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Protein

Type-2 restriction enzyme BsuMI component YdjA

Gene

ydjA

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at transcript leveli

Functioni

Recognizes the double-stranded sequence CTCGAG; the cleavage site is unknown.

Catalytic activityi

Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates.

GO - Molecular functioni

  1. Type II site-specific deoxyribonuclease activity Source: UniProtKB-EC

GO - Biological processi

  1. DNA restriction-modification system Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

Restriction system

Enzyme and pathway databases

BioCyciBSUB:BSU06110-MONOMER.

Protein family/group databases

REBASEi619. BsuMI.

Names & Taxonomyi

Protein namesi
Recommended name:
Type-2 restriction enzyme BsuMI component YdjA (EC:3.1.21.4)
Short name:
R.BsuM
Short name:
R.BsuMI
Alternative name(s):
Endonuclease BsuMI component YdjA
Type II restriction enzyme BsuMI component YdjA
Gene namesi
Name:ydjA
Ordered Locus Names:BSU06110
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
ProteomesiUP000001570 Componenti: Chromosome

Organism-specific databases

GenoListiBSU06110.

Pathology & Biotechi

Disruption phenotypei

Not essential; its disruption results in increased transformation by plasmid DNA carrying multiple BsuMI target sequences.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 465465Type-2 restriction enzyme BsuMI component YdjAPRO_0000379883Add
BLAST

Proteomic databases

PaxDbiO34303.

Expressioni

Developmental stagei

Not expressed during sporulation.1 Publication

Inductioni

Constitutively expressed during exponential growth. Encoded in an operon with ydiR and ydiS.1 Publication

Interactioni

Subunit structurei

BsuMI restriction activity requires YdiR, YdiS and YdjA.

Protein-protein interaction databases

STRINGi224308.BSU06110.

Structurei

3D structure databases

ProteinModelPortaliO34303.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Phylogenomic databases

eggNOGiNOG15592.
HOGENOMiHOG000080449.
OMAiKERWISI.
OrthoDBiEOG6PW23V.

Family and domain databases

InterProiIPR018579. Restrct_endonuc_II_LlaJI.
[Graphical view]
PfamiPF09563. RE_LlaJI. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O34303-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDKSSKFFFE DQKYNKERIV RVLGGNLALL KSKGILYEDS SGDLIFNYVG
60 70 80 90 100
VISNGRNVIF ILPKYCNRHL DEHSKRTLFN KLLKIFKKYS GLNKSRESDY
110 120 130 140 150
FVSELDSDEV SDFMIADYLL NDFSLNGYYQ KKFTEYEIDG EGIIDWSKTV
160 170 180 190 200
NEITPVFSKG VPYYFSTYNE VVQKDEYHLI VKIHKWALSK YFNDFGVILG
210 220 230 240 250
FTGLEFDKSC DGMKILDYAD FFGSVINKEI VNTYVDRDVK LLKALKTAID
260 270 280 290 300
REENQFSKRP TLSLYGTKYF HRVWEEVCKT VFSHVNEYVK KISRPNWINF
310 320 330 340 350
TDIEVNKEKK TLEPDIIKAF EYRSKEYFLI LDAKYYNINF DGKKLEGNPG
360 370 380 390 400
VEDITKQLLY DKALEKLSRG KTKHNAFLFP SSNSTNTFKV FGSVDFDFLD
410 420 430 440 450
IAAVTLVYIS AEQVYNLYLE NKTFSTDDLF KFVSEINKSK KRHSVITSTL
460
YGNMFLFTKR LSDKN
Length:465
Mass (Da):54,336
Last modified:January 1, 1998 - v1
Checksum:iDE93019E964B0E65
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB007637 Genomic DNA. Translation: BAA22755.1.
AL009126 Genomic DNA. Translation: CAB12430.1.
PIRiE69788.
RefSeqiNP_388492.1. NC_000964.3.
WP_003234050.1. NZ_JNCM01000032.1.

Genome annotation databases

EnsemblBacteriaiCAB12430; CAB12430; BSU06110.
GeneIDi939884.
KEGGibsu:BSU06110.
PATRICi18972858. VBIBacSub10457_0643.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB007637 Genomic DNA. Translation: BAA22755.1.
AL009126 Genomic DNA. Translation: CAB12430.1.
PIRiE69788.
RefSeqiNP_388492.1. NC_000964.3.
WP_003234050.1. NZ_JNCM01000032.1.

3D structure databases

ProteinModelPortaliO34303.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.BSU06110.

Protein family/group databases

REBASEi619. BsuMI.

Proteomic databases

PaxDbiO34303.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB12430; CAB12430; BSU06110.
GeneIDi939884.
KEGGibsu:BSU06110.
PATRICi18972858. VBIBacSub10457_0643.

Organism-specific databases

GenoListiBSU06110.

Phylogenomic databases

eggNOGiNOG15592.
HOGENOMiHOG000080449.
OMAiKERWISI.
OrthoDBiEOG6PW23V.

Enzyme and pathway databases

BioCyciBSUB:BSU06110-MONOMER.

Family and domain databases

InterProiIPR018579. Restrct_endonuc_II_LlaJI.
[Graphical view]
PfamiPF09563. RE_LlaJI. 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(1996) [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(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 168.
  3. "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(1987) [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.
  4. "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(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: 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 nameiYDJA_BACSU
AccessioniPrimary (citable) accession number: O34303
Secondary accession number(s): Q797C8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: January 1, 1998
Last modified: January 7, 2015
This is version 72 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList

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.