P50187 (T2N1_NOCAE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Type-2 restriction enzyme NaeI
Short name=R.NaeI
EC=3.1.21.4

Alternative name(s):
Endonuclease NaeI
Type II restriction enzyme NaeI

Gene names

Name:

naeIR

Organism

Lechevalieria aerocolonigenes (Nocardia aerocolonigenes) (Saccharothrix aerocolonigenes)

Taxonomic identifier

68170 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Actinobacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Pseudonocardineae › Pseudonocardiaceae › Lechevalieria

Protein attributes

Sequence length	317 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Recognizes the double-stranded unmethylated sequence GCCGGC and cleaves after C-3.
Catalytic activity	Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates.
Subunit structure	Homodimer.

Ontologies

Keywords
Biological process	Restriction system
Molecular function	Endonuclease Hydrolase Nuclease
Technical term	3D-structure
Gene Ontology (GO)
Biological_process	DNA restriction-modification system Inferred from electronic annotation. Source: UniProtKB-KW nucleic acid phosphodiester bond hydrolysis Inferred from electronic annotation. Source: GOC
Molecular_function	DNA binding Inferred from electronic annotation. Source: InterPro Type II site-specific deoxyribonuclease 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 – 317

317

Type-2 restriction enzyme NaeI

PRO_0000077343

Experimental info

Mutagenesis

43

1

L → K: Change of function; becomes a topoisomerase that recognizes single-stranded mismatched DNA.

Secondary structure

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317

Helix Strand Turn

Details...

Helix

13 – 25

13

Beta strand

26 – 29

4

Helix

30 – 44

15

Helix

46 – 49

4

Helix

54 – 56

3

Helix

59 – 63

5

Helix

65 – 77

13

Beta strand

83 – 89

7

Beta strand

92 – 101

10

Helix

109 – 111

3

Beta strand

114 – 122

9

Turn

123 – 126

4

Beta strand

127 – 134

8

Helix

137 – 139

3

Helix

153 – 156

4

Beta strand

160 – 163

4

Helix

173 – 175

3

Helix

179 – 186

8

Beta strand

191 – 194

4

Helix

196 – 207

12

Beta strand

210 – 213

4

Helix

215 – 222

8

Helix

228 – 230

3

Beta strand

232 – 241

10

Helix

242 – 244

3

Beta strand

246 – 249

4

Helix

255 – 261

7

Beta strand

262 – 264

3

Beta strand

272 – 279

8

Beta strand

288 – 298

11

Sequences

	Sequence		Length	Mass (Da)
	P50187 [UniParc]. Last modified October 1, 1996. Version 1. Checksum: 2D646D6814935B97	FASTA	317	35,335
	10 20 30 40 50 60 MTELPLQFAE PDDDLERVRA TLYSLDPDGD RTAGVLRDTL DQLYDGQRTG RWNFDQLHKT 70 80 90 100 110 120 EKTHMGTLVE INLHREFQFG DGFETDYEIA GVQVDCKFSM SQGAWMLPPE SIGHICLVIW 130 140 150 160 170 180 ASDQQCAWTA GLVKVIPQFL GTANRDLKRR LTPEGRAQVV KLWPDHGKLQ ENLLLHIPGD 190 200 210 220 230 240 VRDQIFSAKS SRGNQHGQAR VNELFRRVHG RLIGRAVIAT VAQQDDFMKR VRGSGGARSI 250 260 270 280 290 300 LRPEGIIILG HQDNDPKVAN DLGLPVPRKG QVVAARVVPA DEGDQRQTAE IQGRRWAVAV 310 PGDPIVEAPV VPRKSAE

References

[1]	"Cloning and expression of the NaeI restriction endonuclease-encoding gene and sequence analysis of the NaeI restriction-modification system." Taron C.H., van Cott E.M., Wilson G.G., Moran L.S., Slatko B.E., Hornstra L.J., Benner J.S., Kucera R.B., Guthrie E.P. Gene 155:19-25(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 23870 / BCRC 13661 / DSM 40034 / JCM 4614 / NBRC 13195 / NCIMB 12944 / NRRL B-3298.
[2]	"DNA topoisomerase and recombinase activities in Nae I restriction endonuclease." Jo K., Topal M.D. Science 267:1817-1820(1995) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION OF MUTANT LYS-43.
[3]	"Effects on NaeI-DNA recognition of the leucine to lysine substitution that transforms restriction endonuclease NaeI to a topoisomerase: a model for restriction endonuclease evolution." Jo K., Topal M.D. Nucleic Acids Res. 24:4171-4175(1996) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION OF MUTANT LYS-43.
[4]	"Crystal structure of NaeI-an evolutionary bridge between DNA endonuclease and topoisomerase." Huai Q., Colandene J.D., Chen Y., Luo F., Zhao Y., Topal M.D., Ke H. EMBO J. 19:3110-3118(2000) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.38 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U09581 Genomic DNA. Translation: AAC43324.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1EV7	X-ray	2.38	A/B	1-317	[»]
1IAW	X-ray	2.40	A/B	1-317	[»]

ProteinModelPortal

P50187.

SMR

P50187. Positions 10-313.

ModBase

Search...

Protein family/group databases

REBASE

1294. NaeI.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

Gene3D

1.10.10.10. 1 hit.
3.40.600.10. 1 hit.

InterPro

IPR011337. DNA_rep_MutH/RE_typeII.
IPR011335. Restrct_endonuc-II-like.
IPR015210. Restrct_endonuc_NaeI.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]

Pfam

PF09126. NaeI. 1 hit.
[Graphical view]

SUPFAM

SSF52980. Restrict_endonuc_II-like_core. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P50187.

Entry information

Entry name

T2N1_NOCAE

Accession

Primary (citable) accession number: P50187

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1996
Last sequence update:	October 1, 1996
Last modified:	May 1, 2013
This is version 69 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program