smc6 (SPCC5E4.06)


Gene Standard Namesmc6 Characterisation Statuspublished
Systematic IDSPCC5E4.06 Feature Typeprotein coding
Synonymsrad18 Name Description
ProductSmc5-6 complex SMC P-loop ATPase 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 binding559
Annotation ExtensionEvidenceWith/FromReference
double-stranded DNA-dependent ATPase activity1
Annotation ExtensionEvidenceWith/FromReference
protein binding863
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
double-strand break repair via homologous recombination36
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
nucleus2691
Annotation ExtensionEvidenceWith/FromReference
Smc5-Smc6 complex8
Annotation ExtensionEvidenceWith/FromReference
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Inviable

Single-allele Phenotypes

Population Phenotype

Term NameGenotypesCount
inviable vegetative cell populationsmc6Δ1444
normal growth on JM216rad18-X10
normal growth on tetraplatinrad18-X14
sensitive to cisplatinrad18-X29
sensitive to hydroxyureasmc6-X542
sensitive to ionizing radiation during vegetative growthrad18-X64
sensitive to JM335rad18-X14
sensitive to oxaliplatinrad18-X16
sensitive to triplatin tetranitraterad18-X7
sensitive to UV during vegetative growthrad18 mutant143
smc6-X
rad18-X

Cell Phenotype

Term NameGenotypesCount
abnormal mitotic cell cyclesmc6Δ834
decreased UV-damage excision repairrad18-X3
inviable after spore germination, single or double cell division, elongated cellsmc6Δ13
inviable elongated mononucleate aseptate cellrad18-X36
inviable elongated vegetative cellsmc6Δ405
inviable vegetative cell, abnormal cell shape, normal cell sizesmc6Δ199
viable elongated vegetative cellrad18-X306
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons652648..652893, 653000..656420
Intron652894..652999
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 5
PTHR19306 HMMPANTHER 25 1139 2
PTHR19306:SF6 HMMPANTHER IPR027132 Structural maintenance of chromosomes protein 6 25 1139 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 Predicted coiled-coil protein (DUF2205) 951 978 1048
Coil ncoils Predicted coiled-coil protein (DUF2205) 715 749 1048
Coil ncoils Predicted coiled-coil protein (DUF2205) 331 365 1048
Coil ncoils Predicted coiled-coil protein (DUF2205) 829 884 1048
Coil ncoils Predicted coiled-coil protein (DUF2205) 787 821 1048
Coil ncoils Predicted coiled-coil protein (DUF2205) 912 932 1048
Coil ncoils Predicted coiled-coil protein (DUF2205) 757 777 1048
Coil ncoils Predicted coiled-coil protein (DUF2205) 264 284 1048
Coil ncoils Predicted coiled-coil protein (DUF2205) 451 485 1048

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: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-serineS27 1674
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
sumoylated lysine 8
Annotation ExtensionEvidenceResidueReference
NAS PMID:15601841
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

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

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
1.9during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
0.73during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
Subunit Composition
DescriptionQualifierReferenceCount
heteromeric(2) PMID:1074703641
Taxonomic Conservation
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3090
conserved in fungi4604
conserved in eukaryotes4514
conserved in bacteria1000
conserved in metazoa3421
conserved in vertebrates3396
conserved in archaea238
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

Load gene that interact physically with SPCC5E4.06 into the Query Builder
View all interactions in esyN
View the HCPIN interactions in esyN

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

Source: BioGRID

Load gene that interact geneitically with SPCC5E4.06 into the Query Builder
View these interactions in esyN

Gene Product Evidence Reference
synthetic lethal withtop2DNA topoisomerase II Synthetic LethalityPMID:10473635
synthetic lethal withnse4Smc5-6 complex non-SMC subunit Nse4 Synthetic LethalityPMID:15485909
synthetic lethal withapn2AP-endonuclease Apn2 Synthetic LethalityPMID:17277362
synthetic lethal withbrc1BRCT domain protein Brc1 Synthetic LethalityPMID:10473635
synthetic lethal withrad60DNA repair protein Rad60 Synthetic LethalityPMID:15485909
synthetic lethal withslx1structure-specific endonuclease catalytic subunit Slx1 Synthetic LethalityPMID:15972456
synthetically rescued byhht2histone H3 h3.2 Synthetic RescuePMID:24687850
synthetically rescued byhst4Sirtuin family histone deacetylase Hst4 Synthetic RescuePMID:24687850
synthetically rescued bypht1histone H2A variant H2A.Z, Pht1 Synthetic RescuePMID:24687850
synthetically rescued byarp8actin-like protein, Ino80 complex subunit Arp8 Synthetic RescuePMID:24687850
synthetically rescued byswr1SNF2 family ATP-dependent DNA helicase Swr1 Synthetic RescuePMID:24687850
rescued by overexpression ofbrc1BRCT domain protein Brc1 Dosage RescuePMID:15972456
rescued by overexpression ofcut1separase/separin Dosage RescuePMID:19528228
rescued by overexpression ofrad60DNA repair protein Rad60 Dosage RescuePMID:20885950
phenotype enhanced byhht2histone H3 h3.2 Phenotypic EnhancementPMID:24687850
phenotype enhanced byrtt109RTT109 family histone lysine acetyltransferase Phenotypic EnhancementPMID:24687850
phenotype enhanced bybrc1BRCT domain protein Brc1 Phenotypic EnhancementPMID:22366461
phenotype enhanced bypht1histone H2A variant H2A.Z, Pht1 Phenotypic EnhancementPMID:24687850
phenotype enhanced byfin1serine/threonine protein kinase, NIMA related Fin1 Phenotypic EnhancementPMID:10473635
phenotype enhanced bytop2DNA topoisomerase II Phenotypic EnhancementPMID:10473635
rescued byhst4Sirtuin family histone deacetylase Hst4 Phenotypic SuppressionPMID:24687850
rescued byswr1SNF2 family ATP-dependent DNA helicase Swr1 Phenotypic SuppressionPMID:24687850
rescued byhht2histone H3 h3.2 Phenotypic SuppressionPMID:24687850
rescued byarp8actin-like protein, Ino80 complex subunit Arp8 Phenotypic SuppressionPMID:24687850
rescued bypht1histone H2A variant H2A.Z, Pht1 Phenotypic SuppressionPMID:24687850
overexpression rescuesrad60DNA repair protein Rad60 Dosage RescuePMID:15485909
overexpression rescuesbrc1BRCT domain protein Brc1 Dosage RescuePMID:15485909
synthetic growth defect withrhp41DNA repair protein Rhp41 Synthetic Growth DefectPMID:17277362
synthetic growth defect withrtt109RTT109 family histone lysine acetyltransferase Synthetic Growth DefectPMID:24687850
synthetic growth defect withhht2histone H3 h3.2 Synthetic Growth DefectPMID:24687850
synthetic growth defect withrhp14XP-A family homolog Rhp14 Synthetic Growth DefectPMID:17277362
synthetic growth defect withrad8ubiquitin-protein ligase E3 Rad8 Synthetic Growth DefectPMID:8290359
synthetic growth defect withswi10DNA repair endonuclease non-catalytic subunit Swi10 Synthetic Growth DefectPMID:17277362
enhances phenotype ofrad13DNA repair nuclease Rad13 Phenotypic EnhancementPMID:8524274
enhances phenotype ofrad60DNA repair protein Rad60 Phenotypic EnhancementPMID:19755492
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 ArchiveCU329672ENA EMBL mapping
European Nucleotide ArchiveX80929ENA EMBL mapping
European Nucleotide ArchiveCAA21961ENA Protein Mapping
European Nucleotide ArchiveCAA21961.1ENA Protein Mapping
European Nucleotide ArchiveCAA56900ENA Protein Mapping
European Nucleotide ArchiveCAA56900.1ENA Protein Mapping
UniParcUPI0000133014UniProt Archive

Literature for smc6

Search: Europe PMC or PubMed

Release Version: PomBase:29_56 - 12 Nov 2015