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O34939

- YDIO_BACSU

UniProt

O34939 - YDIO_BACSU

Protein

Probable BsuMI modification methylase subunit YdiO

Gene

ydiO

Organism
Bacillus subtilis (strain 168)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 88 (01 Oct 2014)
      Sequence version 1 (01 Jan 1998)
      Previous versions | rss
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    Functioni

    This methylase may recognize the double-stranded sequence CTCGAG, causing specific methylation on C-? on both strands, and protects the DNA from cleavage by the BsuMI endonuclease.2 Publications

    Catalytic activityi

    S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei176 – 1761PROSITE-ProRule annotation

    GO - Molecular functioni

    1. DNA (cytosine-5-)-methyltransferase activity Source: UniProtKB-EC
    2. DNA binding Source: InterPro
    3. methyltransferase activity Source: UniProtKB

    GO - Biological processi

    1. DNA methylation on cytosine Source: UniProtKB
    2. DNA restriction-modification system Source: UniProtKB

    Keywords - Molecular functioni

    Methyltransferase, Transferase

    Keywords - Biological processi

    Restriction system

    Keywords - Ligandi

    S-adenosyl-L-methionine

    Enzyme and pathway databases

    BioCyciBSUB:BSU06060-MONOMER.

    Protein family/group databases

    REBASEi3612. M1.BsuMI.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Probable BsuMI modification methylase subunit YdiO (EC:2.1.1.37)
    Short name:
    M1.BsuMI
    Alternative name(s):
    Cytosine-specific methyltransferase M1.BsuMI
    Gene namesi
    Name:ydiO
    Ordered Locus Names:BSU06060
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    ProteomesiUP000001570: Chromosome

    Organism-specific databases

    GenoListiBSU06060.

    Pathology & Biotechi

    Disruption phenotypei

    Essential for growth, it can be disrupted once one of the components of the corresponding BsuMI restriction endonuclease complex (AC O34303, O34885, O35025) has been disrupted.1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 427427Probable BsuMI modification methylase subunit YdiOPRO_0000379884Add
    BLAST

    Proteomic databases

    PaxDbiO34939.

    Expressioni

    Developmental stagei

    Not expressed during sporulation.1 Publication

    Inductioni

    Constitutively expressed during exponential growth. Encoded in an operon with ydiP and in a second with groES, groEL, ydiM and ydiN. This second operon is heat-inducible.1 Publication

    Interactioni

    Subunit structurei

    May form a complex with YdiP, also seems to be active alone.

    Protein-protein interaction databases

    STRINGi224308.BSU06060.

    Structurei

    3D structure databases

    ProteinModelPortaliO34939.
    SMRiO34939. Positions 84-427.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini84 – 427344SAM-dependent MTase C5-typePROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the class I-like SAM-binding methyltransferase superfamily. C5-methyltransferase family.PROSITE-ProRule annotation
    Contains 1 SAM-dependent MTase C5-type domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG0270.
    HOGENOMiHOG000098493.
    KOiK00558.
    OMAiFSAGLEC.
    OrthoDBiEOG6KMB5M.
    PhylomeDBiO34939.

    Family and domain databases

    Gene3Di3.40.50.150. 1 hit.
    InterProiIPR001525. C5_MeTfrase.
    IPR029063. SAM-dependent_MTases-like.
    [Graphical view]
    PANTHERiPTHR10629. PTHR10629. 1 hit.
    PfamiPF00145. DNA_methylase. 1 hit.
    [Graphical view]
    PRINTSiPR00105. C5METTRFRASE.
    SUPFAMiSSF53335. SSF53335. 1 hit.
    TIGRFAMsiTIGR00675. dcm. 1 hit.
    PROSITEiPS51679. SAM_MT_C5. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    O34939-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTNFILNENK QLSLAIEDEN IENFYIDGTD LVRKIIRRSG SGVTSRVPVL    50
    STQDLENKNL HELYDESWLR MKNRPNTELT TESINIADLF SGCGGLSLGV 100
    WEACRALGIN PRFSFACDLN EAALSVYEKN FSPDFSLNES IEKHINGELG 150
    APLTVEEQRI KDKVKKIDFI LAGPPCQGHS DLNNHTRRKD PRNALLMRVS 200
    RVIELFQPSS VLVENVPGII HDKSGSFKEF KNHLKTQGYY FDEIVLNAEK 250
    LGVSQARRRY FIFASKTPVS SLNQINEFYS TNSRPISWAI SDLVENVGDD 300
    IFNTASEHSL ENKRRIEYLF ENNLFELPNS ERPDCHRLKP HSYKSVYGRM 350
    YWDRPAPTIT RGFGSTGQGR FVHSLLKRTI TPHEAARIQF FPDFFNFGDL 400
    RRRQYQDVIG NAVPSKLSYL LALHQLR 427
    Length:427
    Mass (Da):48,909
    Last modified:January 1, 1998 - v1
    Checksum:i3B02F48DD9CF1E30
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB007637 Genomic DNA. Translation: BAA22750.1.
    AL009126 Genomic DNA. Translation: CAB12425.1.
    PIRiH69787.
    RefSeqiNP_388487.1. NC_000964.3.
    WP_003234063.1. NZ_CM000487.1.

    Genome annotation databases

    EnsemblBacteriaiCAB12425; CAB12425; BSU06060.
    GeneIDi939892.
    KEGGibsu:BSU06060.
    PATRICi18972844. VBIBacSub10457_0636.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB007637 Genomic DNA. Translation: BAA22750.1 .
    AL009126 Genomic DNA. Translation: CAB12425.1 .
    PIRi H69787.
    RefSeqi NP_388487.1. NC_000964.3.
    WP_003234063.1. NZ_CM000487.1.

    3D structure databases

    ProteinModelPortali O34939.
    SMRi O34939. Positions 84-427.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 224308.BSU06060.

    Protein family/group databases

    REBASEi 3612. M1.BsuMI.

    Proteomic databases

    PaxDbi O34939.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai CAB12425 ; CAB12425 ; BSU06060 .
    GeneIDi 939892.
    KEGGi bsu:BSU06060.
    PATRICi 18972844. VBIBacSub10457_0636.

    Organism-specific databases

    GenoListi BSU06060.

    Phylogenomic databases

    eggNOGi COG0270.
    HOGENOMi HOG000098493.
    KOi K00558.
    OMAi FSAGLEC.
    OrthoDBi EOG6KMB5M.
    PhylomeDBi O34939.

    Enzyme and pathway databases

    BioCyci BSUB:BSU06060-MONOMER.

    Family and domain databases

    Gene3Di 3.40.50.150. 1 hit.
    InterProi IPR001525. C5_MeTfrase.
    IPR029063. SAM-dependent_MTases-like.
    [Graphical view ]
    PANTHERi PTHR10629. PTHR10629. 1 hit.
    Pfami PF00145. DNA_methylase. 1 hit.
    [Graphical view ]
    PRINTSi PR00105. C5METTRFRASE.
    SUPFAMi SSF53335. SSF53335. 1 hit.
    TIGRFAMsi TIGR00675. dcm. 1 hit.
    PROSITEi PS51679. SAM_MT_C5. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Sequence analysis of the groESL-cotA region of the Bacillus subtilis genome, containing the restriction/modification system genes."
      Kasahara Y., Nakai S., Ogasawara N., Yata K., Sadaie Y.
      DNA Res. 4:335-339(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB 3610 / VKM B-501.
    2. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
      Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
      , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
      Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 168.
    3. "DNA methyltransferase of Bacillus subtilis Marburg: purification, properties and further evidence of specificity."
      Guha S.
      Gene 74:77-81(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
      Strain: 168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB 3610 / VKM B-501.
    4. "Restriction and modification in Bacillus subtilis Marburg 168: target sites and effects on plasmid transformation."
      Bron S., Janniere L., Ehrlich S.D.
      Mol. Gen. Genet. 211:186-189(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: DNA TARGET SEQUENCE.
      Strain: 168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB 3610 / VKM B-501.
    5. "Molecular organization of intrinsic restriction and modification genes BsuM of Bacillus subtilis Marburg."
      Ohshima H., Matsuoka S., Asai K., Sadaie Y.
      J. Bacteriol. 184:381-389(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, DEVELOPMENTAL STAGE, INDUCTION, OPERON STRUCTURE, DISRUPTION PHENOTYPE.
      Strain: 168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB 3610 / VKM B-501.

    Entry informationi

    Entry nameiYDIO_BACSU
    AccessioniPrimary (citable) accession number: O34939
    Secondary accession number(s): Q797D1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 28, 2009
    Last sequence update: January 1, 1998
    Last modified: October 1, 2014
    This is version 88 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Caution

    The characterized enzyme was reported to be a monomer of approximately 45 kDa; it is not clear whether this corresponds to YdiO, YdiP or to another activity altogether.1 Publication

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Bacillus subtilis
      Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3