smc6 (SPCC5E4.06)

Gene Standard Namesmc6 ChromosomeIII
Systematic IDSPCC5E4.06 Gene Start652648
Synonymsrad18 Gene End656420
ProductSmc5-6 complex SMC subunit Smc6 Gene Length3773
Feature Typeprotein coding CDS Start652783
Name Description CDS End656311
Characterisation Statuspublished CDS Length3529

Ensembl Gene Location
  1. cut1
  2. SPCC5E4.05c
  3. SPNCRNA.1149
  4. SPCC5E4.10c
  5. SPNCRNA.1150
  6. smc6
  7. rpl2802
  8. SPCC16C4.19
  9. SPNCRNA.1151
  10. sif2
  11. SPCC16C4.20c
  12. SPCC16C4.02c
Fission Yeast Phenotype Ontology

Ontology Graph

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Term IDTerm NameEvidenceAlleleAllele TypeExpressionConditionReference
FYPO:0001122elongated vegetative cellsmc6delta (deletion)deletionPMID:8524274
FYPO:0001489inviable vegetative cellMicroscopysmc6delta (deletion)deletionPMID:20473289
GO Molecular Function

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Term IDTerm NameEvidenceWith/FromReference
GO:0005515protein bindingIPInse6PMID:16478984
IPInse5PMID:16478984
GO:0005524ATP bindingIEAUniProtKB:KW-0067GO_REF:0000037
GO:0046982protein heterodimerization activityIPIsmc5PMID:10747036
GO Biological Process

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Term IDTerm NameEvidenceWith/FromReference
GO:0000724double-strand break repair via homologous recombinationIEAIPR027132GO_REF:0000002
GO:0006281DNA repairIMPPMID:8524274
GO:0006974response to DNA damage stimulus
requiredIMPPMID:8524274
GO:0048478replication fork protectionICGO:0030915GO_REF:0000001
GO Cellular Component

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Term IDTerm NameEvidenceWith/FromReference
GO:0005634nucleusIDAPMID:16823372
ICGO:0030915GO_REF:0000001
GO:0030915Smc5-Smc6 complexIDAPMID:11927594
Transcript
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Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
1652648652893
2653000656420

References

Region Start End Reference
three_prime_UTR656312656420PMID:21511999
Protein Features
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Graphical View

Ensembl protein image with mapped locations of structural domains

Protein Families and Domains

Feature ID InterPro Database Description Start End All Genes
PF02463 IPR003395 Pfam RecF/RecN/SMC 97 1108 6
G3DSA:3.40.50.300 Gene3D 962 1109 279
G3DSA:3.40.50.300 Gene3D 97 260 279
SSF52540 SuperFamily 97 304 294
SSF52540 SuperFamily 926 1108 294
Coil ncoils Rabaptin coiled-coil domain 951 979 974
Coil ncoils Rabaptin coiled-coil domain 715 750 974
Coil ncoils Rabaptin coiled-coil domain 829 885 974
Coil ncoils Rabaptin coiled-coil domain 451 486 974
Coil ncoils Rabaptin coiled-coil domain 264 285 974
Coil ncoils Rabaptin coiled-coil domain 331 366 974
Coil ncoils Rabaptin coiled-coil domain 912 933 974
Coil ncoils Rabaptin coiled-coil domain 787 822 974
Coil ncoils Rabaptin coiled-coil domain 757 778 974
PTHR19306:SF2 hmmpanther 18 1139 1
PTHR19306 hmmpanther 18 1139 2

View domain organization at Pfam

Protein Modifications (PSI-MOD)

Term IDTerm NameEvidenceResidueReference
MOD:00696phosphorylated residuePMID:18257517
MOD:01149sumoylated lysinePMID:15601841

Manually Curated Family or Sub-families

Term IDTerm NameReferenceAll Genes
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
Sequence
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Gene Expression
DescriptionEvidenceDuringConditionRangeAverage per CellReference
protein levelexperimental evidencevegetative growth of a single-celled organismPECO:0000014,
PECO:0000005		population_wide34.71PMID:23101633
experimental evidencecell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127		population_widePMID:23101633
RNA levelexperimental evidencevegetative growth of a single-celled organismPECO:0000014,
PECO:0000005		population_wide1.9PMID:23101633
experimental evidencecell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005		population_wide0.73PMID:23101633
Species Distribution
DescriptionQualifierReference
predominantly single copy (one to one)
conserved in fungi
conserved in eukaryotes
conserved in bacteria
conserved in metazoa
conserved in vertebrates
conserved in archaea
Manually curated orthologous groups
SpeciesGeneDescription

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Genetic Interactions

Source: BioGRID

Gene Product Evidence Reference
rad13DNA repair nuclease Rad13 Phenotypic EnhancementPMID:8524274
slx1structure-specific endonuclease catalytic subunit Synthetic LethalityPMID:15972456
rad8ubiquitin-protein ligase E3 Rad8 Synthetic Growth DefectPMID:8290359
swi10DNA repair endonuclease Swi10 Synthetic Growth DefectPMID:17277362
brc1BRCT domain protein Brc1 Phenotypic EnhancementPMID:22366461
Dosage Rescue
Dosage RescuePMID:15972456
Dosage RescuePMID:17277362
Synthetic LethalityPMID:10473635
Dosage Rescue
Synthetic LethalityPMID:15485909
Dosage Rescue
Dosage RescuePMID:19528228
top2DNA topoisomerase II Synthetic LethalityPMID:20495382
Phenotypic EnhancementPMID:10473635
Synthetic Lethality
Synthetic LethalityPMID:19528228
nse4Smc5-6 complex non-SMC subunit Nse4 Synthetic LethalityPMID:15485909
rhp14XP-A family homolog Rhp14 Synthetic Growth DefectPMID:17277362
rhp41DNA repair protein Rhp41 Synthetic Growth DefectPMID:17277362
fin1serine/threonine protein kinase, NIMA related Fin1 Phenotypic EnhancementPMID:10473635
apn2AP-endonuclease Apn2 Synthetic LethalityPMID:17277362
rad60DNA repair protein Rad60 Phenotypic EnhancementPMID:19755492
Dosage RescuePMID:20885950
Synthetic LethalityPMID:15485909
Dosage Rescue
cut1separase/separin Dosage RescuePMID:19528228
Physical Interactions

Source: BioGRID

Gene Product Evidence Reference
pli1SUMO E3 ligase Pli1 Biochemical ActivityPMID:18031226
nse4Smc5-6 complex non-SMC subunit Nse4 Affinity Capture-MSPMID:16478984
Reconstituted ComplexPMID:17005570
Affinity Capture-MSPMID:15601840
Affinity Capture-WesternPMID:15485909
smc5Smc5-6 complex SMC subunit Smc5 Affinity Capture-MSPMID:16478984
Reconstituted Complex
Affinity Capture-MSPMID:15331764
Affinity Capture-WesternPMID:10747036
Co-purification
Reconstituted ComplexPMID:15601840
Affinity Capture-MS
nse6Smc5-6 complex non-SMC subunit Nse6 Affinity Capture-WesternPMID:16478984
Reconstituted Complex
Affinity Capture-MS
Reconstituted ComplexPMID:17005570
nse2Smc5-6 complex non-SMC subunit 2 Biochemical ActivityPMID:15601841
Affinity Capture-MSPMID:15601840
Biochemical ActivityPMID:18031226
nse5Smc5-6 complex non-SMC subunit Nse5 Reconstituted ComplexPMID:16478984
Affinity Capture-MS
Reconstituted ComplexPMID:17005570
nse3Smc5-6 complex non-SMC subunit Nse3 Reconstituted ComplexPMID:17005570
Affinity Capture-MSPMID:15601840
nse1Smc5-6 complex non-SMC subunit 1 Affinity Capture-WesternPMID:14701739
Affinity Capture-MSPMID:15601840
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External References
Database Identifier Description
NBRP SPCC5E4.06 Fission yeast strain database, National BioResource Project (Japan)
YOGY SPCC5E4.06 Retrieval of eukaryotic orthologs
BioGrid SPCC5E4.06 BioGRID Interaction Datasets
Bähler Lab SPCC5E4.06 Cell Cycle Expression Profile
Bähler Lab SPCC5E4.06 Meiosis/Sporulation Expression Profies
Bähler Lab SPCC5E4.06 Pheromone response/mating expression profiles
Bähler Lab SPCC5E4.06 Environmental stress expression profiles
Bähler Lab SPCC5E4.06 Bähler Lab Transcriptome Viewer
Cyclebase SPCC5E4.06 Cell Cycle Data
PInt SPCC5E4.06 Bähler Lab Protein-Protein Interaction Predictor
Entrez Gene SPCC5E4.06 Entrez Gene
SPD / RIKEN48/48D06Orfeome Localization Data
EntrezGene2539020Smc5-6 complex SMC subunit Smc6
Uniprot_genenameSMC6
WikiGene2539020Smc5-6 complex SMC subunit Smc6
UniProtKB/SwissProtP53692Structural maintenance of chromosomes protein 6
ModBaseP53692Database of comparative protein structure models
Pfam Protein DomainsP53692Pfam Domain Arrangement
RefSeq PeptideNP_587906Smc5-6 complex SMC subunit Smc6
RefSeq mRNANM_001022898972h- Smc5-6 complex SMC subunit Smc6 (smc6), mRNA
European Nucleotide ArchiveCAA21961ENA Protein Mapping
European Nucleotide ArchiveCAA56900ENA Protein Mapping
SPD / RIKEN48/48D06Orfeome Localization Data

Literature for smc6
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Search: UK PMC or PubMed

Release Version: PomBase:18.34 - 04 Apr 2013