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Protein

Modification methylase DpnIIA

Gene

dpnM

Organism
Streptococcus pneumoniae
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

This methylase recognizes the double-stranded sequence GATC, causes specific methylation on A-2 on both strands, and protects the DNA from cleavage by the DpnII endonuclease.

Catalytic activityi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei17 – 171S-adenosyl-L-methionine
Binding sitei21 – 211S-adenosyl-L-methionine; via amide nitrogen
Binding sitei62 – 621S-adenosyl-L-methionine
Binding sitei194 – 1941S-adenosyl-L-methionine

GO - Molecular functioni

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

BRENDAi2.1.1.72. 1960.

Protein family/group databases

REBASEi3636. M1.DpnII.

Names & Taxonomyi

Protein namesi
Recommended name:
Modification methylase DpnIIA (EC:2.1.1.72)
Short name:
M.DpnIIA
Alternative name(s):
Adenine-specific methyltransferase DpnIIA
M.DpnII 1
Gene namesi
Name:dpnM
OrganismiStreptococcus pneumoniae
Taxonomic identifieri1313 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeStreptococcus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 284284Modification methylase DpnIIAPRO_0000087957Add
BLAST

Interactioni

Subunit structurei

Homodimer.

Structurei

Secondary structure

1
284
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi22 – 243Combined sources
Helixi25 – 317Combined sources
Beta strandi39 – 413Combined sources
Helixi48 – 536Combined sources
Beta strandi56 – 638Combined sources
Helixi65 – 7612Combined sources
Helixi78 – 9114Combined sources
Helixi94 – 1018Combined sources
Helixi102 – 1054Combined sources
Helixi108 – 1114Combined sources
Helixi114 – 12714Combined sources
Helixi129 – 1313Combined sources
Helixi156 – 16813Combined sources
Beta strandi169 – 1768Combined sources
Helixi178 – 1825Combined sources
Beta strandi190 – 1934Combined sources
Helixi216 – 23015Combined sources
Turni231 – 2333Combined sources
Beta strandi235 – 2428Combined sources
Helixi244 – 2496Combined sources
Turni250 – 2523Combined sources
Beta strandi253 – 2586Combined sources
Beta strandi276 – 2816Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2DPMX-ray1.80A1-284[»]
ProteinModelPortaliP04043.
SMRiP04043. Positions 10-284.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP04043.

Family & Domainsi

Sequence similaritiesi

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

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.

P04043-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKIKEIKKVT LQPFTKWTGG KRQLLPVIRE LIPKTYNRYF EPFVGGGALF
60 70 80 90 100
FDLAPKDAVI NDFNAELINC YQQIKDNPQE LIEILKVHQE YNSKEYYLDL
110 120 130 140 150
RSADRDERID MMSEVQRAAR ILYMLRVNFN GLYRVNSKNQ FNVPYGRYKN
160 170 180 190 200
PKIVDEELIS AISVYINNNQ LEIKVGDFEK AIVDVRTGDF VYFDPPYIPL
210 220 230 240 250
SETSAFTSYT HEGFSFADQV RLRDAFKRLS DTGAYVMLSN SSSALVEELY
260 270 280
KDFNIHYVEA TRTNGAKSSS RGKISEIIVT NYEK
Length:284
Mass (Da):32,907
Last modified:November 1, 1986 - v1
Checksum:i9F1525575CFA3E1E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M11226 Genomic DNA. Translation: AAA26872.1.
M14339 Genomic DNA. Translation: AAA88580.1.
PIRiA00556. XYSONA.
RefSeqiWP_000692845.1. NZ_CDQF01000003.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M11226 Genomic DNA. Translation: AAA26872.1.
M14339 Genomic DNA. Translation: AAA88580.1.
PIRiA00556. XYSONA.
RefSeqiWP_000692845.1. NZ_CDQF01000003.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2DPMX-ray1.80A1-284[»]
ProteinModelPortaliP04043.
SMRiP04043. Positions 10-284.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

REBASEi3636. M1.DpnII.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

BRENDAi2.1.1.72. 1960.

Miscellaneous databases

EvolutionaryTraceiP04043.

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

  1. "Nucleotide sequence of the Dpn II DNA methylase gene of Streptococcus pneumoniae and its relationship to the dam gene of Escherichia coli."
    Mannarelli B.M., Balganesh T.S., Greenberg B., Springhorn S.S., Lacks S.A.
    Proc. Natl. Acad. Sci. U.S.A. 82:4468-4472(1985) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Genetic basis of the complementary DpnI and DpnII restriction systems of S. pneumoniae: an intercellular cassette mechanism."
    Lacks S.A., Mannarelli B.M., Springhorn S.S., Greenberg B.
    Cell 46:993-1000(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "Proteins encoded by the DpnII restriction gene cassette. Two methylases and an endonuclease."
    de la Campa A.G., Purushottam K., Springhorn S.S., Lacks S.A.
    J. Mol. Biol. 196:457-469(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-14.
  4. "Crystal structure of the DpnM DNA adenine methyltransferase from the DpnII restriction system of Streptococcus pneumoniae bound to S-adenosylmethionine."
    Tran P.H., Korszun Z.R., Cerritelli S., Springhorn S.S., Lacks S.A.
    Structure 6:1563-1575(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 10-284.
    Strain: HB264.

Entry informationi

Entry nameiMTD21_STREE
AccessioniPrimary (citable) accession number: P04043
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1986
Last sequence update: November 1, 1986
Last modified: July 22, 2015
This is version 103 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The DpnII restriction system has two different methylases.

Keywords - Technical termi

3D-structure, Direct protein sequencing

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.