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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei17S-adenosyl-L-methionine1
Binding sitei21S-adenosyl-L-methionine; via amide nitrogen1
Binding sitei62S-adenosyl-L-methionine1
Binding sitei194S-adenosyl-L-methionine1

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)DescriptionActionsGraphical viewLength
ChainiPRO_00000879571 – 284Modification methylase DpnIIAAdd BLAST284

Interactioni

Subunit structurei

Homodimer.

Structurei

Secondary structure

1284
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi22 – 24Combined sources3
Helixi25 – 31Combined sources7
Beta strandi39 – 41Combined sources3
Helixi48 – 53Combined sources6
Beta strandi56 – 63Combined sources8
Helixi65 – 76Combined sources12
Helixi78 – 91Combined sources14
Helixi94 – 101Combined sources8
Helixi102 – 105Combined sources4
Helixi108 – 111Combined sources4
Helixi114 – 127Combined sources14
Helixi129 – 131Combined sources3
Helixi156 – 168Combined sources13
Beta strandi169 – 176Combined sources8
Helixi178 – 182Combined sources5
Beta strandi190 – 193Combined sources4
Helixi216 – 230Combined sources15
Turni231 – 233Combined sources3
Beta strandi235 – 242Combined sources8
Helixi244 – 249Combined sources6
Turni250 – 252Combined sources3
Beta strandi253 – 258Combined sources6
Beta strandi276 – 281Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2DPMX-ray1.80A1-284[»]
ProteinModelPortaliP04043.
SMRiP04043.
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_MCIW01000071.1.

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_MCIW01000071.1.

3D structure databases

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

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: November 2, 2016
This is version 111 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

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.