P04043 (MTD21_STRPN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Modification methylase DpnIIA
Short name=M.DpnIIA
EC=2.1.1.72

Alternative name(s):
Adenine-specific methyltransferase DpnIIA
M.DpnII 1

Gene names

Name:

dpnM

Organism

Streptococcus pneumoniae

Taxonomic identifier

1313 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Lactobacillales › Streptococcaceae › Streptococcus

Protein attributes

Sequence length	284 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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 activity	S-adenosyl-L-methionine + DNA adenine = S-adenosyl-L-homocysteine + DNA 6-methylaminopurine.
Subunit structure	Homodimer.
Miscellaneous	The DpnII restriction system has two different methylases.
Sequence similarities	Belongs to the N(4)/N(6)-methyltransferase family.

Ontologies

Keywords
Biological process	Restriction system
Ligand	S-adenosyl-L-methionine
Molecular function	Methyltransferase Transferase
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological process	DNA restriction-modification system Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	nucleic acid binding Inferred from electronic annotation. Source: InterPro site-specific DNA-methyltransferase (adenine-specific) activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 284

284

Modification methylase DpnIIA

PRO_0000087957

Sites

Binding site

17

1

S-adenosyl-L-methionine

Binding site

21

1

S-adenosyl-L-methionine; via amide nitrogen

Binding site

62

1

S-adenosyl-L-methionine

Binding site

194

1

S-adenosyl-L-methionine

Secondary structure

1

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284

Helix Strand Turn

Details...

Helix

22 – 24

3

Helix

25 – 31

7

Beta strand

39 – 41

3

Helix

48 – 53

6

Beta strand

56 – 63

8

Helix

65 – 76

12

Helix

78 – 91

14

Helix

94 – 101

8

Helix

102 – 105

4

Helix

108 – 111

4

Helix

114 – 127

14

Helix

129 – 131

3

Helix

156 – 168

13

Beta strand

169 – 176

8

Helix

178 – 182

5

Beta strand

190 – 193

4

Helix

216 – 230

15

Turn

231 – 233

3

Beta strand

235 – 242

8

Helix

244 – 249

6

Turn

250 – 252

3

Beta strand

253 – 258

6

Beta strand

276 – 281

6

Sequences

	Sequence		Length	Mass (Da)
	P04043 [UniParc]. Last modified November 1, 1986. Version 1. Checksum: 9F1525575CFA3E1E	FASTA	284	32,907
	10 20 30 40 50 60 MKIKEIKKVT LQPFTKWTGG KRQLLPVIRE LIPKTYNRYF EPFVGGGALF FDLAPKDAVI 70 80 90 100 110 120 NDFNAELINC YQQIKDNPQE LIEILKVHQE YNSKEYYLDL RSADRDERID MMSEVQRAAR 130 140 150 160 170 180 ILYMLRVNFN GLYRVNSKNQ FNVPYGRYKN PKIVDEELIS AISVYINNNQ LEIKVGDFEK 190 200 210 220 230 240 AIVDVRTGDF VYFDPPYIPL SETSAFTSYT HEGFSFADQV RLRDAFKRLS DTGAYVMLSN 250 260 270 280 SSSALVEELY KDFNIHYVEA TRTNGAKSSS RGKISEIIVT NYEK

References

[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: 2989823] [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: 3019562] [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: 2824782] [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: 9862809] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 10-284. Strain: HB264.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M11226 Genomic DNA. Translation: AAA26872.1.
M14339 Genomic DNA. Translation: AAA88580.1.

PIR

XYSONA. A00556.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2DPM	X-ray	1.80	A	1-284	[»]

ProteinModelPortal

P04043.

SMR

P04043. Positions 10-284.

ModBase

Search...

Protein family/group databases

REBASE

3636. M1.DpnII.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

InterPro

IPR023095. Ade_MeTrfase_dom_2.
IPR002052. DNA_methylase_N6_adenine_CS.
IPR012263. M_m6A_EcoRV.
IPR012327. MeTrfase_D12.
[Graphical view]

Gene3D

G3DSA:1.10.1020.10. Ade_MeTrfase_dom_2. 1 hit.

Pfam

PF02086. MethyltransfD12. 1 hit.
[Graphical view]

PIRSF

PIRSF000398. M_m6A_EcoRV. 1 hit.

PRINTS

PR00505. D12N6MTFRASE.

TIGRFAMs

TIGR00571. Dam. 1 hit.

PROSITE

PS00092. N6_MTASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

MTD21_STRPN

Accession

Primary (citable) accession number: P04043

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1986
Last sequence update:	November 1, 1986
Last modified:	May 31, 2011
This is version 89 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program