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Protein

Probable BsuMI modification methylase subunit YdiO

Gene

ydiO

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

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

  • DNA (cytosine-5-)-methyltransferase activity Source: UniProtKB-EC
  • methyltransferase activity Source: UniProtKB

GO - Biological processi

  • DNA methylation on cytosine Source: UniProtKB
  • DNA restriction-modification system Source: UniProtKB
Complete GO annotation...

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 Componenti: 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.Bsubs1_010100003403.

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.
InParanoidiO34939.
KOiK00558.
OMAiHELYDES.
OrthoDBiEOG6KMB5M.
PhylomeDBiO34939.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR001525. C5_MeTfrase.
IPR029063. SAM-dependent_MTases.
[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

        10         20         30         40         50
MTNFILNENK QLSLAIEDEN IENFYIDGTD LVRKIIRRSG SGVTSRVPVL
60 70 80 90 100
STQDLENKNL HELYDESWLR MKNRPNTELT TESINIADLF SGCGGLSLGV
110 120 130 140 150
WEACRALGIN PRFSFACDLN EAALSVYEKN FSPDFSLNES IEKHINGELG
160 170 180 190 200
APLTVEEQRI KDKVKKIDFI LAGPPCQGHS DLNNHTRRKD PRNALLMRVS
210 220 230 240 250
RVIELFQPSS VLVENVPGII HDKSGSFKEF KNHLKTQGYY FDEIVLNAEK
260 270 280 290 300
LGVSQARRRY FIFASKTPVS SLNQINEFYS TNSRPISWAI SDLVENVGDD
310 320 330 340 350
IFNTASEHSL ENKRRIEYLF ENNLFELPNS ERPDCHRLKP HSYKSVYGRM
360 370 380 390 400
YWDRPAPTIT RGFGSTGQGR FVHSLLKRTI TPHEAARIQF FPDFFNFGDL
410 420
RRRQYQDVIG NAVPSKLSYL LALHQLR
Length:427
Mass (Da):48,909
Last modified:January 1, 1998 - v1
Checksum:i3B02F48DD9CF1E30
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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_JNCM01000032.1.

Genome annotation databases

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

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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_JNCM01000032.1.

3D structure databases

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

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100003403.

Protein family/group databases

REBASEi3612. M1.BsuMI.

Proteomic databases

PaxDbiO34939.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

GenoListiBSU06060.

Phylogenomic databases

eggNOGiCOG0270.
HOGENOMiHOG000098493.
InParanoidiO34939.
KOiK00558.
OMAiHELYDES.
OrthoDBiEOG6KMB5M.
PhylomeDBiO34939.

Enzyme and pathway databases

BioCyciBSUB:BSU06060-MONOMER.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR001525. C5_MeTfrase.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PRINTSiPR00105. C5METTRFRASE.
SUPFAMiSSF53335. SSF53335. 1 hit.
TIGRFAMsiTIGR00675. dcm. 1 hit.
PROSITEiPS51679. SAM_MT_C5. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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: June 24, 2015
This is version 91 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

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 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.