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O34680

- YDIP_BACSU

UniProt

O34680 - YDIP_BACSU

Protein

Probable BsuMI modification methylase subunit YdiP

Gene

ydiP

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 94 (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.PROSITE-ProRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei69 – 691PROSITE-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:BSU06070-MONOMER.

    Protein family/group databases

    REBASEi3613. M2.BsuMI.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Probable BsuMI modification methylase subunit YdiP (EC:2.1.1.37)
    Short name:
    M2.BsuMI
    Alternative name(s):
    Cytosine-specific methyltransferase M2.BsuMI
    Gene namesi
    Name:ydiP
    Ordered Locus Names:BSU06070
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    ProteomesiUP000001570: Chromosome

    Organism-specific databases

    GenoListiBSU06070.

    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 – 389389Probable BsuMI modification methylase subunit YdiPPRO_0000379885Add
    BLAST

    Proteomic databases

    PaxDbiO34680.

    Expressioni

    Developmental stagei

    Not expressed during sporulation.1 Publication

    Inductioni

    Constitutively expressed during exponential growth. Encoded in an operon with ydiO 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 YdiO, also seems to be active alone.

    Protein-protein interaction databases

    STRINGi224308.BSU06070.

    Structurei

    3D structure databases

    ProteinModelPortaliO34680.
    SMRiO34680. Positions 1-296.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini1 – 299299SAM-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.
    HOGENOMiHOG000226162.
    KOiK00558.
    OMAiVAAGFPC.
    OrthoDBiEOG6Z3KHQ.
    PhylomeDBiO34680.

    Family and domain databases

    Gene3Di3.40.50.150. 1 hit.
    InterProiIPR018117. C5_DNA_meth_AS.
    IPR001525. C5_MeTfrase.
    IPR029063. SAM-dependent_MTases-like.
    [Graphical view]
    PANTHERiPTHR10629. PTHR10629. 1 hit.
    PfamiPF00145. DNA_methylase. 2 hits.
    [Graphical view]
    PRINTSiPR00105. C5METTRFRASE.
    SUPFAMiSSF53335. SSF53335. 1 hit.
    TIGRFAMsiTIGR00675. dcm. 1 hit.
    PROSITEiPS00094. C5_MTASE_1. 1 hit.
    PS00095. C5_MTASE_2. 1 hit.
    PS51679. SAM_MT_C5. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    O34680-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKVVSLFSGI GGIELGLHQS GHTTEIFCEV DPLAKAVLSK NFPGVKIEDD    50
    INEIRELPSC DLVAAGFPCQ DLSQAGGKEG IDGSRSGLVK KLFELIEKKE 100
    HANRPPWILI ENVPYMLRLN RGKAMSYLTS VLSELGYTWA YRTVDARCFG 150
    LPQRRHRVIL LASLFEDPKD VIFSQDHSEP DLDGKPSVVD HSNYYGFYWT 200
    EGLRGVGWAR EAVPPIKCGS SVGIASPPAV WSPYEDIVGT INIRDAERLQ 250
    GFPEDWTNIT TETGKDIKEG ARWRLVGNAV SVRVSKWIGE NLSQPKGSIS 300
    DFEGELVTKT WPSAAWGYGD KKYKVPVSKW VANTEQIAIS EFLNHPLKPL 350
    SARALNGFLG RAARCTNVNY SDEFINSLER CKDRQLQKV 389
    Length:389
    Mass (Da):43,284
    Last modified:January 1, 1998 - v1
    Checksum:i16578833225AFE22
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB007637 Genomic DNA. Translation: BAA22751.1.
    AL009126 Genomic DNA. Translation: CAB12426.1.
    PIRiA69788.
    RefSeqiNP_388488.1. NC_000964.3.
    WP_003242904.1. NZ_CM000487.1.

    Genome annotation databases

    EnsemblBacteriaiCAB12426; CAB12426; BSU06070.
    GeneIDi939876.
    KEGGibsu:BSU06070.
    PATRICi18972846. VBIBacSub10457_0637.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB007637 Genomic DNA. Translation: BAA22751.1 .
    AL009126 Genomic DNA. Translation: CAB12426.1 .
    PIRi A69788.
    RefSeqi NP_388488.1. NC_000964.3.
    WP_003242904.1. NZ_CM000487.1.

    3D structure databases

    ProteinModelPortali O34680.
    SMRi O34680. Positions 1-296.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 224308.BSU06070.

    Protein family/group databases

    REBASEi 3613. M2.BsuMI.

    Proteomic databases

    PaxDbi O34680.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai CAB12426 ; CAB12426 ; BSU06070 .
    GeneIDi 939876.
    KEGGi bsu:BSU06070.
    PATRICi 18972846. VBIBacSub10457_0637.

    Organism-specific databases

    GenoListi BSU06070.

    Phylogenomic databases

    eggNOGi COG0270.
    HOGENOMi HOG000226162.
    KOi K00558.
    OMAi VAAGFPC.
    OrthoDBi EOG6Z3KHQ.
    PhylomeDBi O34680.

    Enzyme and pathway databases

    BioCyci BSUB:BSU06070-MONOMER.

    Family and domain databases

    Gene3Di 3.40.50.150. 1 hit.
    InterProi IPR018117. C5_DNA_meth_AS.
    IPR001525. C5_MeTfrase.
    IPR029063. SAM-dependent_MTases-like.
    [Graphical view ]
    PANTHERi PTHR10629. PTHR10629. 1 hit.
    Pfami PF00145. DNA_methylase. 2 hits.
    [Graphical view ]
    PRINTSi PR00105. C5METTRFRASE.
    SUPFAMi SSF53335. SSF53335. 1 hit.
    TIGRFAMsi TIGR00675. dcm. 1 hit.
    PROSITEi PS00094. C5_MTASE_1. 1 hit.
    PS00095. C5_MTASE_2. 1 hit.
    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 nameiYDIP_BACSU
    AccessioniPrimary (citable) accession number: O34680
    Secondary accession number(s): Q797D0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 28, 2009
    Last sequence update: January 1, 1998
    Last modified: October 1, 2014
    This is version 94 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