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 binding848
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
double-strand break repair via homologous recombination32
Annotation ExtensionEvidenceWith/FromReference
meiotic cell cycle441
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
nucleus2690
Annotation ExtensionEvidenceWith/FromReference
Smc5-Smc6 complex8
Annotation ExtensionEvidenceWith/FromReference
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Inviable

Population Phenotype

Term NameAlleleExpressionCount
inviable vegetative cell populationsmc6ΔNull1427
sensitive to ionizing radiation58
expressivity FYPO_EXT:0000001rad18-XNot specified
expressivity FYPO_EXT:0000002rad18-X
sensitive to UV during vegetative growthrad18 mutantNot specified133
expressivity FYPO_EXT:0000001rad18-XNot specified
expressivity FYPO_EXT:0000002rad18-X

Cell Phenotype

Term NameAlleleExpressionCount
abnormal mitotic cell cyclesmc6ΔNull794
decreased UV-damage excision repairrad18-XNot specified3
inviable after spore germination, single or double cell division, elongated cellsmc6ΔNull9
inviable elongated mononucleate aseptate cellrad18-XNot specified37
inviable elongated vegetative cell405
penetrance FYPO_EXT:0000003smc6ΔNull
inviable vegetative cell, abnormal cell shape, normal cell size199
penetrance FYPO_EXT:0000001, expressivity FYPO_EXT:0000003smc6ΔNull
viable elongated vegetative cellrad18-XNot specified231
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
1652648652893
2653000656420

UTRs

Region Coordinates Reference
five_prime_UTR652648..652782PMID:21511999
three_prime_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 HMMPANTHER 6 1127 2
PTHR19306:SF2 HMMPANTHER IPR027132 Structural maintenance of chromosomes protein 6 6 1127 1
3.40.50.300 Gene3D IPR027417 P-loop containing nucleoside triphosphate hydrolase 962 1109 288
3.40.50.300 Gene3D IPR027417 P-loop containing nucleoside triphosphate hydrolase 97 260 288
SSF52540 SuperFamily IPR027417 P-loop containing nucleoside triphosphate hydrolase 926 1108 294
SSF52540 SuperFamily IPR027417 P-loop containing nucleoside triphosphate hydrolase 97 304 294
Coil ncoils Rabaptin coiled-coil domain 829 885 971
Coil ncoils Rabaptin coiled-coil domain 715 750 971
Coil ncoils Rabaptin coiled-coil domain 951 979 971
Coil ncoils Rabaptin coiled-coil domain 787 822 971
Coil ncoils Rabaptin coiled-coil domain 912 933 971
Coil ncoils Rabaptin coiled-coil domain 264 285 971
Coil ncoils Rabaptin coiled-coil domain 331 366 971
Coil ncoils Rabaptin coiled-coil domain 451 486 971
Coil ncoils Rabaptin coiled-coil domain 757 778 971

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_signalPMID:852427421

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-serineS27 1670
present during mitotic M phaseS27
present during cellular response to thiabendazoleS64
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
phosphorylated residue 1922
Annotation ExtensionEvidenceResidueReference
NAS PMID:18257517
sumoylated lysine 4
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 fungi4604
conserved in eukaryotes4516
conserved in bacteria1000
conserved in metazoa3432
conserved in vertebrates3407
conserved in archaea237
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
nse2Smc5-6 complex non-SMC subunit 2, SUMO ligase Biochemical ActivityPMID:15601841
Affinity Capture-MSPMID:15601840
Biochemical ActivityPMID:18031226
nse1Smc5-6 complex ubiquitin-protein ligase E3 subunit 1 Affinity Capture-WesternPMID:14701739
Affinity Capture-MSPMID:15601840
smc5Smc5-6 complex SMC subunit Smc5 Affinity Capture-MSPMID:15331764
Affinity Capture-MSPMID:16478984
Reconstituted Complex
Affinity Capture-WesternPMID:10747036
Co-purification
Affinity Capture-MSPMID:15601840
Reconstituted Complex
nse3Smc5-6 complex non-SMC subunit Nse3 Affinity Capture-MSPMID:15601840
Reconstituted ComplexPMID:17005570
nse4Smc5-6 complex non-SMC subunit Nse4 Affinity Capture-WesternPMID:15485909
Affinity Capture-MSPMID:15601840
Affinity Capture-MSPMID:16478984
Reconstituted ComplexPMID:17005570
nse5Smc5-6 complex non-SMC subunit Nse5 Affinity Capture-MSPMID:16478984
Reconstituted Complex
Reconstituted ComplexPMID:17005570
pli1SUMO E3 ligase Pli1 Biochemical ActivityPMID:18031226
nse6Smc5-6 complex non-SMC subunit Nse6 Reconstituted ComplexPMID:16478984
Affinity Capture-Western
Affinity Capture-MS
Reconstituted ComplexPMID:17005570
Genetic Interactions

Source: BioGRID

View these interactions in esyN

Gene Product Evidence Reference
fin1serine/threonine protein kinase, NIMA related Fin1 Phenotypic EnhancementPMID:10473635
top2DNA topoisomerase II Synthetic LethalityPMID:19528228
Synthetic LethalityPMID:20495382
Synthetic LethalityPMID:10473635
Phenotypic Enhancement
rhp41DNA repair protein Rhp41 Synthetic Growth DefectPMID:17277362
slx1structure-specific endonuclease catalytic subunit Synthetic LethalityPMID:15972456
rhp14XP-A family homolog Rhp14 Synthetic Growth DefectPMID:17277362
apn2AP-endonuclease Apn2 Synthetic LethalityPMID:17277362
hst4Sir2 family histone deacetylase Hst4 Synthetic RescuePMID:24687850
Phenotypic Suppression
rtt109RTT109 family histone lysine acetyltransferase Synthetic Growth DefectPMID:24687850
Phenotypic Enhancement
brc1BRCT domain protein Brc1 Dosage RescuePMID:10473635
Synthetic Lethality
Dosage RescuePMID:17277362
Dosage RescuePMID:19528228
Dosage RescuePMID:15972456
Dosage RescuePMID:22366461
Phenotypic Enhancement
Synthetic LethalityPMID:15485909
Dosage Rescue
nse4Smc5-6 complex non-SMC subunit Nse4 Synthetic LethalityPMID:15485909
swi10DNA repair endonuclease Swi10 Synthetic Growth DefectPMID:17277362
rad13DNA repair nuclease Rad13 Phenotypic EnhancementPMID:8524274
pht1histone H2A variant H2A.Z, Pht1 Phenotypic EnhancementPMID:24687850
Phenotypic Suppression
Synthetic Rescue
arp8actin-like protein, Ino80 complex subunit Arp8 Synthetic RescuePMID:24687850
Phenotypic Suppression
rad60DNA repair protein Rad60 Synthetic LethalityPMID:15485909
Dosage Rescue
Dosage RescuePMID:20885950
Phenotypic EnhancementPMID:19755492
swr1SNF2 family ATP-dependent DNA helicase Swr1 Synthetic RescuePMID:24687850
Phenotypic Suppression
hht2histone H3 h3.2 Synthetic Growth DefectPMID:24687850
Synthetic Rescue
Phenotypic Enhancement
Phenotypic Suppression
rad8ubiquitin-protein ligase E3 Rad8 Synthetic Growth DefectPMID:8290359
cut1separase/separin Dosage RescuePMID:19528228
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)
Cyclebase SPCC5E4.06 Cell Cycle Data
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
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

Search: Europe PMC or PubMed

Release Version: PomBase:25_48 - 10 Jan 2015