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P38257

- MMS4_YEAST

UniProt

P38257 - MMS4_YEAST

Protein

Crossover junction endonuclease MMS4

Gene

MMS4

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 110 (01 Oct 2014)
      Sequence version 2 (13 Apr 2004)
      Previous versions | rss
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    Functioni

    Interacts with MUS81 to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. Typical substrates include 3'-flap structures, D-loops, replication forks with regressed leading strands and nicked Holliday junctions. Cleavage probably occurs approximately half a helical turn upstream of the free 5'-end in these structures. May be required in mitosis for the processing of stalled replication fork intermediates arising spontaneously or subsequent to treatment with DNA damaging agents such as methylmethane sulfonate (MMS), camptothecin (CPT) or UV. May be required in meiosis for the repair of meiosis-specific double strand breaks subsequent to single-end invasion (SEI). This involves consecutive cleavage of D-loops and nicked Holliday junctions leading to sister chromatid crossover. In contrast to MSH4-MSH5 dependent crossover, double Holliday junctions do not seem to be involved. Spore formation and viability are severely impaired in deletion strains.11 Publications

    Cofactori

    Magnesium or manganese.1 Publication

    Kineticsi

    1. KM=31.1 nM for a nicked Holliday junction1 Publication
    2. KM=6.84 nM for a regressed leading strand replication fork1 Publication
    3. KM=4.8 nM for for a 3'-flap structure1 Publication
    4. KM=3.45 nM for a nicked duplex1 Publication
    5. KM=14.0 nM for a regressed lagging strand replication fork1 Publication
    6. KM=245 nM for a Y structure1 Publication
    7. KM=173 nM for a double flap structure1 Publication

    Vmax=55.6 nmol/min/ng enzyme with a nicked Holliday junction as substrate1 Publication

    Vmax=31.3 nmol/min/ng enzyme with a regressed leading strand replication fork as substrate1 Publication

    Vmax=24.4 nmol/min/ng enzyme with a 3'-flap structure as substrate1 Publication

    Vmax=2.21 nmol/min/ng enzyme with a nicked duplex as substrate1 Publication

    Vmax=0.832 nmol/min/ng enzyme with a regressed lagging strand replication fork as subsystrate1 Publication

    Vmax=0.0468 nmol/min/ng enzyme with a Y structure as substrate1 Publication

    Vmax=0.0879 nmol/min/ng enzyme with a double flap structure as substrate1 Publication

    pH dependencei

    Optimum pH is 8.0 for cleavage of a 3'-flap structure.1 Publication

    GO - Molecular functioni

    1. DNA binding Source: InterPro
    2. endonuclease activity Source: UniProtKB-KW
    3. metal ion binding Source: UniProtKB-KW
    4. protein binding Source: IntAct

    GO - Biological processi

    1. cellular response to DNA damage stimulus Source: SGD
    2. DNA catabolic process, endonucleolytic Source: GOC
    3. DNA repair Source: SGD
    4. DNA topological change Source: SGD
    5. reciprocal meiotic recombination Source: SGD
    6. regulation of reciprocal meiotic recombination Source: SGD
    7. resolution of meiotic recombination intermediates Source: SGD

    Keywords - Molecular functioni

    Endonuclease, Hydrolase, Nuclease

    Keywords - Biological processi

    DNA damage, DNA recombination, DNA repair, Meiosis

    Keywords - Ligandi

    Magnesium, Manganese, Metal-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-29062-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Crossover junction endonuclease MMS4 (EC:3.1.22.-)
    Gene namesi
    Name:MMS4
    Synonyms:SLX2
    Ordered Locus Names:YBR098W
    ORF Names:YBR0826, YBR0829, YBR100W
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome II

    Organism-specific databases

    CYGDiYBR098w.
    SGDiS000000302. MMS4.

    Subcellular locationi

    Nucleus 1 Publication

    GO - Cellular componenti

    1. Holliday junction resolvase complex Source: SGD
    2. nucleus Source: SGD

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi173 – 1731G → R in allele MMS4-1; loss of activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 691690Crossover junction endonuclease MMS4PRO_0000096516Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N-acetylserine1 Publication
    Modified residuei48 – 481Phosphoserine1 Publication
    Modified residuei49 – 491Phosphoserine1 Publication
    Modified residuei61 – 611Phosphoserine1 Publication

    Keywords - PTMi

    Acetylation, Phosphoprotein

    Proteomic databases

    MaxQBiP38257.
    PaxDbiP38257.
    PeptideAtlasiP38257.
    PRIDEiP38257.

    Expressioni

    Gene expression databases

    GenevestigatoriP38257.

    Interactioni

    Subunit structurei

    Interacts with MUS81.4 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    MUS81Q041493EBI-21547,EBI-33508

    Protein-protein interaction databases

    BioGridi32804. 125 interactions.
    DIPiDIP-2927N.
    IntActiP38257. 6 interactions.
    MINTiMINT-603238.

    Structurei

    3D structure databases

    ProteinModelPortaliP38257.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni598 – 69194Interaction with MUS81Add
    BLAST

    Coiled coil

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Coiled coili364 – 39128Sequence AnalysisAdd
    BLAST
    Coiled coili507 – 52923Sequence AnalysisAdd
    BLAST

    Sequence similaritiesi

    Belongs to the EME1/MMS4 family.Curated

    Keywords - Domaini

    Coiled coil

    Phylogenomic databases

    eggNOGiNOG40733.
    HOGENOMiHOG000113612.
    OMAiSHMEFIN.
    OrthoDBiEOG7FJHB5.

    Family and domain databases

    InterProiIPR006166. ERCC4_domain.
    [Graphical view]
    PfamiPF02732. ERCC4. 1 hit.
    [Graphical view]
    SMARTiSM00891. ERCC4. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P38257-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSQIVDFVED KDSRNDASIQ IIDGPSNVEI IALSESMDQD ECKRAHVSSA    50
    EMIPSSPQRK SVSNDVENVD LNKSIELSAP FFQDISISKL DDFSTTVNSI 100
    IDSSLRNENN AKGNAKKLLD DLISDEWSAD LESSGKKHNK SQYNLRDIAE 150
    KWGVQSLKNP EPIAVDCEYK TQGIGKTNSD ISDSPKSQIG AADILFDFPL 200
    SPVKHENPTE EKHNSIANEN SSPDNSLKPA GKQNHGEDGT SMAKRVYNKG 250
    EDEQEHLPKG KKRTIALSRT LINSTKLPDT VELNLSKFLD SSDSITTDVL 300
    STPAKGSNIV RTGSQPIFSN ANCFQEAKRS KTLTAEDPKC TKNTAREVSQ 350
    LENYIAYGQY YTREDSKNKI RHLLKENKNA FKRVNQIYRD NIKARSQMII 400
    EFSPSLLQLF KKGDSDLQQQ LAPAVVQSSY NDSMPLLRFL RKCDSIYDFS 450
    NDFYYPCDPK IVEENVLILY YDAQEFFEQY TSQKKELYRK IRFFSKNGKH 500
    VILILSDINK LKRAIFQLEN EKYKARVEQR LSGTEEALRP RSKKSSQVGK 550
    LGIKKFDLEQ RLRFIDREWH VKIHTVNSHM EFINSLPNLV SLIGKQRMDP 600
    AIRYMKYAHL NVKSAQDSTE TLKKTFHQIG RMPEMKANNV VSLYPSFQSL 650
    LEDIEKGRLQ SDNEGKYLMT EAVEKRLYKL FTCTDPNDTI E 691
    Length:691
    Mass (Da):78,764
    Last modified:April 13, 2004 - v2
    Checksum:i3B3918DD3B2E7E0C
    GO

    Sequence cautioni

    The sequence AAT92950.1 differs from that shown. Reason: Frameshift at position 466.
    The sequence CAA55603.1 differs from that shown. Reason: Frameshift at position 466.
    The sequence CAA85051.1 differs from that shown. Reason: Frameshift at position 466.
    The sequence CAA85054.1 differs from that shown. Reason: Erroneous initiation.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U14000 Genomic DNA. Translation: AAF06816.1.
    X78993 Genomic DNA. Translation: CAA55603.1. Frameshift.
    Z35967 Genomic DNA. Translation: CAA85051.1. Frameshift.
    Z35968 Genomic DNA. Translation: CAA85054.1. Different initiation.
    AY692931 Genomic DNA. Translation: AAT92950.1. Frameshift.
    BK006936 Genomic DNA. Translation: DAA07219.1.
    PIRiS45968.
    S48265.
    RefSeqiNP_009656.2. NM_001178446.1.

    Genome annotation databases

    EnsemblFungiiYBR098W; YBR098W; YBR098W.
    GeneIDi852395.
    KEGGisce:YBR098W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U14000 Genomic DNA. Translation: AAF06816.1 .
    X78993 Genomic DNA. Translation: CAA55603.1 . Frameshift.
    Z35967 Genomic DNA. Translation: CAA85051.1 . Frameshift.
    Z35968 Genomic DNA. Translation: CAA85054.1 . Different initiation.
    AY692931 Genomic DNA. Translation: AAT92950.1 . Frameshift.
    BK006936 Genomic DNA. Translation: DAA07219.1 .
    PIRi S45968.
    S48265.
    RefSeqi NP_009656.2. NM_001178446.1.

    3D structure databases

    ProteinModelPortali P38257.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 32804. 125 interactions.
    DIPi DIP-2927N.
    IntActi P38257. 6 interactions.
    MINTi MINT-603238.

    Proteomic databases

    MaxQBi P38257.
    PaxDbi P38257.
    PeptideAtlasi P38257.
    PRIDEi P38257.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YBR098W ; YBR098W ; YBR098W .
    GeneIDi 852395.
    KEGGi sce:YBR098W.

    Organism-specific databases

    CYGDi YBR098w.
    SGDi S000000302. MMS4.

    Phylogenomic databases

    eggNOGi NOG40733.
    HOGENOMi HOG000113612.
    OMAi SHMEFIN.
    OrthoDBi EOG7FJHB5.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-29062-MONOMER.

    Miscellaneous databases

    NextBioi 971222.

    Gene expression databases

    Genevestigatori P38257.

    Family and domain databases

    InterProi IPR006166. ERCC4_domain.
    [Graphical view ]
    Pfami PF02732. ERCC4. 1 hit.
    [Graphical view ]
    SMARTi SM00891. ERCC4. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Mms4, a putative transcriptional (co)activator, protects Saccharomyces cerevisiae cells from endogenous and environmental DNA damage."
      Xiao W., Chow B.L., Milo C.N.
      Mol. Gen. Genet. 257:614-623(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], MUTAGENESIS OF GLY-173.
      Strain: S288c / GRF88.
    2. "Analysis of a 70 kb region on the right arm of yeast chromosome II."
      Mannhaupt G., Stucka R., Ehnle S., Vetter I., Feldmann H.
      Yeast 10:1363-1381(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. "Complete DNA sequence of yeast chromosome II."
      Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C.
      , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K.
      EMBO J. 13:5795-5809(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    4. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    5. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    6. "Functional overlap between Sgs1-Top3 and the Mms4-Mus81 endonuclease."
      Kaliraman V., Mullen J.R., Fricke W.M., Bastin-Shanower S.A., Brill S.J.
      Genes Dev. 15:2730-2740(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, PROCESSING OF STALLED REPLICATION FORK, INTERACTION WITH MUS81.
    7. "Requirement for three novel protein complexes in the absence of the Sgs1 DNA helicase in Saccharomyces cerevisiae."
      Mullen J.R., Kaliraman V., Ibrahim S.S., Brill S.J.
      Genetics 157:103-118(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH MUS81.
    8. "A role for MMS4 in the processing of recombination intermediates during meiosis in Saccharomyces cerevisiae."
      de los Santos T., Loidl J., Larkin B., Hollingsworth N.M.
      Genetics 159:1511-1525(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    9. "Alternate pathways involving Sgs1/Top3, Mus81/ Mms4, and Srs2 prevent formation of toxic recombination intermediates from single-stranded gaps created by DNA replication."
      Fabre F., Chan A., Heyer W.-D., Gangloff S.
      Proc. Natl. Acad. Sci. U.S.A. 99:16887-16892(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    10. Erratum
      Fabre F., Chan A., Heyer W.-D., Gangloff S.
      Proc. Natl. Acad. Sci. U.S.A. 100:1462-1462(2002)
    11. "Functional domains required for the Saccharomyces cerevisiae Mus81-Mms4 endonuclease complex formation and nuclear localization."
      Fu Y., Xiao W.
      DNA Repair 2:1435-1447(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH MUS81, SUBCELLULAR LOCATION, CHARACTERIZATION OF MUTANT ARG-173.
    12. "The Mus81/Mms4 endonuclease acts independently of double-Holliday junction resolution to promote a distinct subset of crossovers during meiosis in budding yeast."
      de los Santos T., Hunter N., Lee C., Larkin B., Loidl J., Hollingsworth N.M.
      Genetics 164:81-94(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CROSSOVER WITHOUT DOUBLE HOLLIDAY JUNCTION.
    13. "Cleavage of model replication forks by fission yeast Mus81-Eme1 and budding yeast Mus81-Mms4."
      Whitby M.C., Osman F., Dixon J.
      J. Biol. Chem. 278:6928-6935(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    14. "The mechanism of Mus81-Mms4 cleavage site selection distinguishes it from the homologous endonuclease Rad1-Rad10."
      Bastin-Shanower S.A., Fricke W.M., Mullen J.R., Brill S.J.
      Mol. Cell. Biol. 23:3487-3496(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CLEAVAGE SITE SELECTION.
    15. "Generating crossovers by resolution of nicked Holliday junctions: a role for Mus81-Eme1 in meiosis."
      Osman F., Dixon J., Doe C.L., Whitby M.C.
      Mol. Cell 12:761-774(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CROSSOVER WITHOUT DOUBLE HOLLIDAY JUNCTION.
    16. "Competing crossover pathways act during meiosis in Saccharomyces cerevisiae."
      Argueso J.L., Wanat J., Gemici Z., Alani E.
      Genetics 168:1805-1816(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    17. "Substrate specificity of the Saccharomyces cerevisiae Mus81-Mms4 endonuclease."
      Fricke W.M., Bastin-Shanower S.A., Brill S.J.
      DNA Repair 4:243-251(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, INTERACTION WITH MUS81.
    18. "The Mus81 solution to resolution: generating meiotic crossovers without Holliday junctions."
      Hollingsworth N.M., Brill S.J.
      Genes Dev. 18:117-125(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: REVIEW.
    19. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
      Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
      Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    20. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
      Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
      Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-48; SER-49 AND SER-61, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    21. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiMMS4_YEAST
    AccessioniPrimary (citable) accession number: P38257
    Secondary accession number(s): D6VQ99
    , P38259, Q6B1Z9, Q9URQ2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1994
    Last sequence update: April 13, 2004
    Last modified: October 1, 2014
    This is version 110 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Two distinct classes of meiotic crossovers have been demonstrated in budding yeast. Class I crossovers exhibit crossover interference and require MSH4 and MSH5 for their resolution, while class II crossovers exhibit no crossover interference and require MUS81 and MMS4. While class I crossovers represent the majority of crossovers in S.cerevisiae, they are virtually absent in S.pombe which lacks orthologs of MSH4 and MSH5.

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

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

    External Data

    Dasty 3