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Protein

Type-2 restriction enzyme NgoMIV

Gene

ngoMIVR

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

Functioni

Recognizes the double-stranded sequence GCCGGC and cleaves after G-1.

Catalytic activityi

Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates.

Cofactori

Mg2+Note: Binds 2 magnesium ions per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi140 – 1401Magnesium 1
Metal bindingi140 – 1401Magnesium 2
Metal bindingi186 – 1861Magnesium 1; via carbonyl oxygen

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

Restriction system

Keywords - Ligandi

Magnesium, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Type-2 restriction enzyme NgoMIV (EC:3.1.21.4)
Short name:
R.NgoMIV
Alternative name(s):
Endonuclease NgoMIV
Type II restriction enzyme NgoMIV
Gene namesi
Name:ngoMIVR
OrganismiNeisseria gonorrhoeae
Taxonomic identifieri485 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaNeisserialesNeisseriaceaeNeisseria

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 286286Type-2 restriction enzyme NgoMIVPRO_0000077347Add
BLAST

Interactioni

Subunit structurei

Homotetramer.

Structurei

Secondary structure

1
286
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 1815Combined sources
Helixi38 – 5013Combined sources
Helixi62 – 8120Combined sources
Helixi82 – 843Combined sources
Turni85 – 873Combined sources
Beta strandi92 – 965Combined sources
Beta strandi99 – 1013Combined sources
Helixi104 – 1074Combined sources
Helixi109 – 1124Combined sources
Helixi113 – 1219Combined sources
Helixi125 – 1317Combined sources
Beta strandi140 – 1456Combined sources
Helixi150 – 1534Combined sources
Beta strandi155 – 1573Combined sources
Beta strandi179 – 18911Combined sources
Helixi194 – 1963Combined sources
Helixi197 – 20812Combined sources
Beta strandi210 – 2123Combined sources
Beta strandi215 – 2206Combined sources
Helixi225 – 2328Combined sources
Beta strandi233 – 2375Combined sources
Beta strandi239 – 2435Combined sources
Helixi246 – 25611Combined sources
Helixi259 – 27012Combined sources
Beta strandi273 – 2764Combined sources
Helixi277 – 2793Combined sources
Helixi280 – 2834Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1FIUX-ray1.60A/B/C/D1-286[»]
4ABTX-ray2.22A/B3-286[»]
ProteinModelPortaliP31032.
SMRiP31032. Positions 1-286.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP31032.

Family & Domainsi

Family and domain databases

Gene3Di3.40.50.10010. 1 hit.
InterProiIPR011335. Restrct_endonuc-II-like.
IPR015105. Restrct_endonuc_II_NgoMIV.
[Graphical view]
PfamiPF09015. NgoMIV_restric. 1 hit.
[Graphical view]
SUPFAMiSSF52980. SSF52980. 1 hit.

Sequencei

Sequence statusi: Complete.

P31032-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNPLFTQERR IFHKKLLDGN ILATNNRGVV SNADGSNTRS FNIAKGIADL
60 70 80 90 100
LHSETVSERL PGQTSGNAFE AICSEFVQSA FEKLQHIRPG DWNVKQVGSR
110 120 130 140 150
NRLEIARYQQ YAHLTALAKA AEENPELAAA LGSDYTITPD IIVTRNLIAD
160 170 180 190 200
AEINRNEFLV DENIATYASL RAGNGNMPLL HASISCKWTI RSDRAQNARS
210 220 230 240 250
EGLNLVRNRK GRLPHIVVVT AEPTPSRISS IALGTGEIDC VYHFALYELE
260 270 280
QILQSLNYED ALDLFYIMVN GKRLKDISDL PLDLAV
Length:286
Mass (Da):31,760
Last modified:July 1, 1993 - v1
Checksum:i6609772EF21083F6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M86915 Genomic DNA. No translation available.
PIRiB42709.
RefSeqiWP_003688519.1. NZ_JIBZ01000002.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M86915 Genomic DNA. No translation available.
PIRiB42709.
RefSeqiWP_003688519.1. NZ_JIBZ01000002.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1FIUX-ray1.60A/B/C/D1-286[»]
4ABTX-ray2.22A/B3-286[»]
ProteinModelPortaliP31032.
SMRiP31032. Positions 1-286.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP31032.

Family and domain databases

Gene3Di3.40.50.10010. 1 hit.
InterProiIPR011335. Restrct_endonuc-II-like.
IPR015105. Restrct_endonuc_II_NgoMIV.
[Graphical view]
PfamiPF09015. NgoMIV_restric. 1 hit.
[Graphical view]
SUPFAMiSSF52980. SSF52980. 1 hit.
ProtoNetiSearch...

Publicationsi

  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).

Entry informationi

Entry nameiT2M4_NEIGO
AccessioniPrimary (citable) accession number: P31032
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: July 1, 1993
Last modified: March 4, 2015
This is version 88 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Caution

Was originally known as R.ngomI.1 Publication

Keywords - Technical termi

3D-structure

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

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.