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O34680

- YDIP_BACSU

UniProt

O34680 - YDIP_BACSU

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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

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
Complete GO annotation...

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.
InParanoidiO34680.
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

        10         20         30         40         50
MKVVSLFSGI GGIELGLHQS GHTTEIFCEV DPLAKAVLSK NFPGVKIEDD
60 70 80 90 100
INEIRELPSC DLVAAGFPCQ DLSQAGGKEG IDGSRSGLVK KLFELIEKKE
110 120 130 140 150
HANRPPWILI ENVPYMLRLN RGKAMSYLTS VLSELGYTWA YRTVDARCFG
160 170 180 190 200
LPQRRHRVIL LASLFEDPKD VIFSQDHSEP DLDGKPSVVD HSNYYGFYWT
210 220 230 240 250
EGLRGVGWAR EAVPPIKCGS SVGIASPPAV WSPYEDIVGT INIRDAERLQ
260 270 280 290 300
GFPEDWTNIT TETGKDIKEG ARWRLVGNAV SVRVSKWIGE NLSQPKGSIS
310 320 330 340 350
DFEGELVTKT WPSAAWGYGD KKYKVPVSKW VANTEQIAIS EFLNHPLKPL
360 370 380
SARALNGFLG RAARCTNVNY SDEFINSLER CKDRQLQKV
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.
InParanoidi O34680.
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

« 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 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 29, 2014
This is version 95 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