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Protein

Type-2 restriction enzyme NaeI

Gene

naeIR

Organism
Lechevalieria aerocolonigenes (Nocardia aerocolonigenes) (Saccharothrix aerocolonigenes)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Recognizes the double-stranded unmethylated sequence GCCGGC and cleaves after C-3.

Catalytic activityi

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

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

Restriction system

Protein family/group databases

REBASEi1294. NaeI.

Names & Taxonomyi

Protein namesi
Recommended name:
Type-2 restriction enzyme NaeI (EC:3.1.21.4)
Short name:
R.NaeI
Alternative name(s):
Endonuclease NaeI
Type II restriction enzyme NaeI
Gene namesi
Name:naeIR
OrganismiLechevalieria aerocolonigenes (Nocardia aerocolonigenes) (Saccharothrix aerocolonigenes)
Taxonomic identifieri68170 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesPseudonocardineaePseudonocardiaceaeLechevalieria

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi43 – 431L → K: Change of function; becomes a topoisomerase that recognizes single-stranded mismatched DNA.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 317317Type-2 restriction enzyme NaeIPRO_0000077343Add
BLAST

Interactioni

Subunit structurei

Homodimer.

Structurei

Secondary structure

1
317
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi13 – 2513Combined sources
Beta strandi26 – 294Combined sources
Helixi30 – 4415Combined sources
Helixi46 – 494Combined sources
Helixi54 – 563Combined sources
Helixi59 – 635Combined sources
Helixi65 – 7713Combined sources
Beta strandi83 – 897Combined sources
Beta strandi92 – 10110Combined sources
Helixi109 – 1113Combined sources
Beta strandi114 – 1229Combined sources
Turni123 – 1264Combined sources
Beta strandi127 – 1348Combined sources
Helixi137 – 1393Combined sources
Helixi153 – 1564Combined sources
Beta strandi160 – 1634Combined sources
Helixi173 – 1753Combined sources
Helixi179 – 1868Combined sources
Beta strandi191 – 1944Combined sources
Helixi196 – 20712Combined sources
Beta strandi210 – 2134Combined sources
Helixi215 – 2228Combined sources
Helixi228 – 2303Combined sources
Beta strandi232 – 24110Combined sources
Helixi242 – 2443Combined sources
Beta strandi246 – 2494Combined sources
Helixi255 – 2617Combined sources
Beta strandi262 – 2643Combined sources
Beta strandi272 – 2798Combined sources
Beta strandi288 – 29811Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1EV7X-ray2.38A/B1-317[»]
1IAWX-ray2.40A/B1-317[»]
ProteinModelPortaliP50187.
SMRiP50187. Positions 10-313.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP50187.

Family & Domainsi

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
3.40.600.10. 1 hit.
InterProiIPR011337. DNA_rep_MutH/RE_typeII.
IPR011335. Restrct_endonuc-II-like.
IPR015210. Restrct_endonuc_NaeI.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF09126. NaeI. 1 hit.
[Graphical view]
SUPFAMiSSF52980. SSF52980. 1 hit.

Sequencei

Sequence statusi: Complete.

P50187-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTELPLQFAE PDDDLERVRA TLYSLDPDGD RTAGVLRDTL DQLYDGQRTG
60 70 80 90 100
RWNFDQLHKT EKTHMGTLVE INLHREFQFG DGFETDYEIA GVQVDCKFSM
110 120 130 140 150
SQGAWMLPPE SIGHICLVIW ASDQQCAWTA GLVKVIPQFL GTANRDLKRR
160 170 180 190 200
LTPEGRAQVV KLWPDHGKLQ ENLLLHIPGD VRDQIFSAKS SRGNQHGQAR
210 220 230 240 250
VNELFRRVHG RLIGRAVIAT VAQQDDFMKR VRGSGGARSI LRPEGIIILG
260 270 280 290 300
HQDNDPKVAN DLGLPVPRKG QVVAARVVPA DEGDQRQTAE IQGRRWAVAV
310
PGDPIVEAPV VPRKSAE
Length:317
Mass (Da):35,335
Last modified:October 1, 1996 - v1
Checksum:i2D646D6814935B97
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U09581 Genomic DNA. Translation: AAC43324.1.
RefSeqiWP_030468110.1. NZ_JOFI01000013.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U09581 Genomic DNA. Translation: AAC43324.1.
RefSeqiWP_030468110.1. NZ_JOFI01000013.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1EV7X-ray2.38A/B1-317[»]
1IAWX-ray2.40A/B1-317[»]
ProteinModelPortaliP50187.
SMRiP50187. Positions 10-313.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

REBASEi1294. NaeI.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP50187.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
3.40.600.10. 1 hit.
InterProiIPR011337. DNA_rep_MutH/RE_typeII.
IPR011335. Restrct_endonuc-II-like.
IPR015210. Restrct_endonuc_NaeI.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF09126. NaeI. 1 hit.
[Graphical view]
SUPFAMiSSF52980. SSF52980. 1 hit.
ProtoNetiSearch...

Publicationsi

  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).

Entry informationi

Entry nameiT2N1_NOCAE
AccessioniPrimary (citable) accession number: P50187
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: May 27, 2015
This is version 76 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.