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
protein binding831
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
cellular response to DNA damage stimulus211
Annotation ExtensionEvidenceWith/FromReference
DNA repair165
Annotation ExtensionEvidenceWith/FromReference
double-strand break repair via homologous recombination32
Annotation ExtensionEvidenceWith/FromReference
meiotic cell cycle437
Annotation ExtensionEvidenceWith/FromReference
replication fork protection12
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
nucleus2740
Annotation ExtensionEvidenceWith/FromReference
Smc5-Smc6 complex8
Annotation ExtensionEvidenceWith/FromReference
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Inviable

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002061inviable vegetative cell populationMicroscopysmc6ΔNullPMID:204732891338
Microscopysmc6ΔNullPECO:0000005, PECO:0000137PMID:23697806
FYPO:0000268sensitive to UV during vegetative growthCell growth assayrad18 mutantNot specifiedPMID:8290359123

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0000059abnormal mitotic cell cycleMicroscopysmc6ΔNullPECO:0000004, PECO:0000137PMID:23697806686
FYPO:0001122elongated vegetative cellMicroscopysmc6ΔNullPMID:8524274685
FYPO:0001490inviable elongated vegetative cell393
penetrance FYPO_EXT:0000003Microscopysmc6ΔNullPECO:0000005, PECO:0000137PMID:23697806
FYPO:0001511inviable vegetative cell, abnormal cell shape, normal cell size199
expressivity FYPO_EXT:0000003
penetrance FYPO_EXT:0000001
Microscopysmc6ΔNullPECO:0000137, PECO:0000005PMID:23697806
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:SF2 HMMPANTHER IPR027132 Structural maintenance of chromosomes protein 6 1 1138 1
PTHR19306 HMMPANTHER 1 1138 2
3.40.50.300 Gene3D 97 260 288
3.40.50.300 Gene3D 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 951 979 968
Coil ncoils Rabaptin coiled-coil domain 715 750 968
Coil ncoils Rabaptin coiled-coil domain 829 885 968
Coil ncoils Rabaptin coiled-coil domain 264 285 968
Coil ncoils Rabaptin coiled-coil domain 451 486 968
Coil ncoils Rabaptin coiled-coil domain 331 366 968
Coil ncoils Rabaptin coiled-coil domain 912 933 968
Coil ncoils Rabaptin coiled-coil domain 787 822 968
Coil ncoils Rabaptin coiled-coil domain 757 778 968

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

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 IDTerm NameEvidenceResidueReferenceCount
MOD:00046O-phospho-L-serineIDAS64PMID:182575171670
present during cellular response to thiabendazole
experimental evidenceS27PMID:24763107
present during mitotic M phaseexperimental evidenceS27PMID:21712547
MOD:00696phosphorylated residueNASPMID:182575171922
MOD:01149sumoylated lysineNASPMID:156018414
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
4373during GO:0072690PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
34.71during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
NDduring cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633

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:1074703642
Species Distribution
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3092
conserved in fungi4600
conserved in eukaryotes4514
conserved in bacteria1000
conserved in metazoa3425
conserved in vertebrates3400
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
Reconstituted ComplexPMID:15601840
Affinity Capture-MS
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 Reconstituted ComplexPMID:16478984
Affinity Capture-MS
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
Phenotypic EnhancementPMID:10473635
Synthetic Lethality
rhp41DNA repair protein Rhp41 Synthetic Growth DefectPMID:17277362
slx1structure-specific endonuclease catalytic subunit Synthetic LethalityPMID:15972456
cut1separase/separin Dosage RescuePMID:19528228
apn2AP-endonuclease Apn2 Synthetic LethalityPMID:17277362
brc1BRCT domain protein Brc1 Dosage RescuePMID:10473635
Synthetic Lethality
Dosage RescuePMID:17277362
Dosage RescuePMID:19528228
Dosage RescuePMID:15972456
Phenotypic EnhancementPMID:22366461
Dosage Rescue
Dosage RescuePMID:15485909
Synthetic Lethality
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
rhp14XP-A family homolog Rhp14 Synthetic Growth DefectPMID:17277362
rad60DNA repair protein Rad60 Synthetic LethalityPMID:15485909
Dosage Rescue
Dosage RescuePMID:20885950
Phenotypic EnhancementPMID:19755492
rad8ubiquitin-protein ligase E3 Rad8 Synthetic Growth DefectPMID:8290359
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:23_47 - 27 Oct 2014