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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: 4 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 + adenine in DNA = S-adenosyl-L-homocysteine + N-6-methyladenine in DNA.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei216S-adenosyl-L-methionineBy similarity1

GO - Molecular functioni

  • DNA binding Source: InterPro
  • N-methyltransferase activity Source: EcoliWiki
  • site-specific DNA-methyltransferase (adenine-specific) activity Source: UniProtKB-EC

GO - Biological processi

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10458. hsdM.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000880221 – 529Type I restriction enzyme EcoKI M proteinAdd BLAST529

Proteomic databases

EPDiP08957.
PaxDbiP08957.
PRIDEiP08957.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

BioGridi4262768. 97 interactors.
DIPiDIP-9943N.
IntActiP08957. 14 interactors.
MINTiMINT-1252160.
STRINGi511145.b4349.

Structurei

Secondary structure

1529
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi5 – 18Combined sources14
Turni19 – 21Combined sources3
Helixi27 – 43Combined sources17
Helixi46 – 49Combined sources4
Helixi56 – 60Combined sources5
Helixi64 – 78Combined sources15
Beta strandi80 – 82Combined sources3
Helixi84 – 90Combined sources7
Helixi100 – 111Combined sources12
Helixi153 – 163Combined sources11
Beta strandi171 – 173Combined sources3
Turni177 – 179Combined sources3
Helixi180 – 190Combined sources11
Turni191 – 198Combined sources8
Helixi201 – 209Combined sources9
Beta strandi211 – 217Combined sources7
Helixi219 – 230Combined sources12
Turni231 – 233Combined sources3
Helixi238 – 240Combined sources3
Beta strandi242 – 247Combined sources6
Helixi252 – 255Combined sources4
Beta strandi260 – 265Combined sources6
Helixi288 – 299Combined sources12
Beta strandi300 – 311Combined sources12
Helixi312 – 316Combined sources5
Helixi320 – 331Combined sources12
Beta strandi332 – 339Combined sources8
Beta strandi345 – 347Combined sources3
Beta strandi352 – 360Combined sources9
Beta strandi374 – 379Combined sources6
Beta strandi388 – 391Combined sources4
Helixi395 – 397Combined sources3
Helixi399 – 405Combined sources7
Beta strandi427 – 429Combined sources3
Helixi433 – 435Combined sources3
Helixi442 – 444Combined sources3
Beta strandi446 – 451Combined sources6
Helixi452 – 457Combined sources6
Beta strandi459 – 461Combined sources3
Helixi482 – 505Combined sources24
Helixi511 – 521Combined sources11

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP08957.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni148 – 153S-adenosyl-L-methionine bindingBy similarity6
Regioni178 – 180S-adenosyl-L-methionine bindingBy similarity3

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105CVR. Bacteria.
COG0286. LUCA.
HOGENOMiHOG000295041.
InParanoidiP08957.
KOiK03427.
OMAiINYSDYV.
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.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF12161. HsdM_N. 1 hit.
PF02384. N6_Mtase. 1 hit.
[Graphical view]
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:November 1, 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.
WP_001063204.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC77305; AAC77305; b4349.
BAE78339; BAE78339; BAE78339.
GeneIDi948872.
KEGGiecj:JW4312.
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.
WP_001063204.1. NZ_LN832404.1.

3D structure databases

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

Protein-protein interaction databases

BioGridi4262768. 97 interactors.
DIPiDIP-9943N.
IntActiP08957. 14 interactors.
MINTiMINT-1252160.
STRINGi511145.b4349.

Protein family/group databases

REBASEi3387. M.EcoKI.

Proteomic databases

EPDiP08957.
PaxDbiP08957.
PRIDEiP08957.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC77305; AAC77305; b4349.
BAE78339; BAE78339; BAE78339.
GeneIDi948872.
KEGGiecj:JW4312.
eco:b4349.
PATRICi32124304. VBIEscCol129921_4495.

Organism-specific databases

EchoBASEiEB0453.
EcoGeneiEG10458. hsdM.

Phylogenomic databases

eggNOGiENOG4105CVR. Bacteria.
COG0286. LUCA.
HOGENOMiHOG000295041.
InParanoidiP08957.
KOiK03427.
OMAiINYSDYV.
PhylomeDBiP08957.

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiP08957.
PROiP08957.

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.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF12161. HsdM_N. 1 hit.
PF02384. N6_Mtase. 1 hit.
[Graphical view]
SUPFAMiSSF53335. SSF53335. 1 hit.
PROSITEiPS00092. N6_MTASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiT1MK_ECOLI
AccessioniPrimary (citable) accession number: P08957
Secondary accession number(s): Q2M5W7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1988
Last sequence update: November 1, 1988
Last modified: November 2, 2016
This is version 145 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

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 one 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.