P31032 (T2M4_NEIGO) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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

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

Gene names

Name:

ngoMIVR

Organism

Neisseria gonorrhoeae

Taxonomic identifier

485 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Betaproteobacteria › Neisseriales › Neisseriaceae › Neisseria

Protein attributes

Sequence length	286 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Recognizes the double-stranded sequence GCCGGC and cleaves after G-1.
Catalytic activity	Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates.
Cofactor	Binds 2 magnesium ions per subunit.
Subunit structure	Homotetramer.
Caution	Was originally (Ref.1) known as R.ngomI.

Ontologies

Keywords
Biological process	Restriction system
Ligand	Magnesium Metal-binding
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	Type II site-specific deoxyribonuclease activity Inferred from electronic annotation. Source: EC metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 286

286

Type-2 restriction enzyme NgoMIV

PRO_0000077347

Sites

Metal binding

140

1

Magnesium 1

Metal binding

140

1

Magnesium 2

Metal binding

186

1

Magnesium 1; via carbonyl oxygen

Secondary structure

1

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286

Helix Strand Turn

Details...

Helix

4 – 18

15

Helix

38 – 50

13

Helix

62 – 81

20

Helix

82 – 84

3

Turn

85 – 87

3

Beta strand

92 – 96

5

Beta strand

99 – 101

3

Helix

104 – 107

4

Helix

109 – 112

4

Helix

113 – 121

9

Helix

125 – 131

7

Beta strand

140 – 145

6

Helix

150 – 153

4

Beta strand

155 – 157

3

Beta strand

179 – 189

11

Helix

194 – 196

3

Helix

197 – 208

12

Beta strand

210 – 212

3

Beta strand

215 – 220

6

Helix

225 – 232

8

Beta strand

233 – 237

5

Beta strand

239 – 243

5

Helix

246 – 256

11

Helix

259 – 270

12

Beta strand

273 – 276

4

Helix

277 – 279

3

Helix

280 – 283

4

Sequences

	Sequence		Length	Mass (Da)
	P31032 [UniParc]. Last modified July 1, 1993. Version 1. Checksum: 6609772EF21083F6	FASTA	286	31,760
	10 20 30 40 50 60 MNPLFTQERR IFHKKLLDGN ILATNNRGVV SNADGSNTRS FNIAKGIADL LHSETVSERL 70 80 90 100 110 120 PGQTSGNAFE AICSEFVQSA FEKLQHIRPG DWNVKQVGSR NRLEIARYQQ YAHLTALAKA 130 140 150 160 170 180 AEENPELAAA LGSDYTITPD IIVTRNLIAD AEINRNEFLV DENIATYASL RAGNGNMPLL 190 200 210 220 230 240 HASISCKWTI RSDRAQNARS EGLNLVRNRK GRLPHIVVVT AEPTPSRISS IALGTGEIDC 250 260 270 280 VYHFALYELE QILQSLNYED ALDLFYIMVN GKRLKDISDL PLDLAV

References

[1]	"Construction of a Neisseria gonorrhoeae MS11 derivative deficient in NgoMI restriction and modification." Stein D.C., Chien R., Seifert H.S. J. Bacteriol. 174:4899-4906(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: MS11.
[2]	"Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA." Deibert M., Grazulis S., Sasnauskas G., Siksnys V., Huber R. Nat. Struct. Biol. 7:792-799(2000) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M86915 Genomic DNA. No translation available.

PIR

B42709.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1FIU	X-ray	1.60	A/B/C/D	3-286	[»]
4ABT	X-ray	2.22	A/B	3-286	[»]

ProteinModelPortal

P31032.

SMR

P31032. Positions 1-286.

ModBase

Search...

Protein family/group databases

REBASE

1330. NgoMIV.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

Gene3D

3.40.50.10010. 1 hit.

InterPro

IPR011335. Restrct_endonuc-II-like.
IPR015105. Restrct_endonuc_II_NgoMIV.
[Graphical view]

Pfam

PF09015. NgoMIV_restric. 1 hit.
[Graphical view]

SUPFAM

SSF52980. Restrict_endonuc_II-like_core. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P31032.

Entry information

Entry name

T2M4_NEIGO

Accession

Primary (citable) accession number: P31032

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 1993
Last sequence update:	July 1, 1993
Last modified:	April 3, 2013
This is version 80 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program