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Protein

Structural maintenance of chromosomes protein 5

Gene

SMC5

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Acts in a DNA repair pathway for removal of UV-induced DNA damage that is distinct from classical nucleotide excision repair and in repair of ionizing radiation damage. Functions in homologous recombination repair of DNA double strand breaks and in recovery of stalled replication forks.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi69 – 768ATPSequence analysis

GO - Molecular functioni

  • ATPase activity Source: SGD
  • ATP binding Source: UniProtKB-KW
  • damaged DNA binding Source: SGD
  • single-stranded DNA binding Source: SGD

GO - Biological processi

  • chromosome separation Source: SGD
  • DNA repair Source: SGD
  • double-strand break repair via homologous recombination Source: InterPro
  • recombinational repair Source: SGD
  • resolution of recombination intermediates Source: SGD
Complete GO annotation...

Keywords - Biological processi

DNA damage, DNA recombination, DNA repair

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-33450-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Structural maintenance of chromosomes protein 5
Gene namesi
Name:SMC5
Ordered Locus Names:YOL034W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XV

Organism-specific databases

EuPathDBiFungiDB:YOL034W.
SGDiS000005394. SMC5.

Subcellular locationi

GO - Cellular componenti

  • nucleus Source: SGD
  • Smc5-Smc6 complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10931093Structural maintenance of chromosomes protein 5PRO_0000119020Add
BLAST

Post-translational modificationi

Sumoylated by MMS21.1 Publication

Keywords - PTMi

Ubl conjugation

Proteomic databases

MaxQBiQ08204.
PRIDEiQ08204.

Interactioni

Subunit structurei

Component of the Smc5-Smc6 complex which consists of KRE29, MMS21, NSE1, NSE3, NSE4, NSE5, SMC5 and SMC6.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
NSE1Q079135EBI-34125,EBI-30144

Protein-protein interaction databases

BioGridi34366. 44 interactions.
DIPiDIP-1979N.
IntActiQ08204. 17 interactions.
MINTiMINT-404105.

Structurei

Secondary structure

1
1093
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi307 – 36054Combined sources
Turni740 – 7423Combined sources
Helixi743 – 80866Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3HTKX-ray2.31A304-363[»]
B739-811[»]
ProteinModelPortaliQ08204.
SMRiQ08204. Positions 304-363, 739-1048.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ08204.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni442 – 650209Flexible hingeAdd
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili208 – 354147Sequence analysisAdd
BLAST
Coiled coili404 – 44138Sequence analysisAdd
BLAST
Coiled coili651 – 757107Sequence analysisAdd
BLAST
Coiled coili884 – 92643Sequence analysisAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi986 – 102136Ala/Asp-rich (DA-box)Add
BLAST

Domaini

The flexible hinge domain, which separates the large intramolecular coiled coil regions, allows the heterotypic interaction with the corresponding domain of smc6, forming a V-shaped heterodimer.By similarity

Sequence similaritiesi

Belongs to the SMC family. SMC5 subfamily.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

GeneTreeiENSGT00550000074963.
HOGENOMiHOG000141775.
InParanoidiQ08204.
OMAiHTSQYFL.
OrthoDBiEOG7Q8CWQ.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR027417. P-loop_NTPase.
IPR003395. RecF/RecN/SMC_N.
IPR027131. SMC5.
IPR033268. Smc5/Smc6.
[Graphical view]
PANTHERiPTHR19306. PTHR19306. 1 hit.
PTHR19306:SF1. PTHR19306:SF1. 1 hit.
PfamiPF02463. SMC_N. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.

Sequencei

Sequence statusi: Complete.

Q08204-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTSLIDLGRY VERTHHGEDT EPRSKRVKIA KPDLSSFQPG SIIKIRLQDF
60 70 80 90 100
VTYTLTEFNL SPSLNMIIGP NGSGKSTFVC AVCLGLAGKP EYIGRSKKVE
110 120 130 140 150
DFIKNGQDVS KIEITLKNSP NVTDIEYIDA RDETIKITRI ITRSKRRSDY
160 170 180 190 200
LINDYQVSES VVKTLVAQLN IQLDNLCQFL SQERVEEFAR LKSVKLLVET
210 220 230 240 250
IRSIDASLLD VLDELRELQG NEQSLQKDLD FKKAKIVHLR QESDKLRKSV
260 270 280 290 300
ESLRDFQNKK GEIELHSQLL PYVKVKDHKE KLNIYKEEYE RAKANLRAIL
310 320 330 340 350
KDKKPFANTK KTLENQVEEL TEKCSLKTDE FLKAKEKINE IFEKLNTIRD
360 370 380 390 400
EVIKKKNQNE YYRGRTKKLQ ATIISTKEDF LRSQEILAQT HLPEKSVFED
410 420 430 440 450
IDIKRKEIIN KEGEIRDLIS EIDAKANAIN HEMRSIQRQA ESKTKSLTTT
460 470 480 490 500
DKIGILNQDQ DLKEVRDAVL MVREHPEMKD KILEPPIMTV SAINAQFAAY
510 520 530 540 550
LAQCVDYNTS KALTVVDSDS YKLFANPILD KFKVNLRELS SADTTPPVPA
560 570 580 590 600
ETVRDLGFEG YLSDFITGDK RVMKMLCQTS KIHTIPVSRR ELTPAQIKKL
610 620 630 640 650
ITPRPNGKIL FKRIIHGNRL VDIKQSAYGS KQVFPTDVSI KQTNFYQGSI
660 670 680 690 700
MSNEQKIRIE NEIINLKNEY NDRKSTLDAL SNQKSGYRHE LSELASKNDD
710 720 730 740 750
INREAHQLNE IRKKYTMRKS TIETLREKLD QLKREARKDV SQKIKDIDDQ
760 770 780 790 800
IQQLLLKQRH LLSKMASSMK SLKNCQKELI STQILQFEAQ NMDVSMNDVI
810 820 830 840 850
GFFNEREADL KSQYEDKKKF VKEMRDTPEF QSWMREIRSY DQDTKEKLNK
860 870 880 890 900
VAEKYEEEGN FNLSFVQDVL DKLESEIAMV NHDESAVTIL DQVTAELREL
910 920 930 940 950
EHTVPQQSKD LETIKAKLKE DHAVLEPKLD DIVSKISARF ARLFNNVGSA
960 970 980 990 1000
GAVRLEKPKD YAEWKIEIMV KFRDNAPLKK LDSHTQSGGE RAVSTVLYMI
1010 1020 1030 1040 1050
ALQEFTSAPF RVVDEINQGM DSRNERIVHK AMVENACAEN TSQYFLITPK
1060 1070 1080 1090
LLTGLHYHEK MRIHCVMAGS WIPNPSEDPK MIHFGETSNY SFD
Length:1,093
Mass (Da):126,037
Last modified:November 1, 1996 - v1
Checksum:i6752B96438CFB549
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z74776 Genomic DNA. Translation: CAA99034.1.
BK006948 Genomic DNA. Translation: DAA10747.1.
PIRiS66717.
RefSeqiNP_014608.1. NM_001183288.1.

Genome annotation databases

EnsemblFungiiYOL034W; YOL034W; YOL034W.
GeneIDi854123.
KEGGisce:YOL034W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z74776 Genomic DNA. Translation: CAA99034.1.
BK006948 Genomic DNA. Translation: DAA10747.1.
PIRiS66717.
RefSeqiNP_014608.1. NM_001183288.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3HTKX-ray2.31A304-363[»]
B739-811[»]
ProteinModelPortaliQ08204.
SMRiQ08204. Positions 304-363, 739-1048.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34366. 44 interactions.
DIPiDIP-1979N.
IntActiQ08204. 17 interactions.
MINTiMINT-404105.

Proteomic databases

MaxQBiQ08204.
PRIDEiQ08204.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYOL034W; YOL034W; YOL034W.
GeneIDi854123.
KEGGisce:YOL034W.

Organism-specific databases

EuPathDBiFungiDB:YOL034W.
SGDiS000005394. SMC5.

Phylogenomic databases

GeneTreeiENSGT00550000074963.
HOGENOMiHOG000141775.
InParanoidiQ08204.
OMAiHTSQYFL.
OrthoDBiEOG7Q8CWQ.

Enzyme and pathway databases

BioCyciYEAST:G3O-33450-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ08204.
NextBioi975828.
PROiQ08204.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR027417. P-loop_NTPase.
IPR003395. RecF/RecN/SMC_N.
IPR027131. SMC5.
IPR033268. Smc5/Smc6.
[Graphical view]
PANTHERiPTHR19306. PTHR19306. 1 hit.
PTHR19306:SF1. PTHR19306:SF1. 1 hit.
PfamiPF02463. SMC_N. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV."
    Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D.
    , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.
    Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  3. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  4. "A SUMO ligase is part of a nuclear multiprotein complex that affects DNA repair and chromosomal organization."
    Zhao X., Blobel G.
    Proc. Natl. Acad. Sci. U.S.A. 102:4777-4782(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT, SUMOYLATION BY MMS21.

Entry informationi

Entry nameiSMC5_YEAST
AccessioniPrimary (citable) accession number: Q08204
Secondary accession number(s): D6W231
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 25, 2005
Last sequence update: November 1, 1996
Last modified: May 11, 2016
This is version 110 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 892 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XV
    Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.