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Protein

Type I restriction enzyme EcoKI M protein

Gene

hsdM

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

The M and S subunits together form a methyltransferase (MTase) that methylates two adenine residues in complementary strands of a bipartite DNA recognition sequence. In the presence of the R subunit the complex can also act as an endonuclease, binding to the same target sequence but cutting the DNA some distance from this site. Whether the DNA is cut or modified depends on the methylation state of the target sequence. When the target site is unmodified, the DNA is cut. When the target site is hemimethylated, the complex acts as a maintenance MTase modifying the DNA so that both strands become methylated. The EcoKI enzyme recognizes 5'-AACN6GTGC-3'.

Catalytic activityi

S-adenosyl-L-methionine + DNA adenine = S-adenosyl-L-homocysteine + DNA 6-methylaminopurine.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei216 – 2161S-adenosyl-L-methionineBy similarity

GO - Molecular functioni

  1. DNA binding Source: InterPro
  2. N-methyltransferase activity Source: EcoliWiki
  3. site-specific DNA-methyltransferase (adenine-specific) activity Source: UniProtKB-EC

GO - Biological processi

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

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

Restriction system

Keywords - Ligandi

S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciEcoCyc:EG10458-MONOMER.
ECOL316407:JW4312-MONOMER.
MetaCyc:EG10458-MONOMER.

Protein family/group databases

REBASEi3387. M.EcoKI.

Names & Taxonomyi

Protein namesi
Recommended name:
Type I restriction enzyme EcoKI M protein (EC:2.1.1.72)
Short name:
M.EcoKI
Gene namesi
Name:hsdM
Synonyms:hsm
Ordered Locus Names:b4349, JW4312
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10458. hsdM.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 529529Type I restriction enzyme EcoKI M proteinPRO_0000088022Add
BLAST

Proteomic databases

PaxDbiP08957.
PRIDEiP08957.

Expressioni

Gene expression databases

GenevestigatoriP08957.

Interactioni

Subunit structurei

The type I restriction/modification system is composed of three polypeptides R, M and S.

Protein-protein interaction databases

DIPiDIP-9943N.
IntActiP08957. 14 interactions.
MINTiMINT-1252160.
STRINGi511145.b4349.

Structurei

Secondary structure

1
529
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi5 – 1814Combined sources
Turni19 – 213Combined sources
Helixi27 – 4317Combined sources
Helixi46 – 494Combined sources
Helixi56 – 605Combined sources
Helixi64 – 7815Combined sources
Beta strandi80 – 823Combined sources
Helixi84 – 907Combined sources
Helixi100 – 11112Combined sources
Helixi153 – 16311Combined sources
Beta strandi171 – 1733Combined sources
Turni177 – 1793Combined sources
Helixi180 – 19011Combined sources
Turni191 – 1988Combined sources
Helixi201 – 2099Combined sources
Beta strandi211 – 2177Combined sources
Helixi219 – 23012Combined sources
Turni231 – 2333Combined sources
Helixi238 – 2403Combined sources
Beta strandi242 – 2476Combined sources
Helixi252 – 2554Combined sources
Beta strandi260 – 2656Combined sources
Helixi288 – 29912Combined sources
Beta strandi300 – 31112Combined sources
Helixi312 – 3165Combined sources
Helixi320 – 33112Combined sources
Beta strandi332 – 3398Combined sources
Beta strandi345 – 3473Combined sources
Beta strandi352 – 3609Combined sources
Beta strandi374 – 3796Combined sources
Beta strandi388 – 3914Combined sources
Helixi395 – 3973Combined sources
Helixi399 – 4057Combined sources
Beta strandi427 – 4293Combined sources
Helixi433 – 4353Combined sources
Helixi442 – 4443Combined sources
Beta strandi446 – 4516Combined sources
Helixi452 – 4576Combined sources
Beta strandi459 – 4613Combined sources
Helixi482 – 50524Combined sources
Helixi511 – 52111Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2AR0X-ray2.80A/B2-527[»]
2Y7Celectron microscopy18.00B/C1-529[»]
2Y7Helectron microscopy18.00B/C1-529[»]
ProteinModelPortaliP08957.
SMRiP08957. Positions 1-529.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP08957.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni148 – 1536S-adenosyl-L-methionine bindingBy similarity
Regioni178 – 1803S-adenosyl-L-methionine bindingBy similarity

Sequence similaritiesi

Belongs to the N(4)/N(6)-methyltransferase family.Curated

Phylogenomic databases

eggNOGiCOG0286.
HOGENOMiHOG000295041.
InParanoidiP08957.
KOiK03427.
OMAiLCNVLRD.
OrthoDBiEOG686NCV.
PhylomeDBiP08957.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR022749. D12N6_MeTrfase_N.
IPR003356. DNA_methylase_A-5.
IPR002052. DNA_methylase_N6_adenine_CS.
IPR002296. N12N6_MeTrfase.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF12161. HsdM_N. 1 hit.
PF02384. N6_Mtase. 1 hit.
[Graphical view]
PRINTSiPR00507. N12N6MTFRASE.
SUPFAMiSSF53335. SSF53335. 1 hit.
PROSITEiPS00092. N6_MTASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P08957-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNNNDLVAKL WKLCDNLRDG GVSYQNYVNE LASLLFLKMC KETGQEAEYL
60 70 80 90 100
PEGYRWDDLK SRIGQEQLQF YRKMLVHLGE DDKKLVQAVF HNVSTTITEP
110 120 130 140 150
KQITALVSNM DSLDWYNGAH GKSRDDFGDM YEGLLQKNAN ETKSGAGQYF
160 170 180 190 200
TPRPLIKTII HLLKPQPREV VQDPAAGTAG FLIEADRYVK SQTNDLDDLD
210 220 230 240 250
GDTQDFQIHR AFIGLELVPG TRRLALMNCL LHDIEGNLDH GGAIRLGNTL
260 270 280 290 300
GSDGENLPKA HIVATNPPFG SAAGTNITRT FVHPTSNKQL CFMQHIIETL
310 320 330 340 350
HPGGRAAVVV PDNVLFEGGK GTDIRRDLMD KCHLHTILRL PTGIFYAQGV
360 370 380 390 400
KTNVLFFTKG TVANPNQDKN CTDDVWVYDL RTNMPSFGKR TPFTDEHLQP
410 420 430 440 450
FERVYGEDPH GLSPRTEGEW SFNAEETEVA DSEENKNTDQ HLATSRWRKF
460 470 480 490 500
SREWIRTAKS DSLDISWLKD KDSIDADSLP EPDVLAAEAM GELVQALSEL
510 520
DALMRELGAS DEADLQRQLL EEAFGGVKE
Length:529
Mass (Da):59,307
Last modified:October 31, 1988 - v1
Checksum:iD41C02203747C965
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X06545 Genomic DNA. Translation: CAA29792.1.
U14003 Genomic DNA. Translation: AAA97246.1.
U00096 Genomic DNA. Translation: AAC77305.1.
AP009048 Genomic DNA. Translation: BAE78339.1.
PIRiB30375. XYECHM.
RefSeqiNP_418769.1. NC_000913.3.
YP_492480.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC77305; AAC77305; b4349.
BAE78339; BAE78339; BAE78339.
GeneIDi12933774.
948872.
KEGGiecj:Y75_p4234.
eco:b4349.
PATRICi32124304. VBIEscCol129921_4495.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X06545 Genomic DNA. Translation: CAA29792.1.
U14003 Genomic DNA. Translation: AAA97246.1.
U00096 Genomic DNA. Translation: AAC77305.1.
AP009048 Genomic DNA. Translation: BAE78339.1.
PIRiB30375. XYECHM.
RefSeqiNP_418769.1. NC_000913.3.
YP_492480.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2AR0X-ray2.80A/B2-527[»]
2Y7Celectron microscopy18.00B/C1-529[»]
2Y7Helectron microscopy18.00B/C1-529[»]
ProteinModelPortaliP08957.
SMRiP08957. Positions 1-529.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-9943N.
IntActiP08957. 14 interactions.
MINTiMINT-1252160.
STRINGi511145.b4349.

Protein family/group databases

REBASEi3387. M.EcoKI.

Proteomic databases

PaxDbiP08957.
PRIDEiP08957.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC77305; AAC77305; b4349.
BAE78339; BAE78339; BAE78339.
GeneIDi12933774.
948872.
KEGGiecj:Y75_p4234.
eco:b4349.
PATRICi32124304. VBIEscCol129921_4495.

Organism-specific databases

EchoBASEiEB0453.
EcoGeneiEG10458. hsdM.

Phylogenomic databases

eggNOGiCOG0286.
HOGENOMiHOG000295041.
InParanoidiP08957.
KOiK03427.
OMAiLCNVLRD.
OrthoDBiEOG686NCV.
PhylomeDBiP08957.

Enzyme and pathway databases

BioCyciEcoCyc:EG10458-MONOMER.
ECOL316407:JW4312-MONOMER.
MetaCyc:EG10458-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP08957.
PROiP08957.

Gene expression databases

GenevestigatoriP08957.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR022749. D12N6_MeTrfase_N.
IPR003356. DNA_methylase_A-5.
IPR002052. DNA_methylase_N6_adenine_CS.
IPR002296. N12N6_MeTrfase.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF12161. HsdM_N. 1 hit.
PF02384. N6_Mtase. 1 hit.
[Graphical view]
PRINTSiPR00507. N12N6MTFRASE.
SUPFAMiSSF53335. SSF53335. 1 hit.
PROSITEiPS00092. N6_MTASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Organization and sequence of the hsd genes of Escherichia coli K-12."
    Loenen W.A.M., Daniel A.S., Braymer H.D., Murray N.E.
    J. Mol. Biol. 198:159-170(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  2. "Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes."
    Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.
    Nucleic Acids Res. 23:2105-2119(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Escherichia coli proteome analysis using the gene-protein database."
    VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
    Electrophoresis 18:1243-1251(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY 2D-GEL.

Entry informationi

Entry nameiT1MK_ECOLI
AccessioniPrimary (citable) accession number: P08957
Secondary accession number(s): Q2M5W7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 31, 1988
Last sequence update: October 31, 1988
Last modified: January 6, 2015
This is version 131 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Type I restriction and modification enzymes are complex, multifunctional systems which require ATP, S-adenosyl methionine and Mg2+ as cofactors and, in addition to their endonucleolytic and methylase activities, are potent DNA-dependent ATPases.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Restriction enzymes and methylases
    Classification of restriction enzymes and methylases and list of entries
  4. 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.