chromosomes protein 6
ModBaseP53692Database of comparative protein structure models
STRINGP53692Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_587906Smc5-6 complex SMC subunit Smc6
RefSeq mRNANM_001022898972h- Smc5-6 complex SMC subunit Smc6 (smc6), mRNA
European Nucleotide ArchiveCAA21961.1ENA Protein Mapping
European Nucleotide ArchiveCAA56900.1ENA Protein Mapping
UniParcUPI0000133014UniProt Archive

Literature for smc6

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Release Version: PomBase:26_53 - 27 May 2015