Q975R3 (ENDA_SULTO) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
tRNA-splicing endonuclease
EC=3.1.27.9

Alternative name(s):
tRNA-intron endonuclease

Gene names

Name:	endA
Ordered Locus Names:	STK_03580

Organism

Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) [Complete proteome] [HAMAP]

Taxonomic identifier

273063 [NCBI]

Taxonomic lineage

cellular organisms › Archaea › Crenarchaeota › Thermoprotei › Sulfolobales › Sulfolobaceae › Sulfolobus › Sulfolobus tokodaii

Protein attributes

Sequence length	180 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Endonuclease that removes tRNA introns. Cleaves pre-tRNA at the 5'- and 3'-splice sites to release the intron. The products are an intron and two tRNA half-molecules bearing 2',3' cyclic phosphate and 5'-OH termini. Recognizes a pseudosymmetric substrate in which 2 bulged loops of 3 bases are separated by a stem of 4 bp By similarity. HAMAP-Rule MF_01833
Catalytic activity	Endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxy and 2',3'-cyclic phosphate termini, and specifically removing the intron. HAMAP-Rule MF_01833
Subunit structure	Homotetramer; although the tetramer contains four active sites, only two participate in the cleavage. Therefore, it should be considered as a dimer of dimers By similarity.
Sequence similarities	Belongs to the tRNA-intron endonuclease family. Archaeal short subfamily.

Ontologies

Keywords
Biological process	tRNA processing
Molecular function	Endonuclease Hydrolase Nuclease
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological_process	nucleic acid phosphodiester bond hydrolysis Inferred from electronic annotation. Source: GOC tRNA splicing, via endonucleolytic cleavage and ligation Inferred from electronic annotation. Source: HAMAP
Molecular_function	nucleic acid binding Inferred from electronic annotation. Source: InterPro tRNA-intron endonuclease activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 180

180

tRNA-splicing endonuclease HAMAP-Rule MF_01833

PRO_0000109482

Sites

Active site

117

1

By similarity

Active site

125

1

By similarity

Active site

156

1

By similarity

Secondary structure

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180

Helix Strand Turn

Details...

Beta strand

2 – 6

5

Beta strand

9 – 12

4

Helix

15 – 25

11

Beta strand

28 – 30

3

Beta strand

46 – 49

4

Helix

50 – 58

9

Beta strand

63 – 66

4

Beta strand

69 – 71

3

Helix

73 – 83

11

Helix

87 – 99

13

Beta strand

103 – 106

4

Helix

108 – 110

3

Beta strand

112 – 117

6

Beta strand

128 – 134

7

Beta strand

138 – 140

3

Helix

141 – 144

4

Beta strand

147 – 149

3

Beta strand

157 – 163

7

Turn

165 – 167

3

Beta strand

170 – 178

9

Sequences

	Sequence		Length	Mass (Da)
	Q975R3 [UniParc]. Last modified December 1, 2001. Version 1. Checksum: 40615B98F1C05085	FASTA	180	20,507
	10 20 30 40 50 60 MIGELVKDKI LIKNIEDARL IYKMGYYGKP IGISKPKSAE EINSELILSL IEGVYLVKKG 70 80 90 100 110 120 KLEIVSNGER LDFERLYQIG VTQIPRFRIL YSVYEDLREK GYVVRSGIKY GADFAVYTIG 130 140 150 160 170 180 PGIEHAPYLV IALDENSQIS SNEILGFGRV SHSTRKELIL GIVNLTNGKI RYIMFKWLKM

References

[1]

"Complete genome sequence of an aerobic thermoacidophilic Crenarchaeon, Sulfolobus tokodaii strain7." Kawarabayasi Y., Hino Y., Horikawa H., Jin-no K., Takahashi M., Sekine M., Baba S., Ankai A., Kosugi H., Hosoyama A., Fukui S., Nagai Y., Nishijima K., Otsuka R., Nakazawa H., Takamiya M., Kato Y., Yoshizawa T. , Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Masuda S., Yanagii M., Nishimura M., Yamagishi A., Oshima T., Kikuchi H. DNA Res. 8:123-140(2001) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

BA000023 Genomic DNA. Translation: BAK54248.1.

RefSeq

NP_376228.1. NC_003106.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2CV8	X-ray	2.80	A/B	1-180	[»]

ProteinModelPortal

Q975R3.

SMR

Q975R3. Positions 1-180.

ModBase

Search...

Protein-protein interaction databases

STRING

273063.ST0358.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

BAK54248; BAK54248; STK_03580.

GeneID

1458281.

KEGG

sto:ST0358.

Organism-specific databases

CMR

Search...

Phylogenomic databases

eggNOG

COG1676.

HOGENOM

HOG000107823.

KO

K01170.

OMA

FVRVAHS.

ProtClustDB

PRK09297.

Family and domain databases

Gene3D

3.40.1350.10. 1 hit.

HAMAP

MF_01833. EndA_short.

InterPro

IPR011856. tRNA_endonuc-like_dom.
IPR006677. tRNA_intron_Endonuc_cat-like.
IPR006678. tRNA_intron_Endonuc_N.
IPR006676. tRNA_splic.
IPR016442. tRNA_splic_arch_short.
[Graphical view]

Pfam

PF01974. tRNA_int_endo. 1 hit.
PF02778. tRNA_int_endo_N. 1 hit.
[Graphical view]

PIRSF

PIRSF005285. tRNA_splic_archaea. 1 hit.

SUPFAM

SSF53032. tRNA_int_endo_C. 1 hit.
SSF55267. tRNA_int_endo_N. 1 hit.

TIGRFAMs

TIGR00324. endA. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

Q975R3.

Entry information

Entry name

ENDA_SULTO

Accession

Primary (citable) accession number: Q975R3
Secondary accession number(s): F9VMV1

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 11, 2004
Last sequence update:	December 1, 2001
Last modified:	May 1, 2013
This is version 71 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program