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Protein

DNA adenine methylase

Gene

DAM

Organism
Enterobacteria phage T4 (Bacteriophage T4)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Methyltransferase that methylates adenine residues in the dsDNA sequence GATC. May prevents degradation of viral DNA by the host restriction-modification antiviral defense system.Curated1 Publication

Catalytic activityi

S-adenosyl-L-methionine + DNA adenine = S-adenosyl-L-homocysteine + DNA 6-methylaminopurine.1 Publication

Kineticsi

  1. KM=0.1 µM for S-adenosylmethionine1 Publication

    pH dependencei

    Optimum pH is 7.0-8.5.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei7 – 71S-adenosyl-L-homocysteineCombined sources
    Binding sitei11 – 111S-adenosyl-L-homocysteine; via amide nitrogenCombined sources
    Binding sitei50 – 501S-adenosyl-L-methionineCombined sources
    Binding sitei171 – 1711S-adenosyl-L-methionineCombined sources
    Binding sitei181 – 1811S-adenosyl-L-homocysteineCombined sources

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Methyltransferase, Transferase

    Keywords - Biological processi

    DNA replication, Host-virus interaction, Restriction-modification system evasion by virus

    Keywords - Ligandi

    S-adenosyl-L-methionine

    Enzyme and pathway databases

    BRENDAi2.1.1.72. 732.

    Protein family/group databases

    REBASEi2837. M.EcoT4Dam.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA adenine methylase (EC:2.1.1.721 Publication)
    Alternative name(s):
    DNA-(N(6)-adenine)-methyltransferase1 Publication
    Deoxyadenosyl-methyltransferase
    M.EcoT4Dam
    Gene namesi
    Name:DAM
    OrganismiEnterobacteria phage T4 (Bacteriophage T4)
    Taxonomic identifieri10665 [NCBI]
    Taxonomic lineageiVirusesdsDNA viruses, no RNA stageCaudoviralesMyoviridaeTevenvirinaeT4likevirus
    Virus hostiEscherichia coli [TaxID: 562]
    ProteomesiUP000009087 Componenti: Genome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi126 – 1261P → S in damh; hypermethylating mutant.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 259259DNA adenine methylasePRO_0000087990Add
    BLAST

    Interactioni

    Subunit structurei

    Monomer.2 Publications

    Structurei

    Secondary structure

    1
    259
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Turni12 – 143Combined sources
    Helixi15 – 206Combined sources
    Beta strandi26 – 305Combined sources
    Helixi39 – 413Combined sources
    Beta strandi44 – 496Combined sources
    Helixi53 – 6210Combined sources
    Helixi67 – 7610Combined sources
    Helixi84 – 9714Combined sources
    Helixi100 – 1078Combined sources
    Helixi111 – 1133Combined sources
    Helixi136 – 14611Combined sources
    Helixi147 – 1493Combined sources
    Beta strandi150 – 1534Combined sources
    Helixi157 – 1593Combined sources
    Beta strandi166 – 1705Combined sources
    Beta strandi175 – 1773Combined sources
    Helixi180 – 1845Combined sources
    Helixi187 – 20115Combined sources
    Turni202 – 2043Combined sources
    Beta strandi206 – 21510Combined sources
    Helixi221 – 2277Combined sources
    Beta strandi230 – 2345Combined sources
    Helixi237 – 2426Combined sources
    Beta strandi254 – 2585Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1Q0SX-ray2.30A1-259[»]
    1Q0TX-ray3.10A/B1-259[»]
    1YF3X-ray2.29A/B1-259[»]
    1YFJX-ray2.69A/B/C/D/E/F1-259[»]
    1YFLX-ray3.09A/B/D/E1-259[»]
    ProteinModelPortaliP04392.
    SMRiP04392. Positions 1-259.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP04392.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni32 – 376S-adenosyl-L-homocysteine bindingCombined sources
    Regioni156 – 1572S-adenosyl-L-homocysteine bindingCombined sources

    Sequence similaritiesi

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

    Phylogenomic databases

    KOiK06223.

    Family and domain databases

    Gene3Di1.10.1020.10. 1 hit.
    3.40.50.150. 2 hits.
    InterProiIPR023095. Ade_MeTrfase_dom_2.
    IPR002052. DNA_methylase_N6_adenine_CS.
    IPR012263. M_m6A_EcoRV.
    IPR012327. MeTrfase_D12.
    IPR029063. SAM-dependent_MTases.
    [Graphical view]
    PfamiPF02086. MethyltransfD12. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000398. M_m6A_EcoRV. 1 hit.
    PRINTSiPR00505. D12N6MTFRASE.
    SUPFAMiSSF53335. SSF53335. 1 hit.
    TIGRFAMsiTIGR00571. dam. 1 hit.
    PROSITEiPS00092. N6_MTASE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P04392-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MLGAIAYTGN KQSLLPELKS HFPKYNRFVD LFCGGLSVSL NVNGPVLAND
    60 70 80 90 100
    IQEPIIEMYK RLINVSWDDV LKVIKQYKLS KTSKEEFLKL REDYNKTRDP
    110 120 130 140 150
    LLLYVLHFHG FSNMIRINDK GNFTTPFGKR TINKNSEKQY NHFKQNCDKI
    160 170 180 190 200
    IFSSLHFKDV KILDGDFVYV DPPYLITVAD YNKFWSEDEE KDLLNLLDSL
    210 220 230 240 250
    NDRGIKFGQS NVLEHHGKEN TLLKEWSKKY NVKHLNKKYV FNIYHSKEKN

    GTDEVYIFN
    Length:259
    Mass (Da):30,417
    Last modified:March 20, 1987 - v1
    Checksum:iA49401D059A4388D
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti139 – 1402QY → RF in X17641 (PubMed:2510127).Curated
    Sequence conflicti209 – 2091Q → L in X17641 (PubMed:2510127).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X01416 Genomic DNA. Translation: CAA25660.1.
    X17641 Genomic DNA. No translation available.
    K03113 Genomic DNA. Translation: AAA32555.1.
    AF158101 Genomic DNA. Translation: AAD42553.1.
    PIRiA00554. XYBPT4.
    RefSeqiNP_049647.1. NC_000866.4.

    Genome annotation databases

    GeneIDi1258548.
    KEGGivg:1258548.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X01416 Genomic DNA. Translation: CAA25660.1.
    X17641 Genomic DNA. No translation available.
    K03113 Genomic DNA. Translation: AAA32555.1.
    AF158101 Genomic DNA. Translation: AAD42553.1.
    PIRiA00554. XYBPT4.
    RefSeqiNP_049647.1. NC_000866.4.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1Q0SX-ray2.30A1-259[»]
    1Q0TX-ray3.10A/B1-259[»]
    1YF3X-ray2.29A/B1-259[»]
    1YFJX-ray2.69A/B/C/D/E/F1-259[»]
    1YFLX-ray3.09A/B/D/E1-259[»]
    ProteinModelPortaliP04392.
    SMRiP04392. Positions 1-259.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein family/group databases

    REBASEi2837. M.EcoT4Dam.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    GeneIDi1258548.
    KEGGivg:1258548.

    Phylogenomic databases

    KOiK06223.

    Enzyme and pathway databases

    BRENDAi2.1.1.72. 732.

    Miscellaneous databases

    EvolutionaryTraceiP04392.

    Family and domain databases

    Gene3Di1.10.1020.10. 1 hit.
    3.40.50.150. 2 hits.
    InterProiIPR023095. Ade_MeTrfase_dom_2.
    IPR002052. DNA_methylase_N6_adenine_CS.
    IPR012263. M_m6A_EcoRV.
    IPR012327. MeTrfase_D12.
    IPR029063. SAM-dependent_MTases.
    [Graphical view]
    PfamiPF02086. MethyltransfD12. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000398. M_m6A_EcoRV. 1 hit.
    PRINTSiPR00505. D12N6MTFRASE.
    SUPFAMiSSF53335. SSF53335. 1 hit.
    TIGRFAMsiTIGR00571. dam. 1 hit.
    PROSITEiPS00092. N6_MTASE. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Regulation of a new bacteriophage T4 gene, 69, that spans an origin of DNA replication."
      McDonald P.M., Mosig G.
      EMBO J. 3:2863-2871(1984) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Single amino acid changes that alter the DNA sequence specificity of the DNA-[N6-adenine] methyltransferase (Dam) of bacteriophage T4."
      Miner Z., Schlagman S.L., Hattman S.
      Nucleic Acids Res. 17:8149-8157(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], MUTANT DAMH.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    4. "Phage T4 DNA [N6-adenine]methyltransferase. Overexpression, purification, and characterization."
      Kossykh V.G., Schlagman S.L., Hattman S.
      J. Biol. Chem. 270:14389-14393(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES, CATALYTIC ACTIVITY.
    5. "Bacteriophage T4 Dam DNA-(N6-adenine)-methyltransferase. Processivity and orientation to the methylation target."
      Zinoviev V.V., Evdokimov A.A., Malygin E.G., Schlagman S.L., Hattman S.
      J. Biol. Chem. 278:7829-7833(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    6. Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE, SUBUNIT.
    7. "Transition from nonspecific to specific DNA interactions along the substrate-recognition pathway of dam methyltransferase."
      Horton J.R., Liebert K., Hattman S., Jeltsch A., Cheng X.
      Cell 121:349-361(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.29 ANGSTROMS) IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE.

    Entry informationi

    Entry nameiDMA_BPT4
    AccessioniPrimary (citable) accession number: P04392
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 20, 1987
    Last sequence update: March 20, 1987
    Last modified: July 22, 2015
    This is version 105 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programViral Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. Restriction enzymes and methylases
      Classification of restriction enzymes and methylases and list of entries
    3. 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.