Q58819 (ENDA_METJA) 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:	MJ1424

Organism

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii) [Reference proteome] [HAMAP]

Taxonomic identifier

243232 [NCBI]

Taxonomic lineage

cellular organisms › Archaea › Euryarchaeota › Methanococci › Methanococcales › Methanocaldococcaceae › Methanocaldococcus › Methanocaldococcus jannaschii

Protein attributes

Sequence length	179 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. Ref.2
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. Ref.2
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 Reference 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 – 179

179

tRNA-splicing endonuclease HAMAP-Rule MF_01833

PRO_0000109470

Sites

Active site

115

1

Active site

125

1

Active site

156

1

Experimental info

Mutagenesis

125

1

H → A: Induces a strong decrease in activity. Ref.2

Secondary structure

1

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179

Helix Strand Turn

Details...

Beta strand

10 – 15

6

Beta strand

18 – 21

4

Helix

24 – 32

9

Beta strand

36 – 38

3

Beta strand

43 – 46

4

Helix

47 – 55

9

Beta strand

59 – 62

4

Beta strand

64 – 67

4

Helix

71 – 81

11

Helix

85 – 97

13

Beta strand

101 – 104

4

Helix

106 – 108

3

Beta strand

110 – 115

6

Turn

121 – 123

3

Beta strand

127 – 134

8

Beta strand

137 – 139

3

Helix

142 – 153

12

Beta strand

157 – 163

7

Beta strand

169 – 177

9

Sequences

	Sequence		Length	Mass (Da)
	Q58819 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: BCC4675E4AD21BE6	FASTA	179	20,664
	10 20 30 40 50 60 MVRDKMGKKI TGLLDGDRVI VFDKNGISKL SARHYGNVEG NFLSLSLVEA LYLINLGWLE 70 80 90 100 110 120 VKYKDNKPLS FEELYEYARN VEERLCLKYL VYKDLRTRGY IVKTGLKYGA DFRLYERGAN 130 140 150 160 170 IDKEHSVYLV KVFPEDSSFL LSELTGFVRV AHSVRKKLLI AIVDADGDIV YYNMTYVKP

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii." Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G., Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R., Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R., Kirkness E.F., Weinstock K.G. , Merrick J.M., Glodek A., Scott J.L., Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R., Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D., Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P., Fraser C.M., Smith H.O., Woese C.R., Venter J.C. Science 273:1058-1073(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.
[2]	"RNA-protein interactions of an archaeal homotetrameric splicing endoribonuclease with an exceptional evolutionary history." Lykke-Andersen J., Garrett R.A. EMBO J. 16:6290-6300(1997) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBUNIT, MUTAGENESIS OF HIS-125.
[3]	"Crystal structure and evolution of a transfer RNA splicing enzyme." Li H., Trotta C.R., Abelson J. Science 280:279-284(1998) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

L77117 Genomic DNA. Translation: AAB99435.1.

PIR

G64477.

RefSeq

NP_248428.1. NC_000909.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1A79	X-ray	2.28	A/B/C/D	9-179	[»]

ProteinModelPortal

Q58819.

SMR

Q58819. Positions 9-179.

ModBase

Search...

Protein-protein interaction databases

STRING

243232.MJ1424.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAB99435; AAB99435; MJ_1424.

GeneID

1452328.

KEGG

mja:MJ_1424.

Phylogenomic databases

eggNOG

COG1676.

KO

K01170.

OMA

FVRVAHS.

ProtClustDB

PRK09297.

Enzyme and pathway databases

BRENDA

1.14.12.3. 5393.

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

Q58819.

Entry information

Entry name

ENDA_METJA

Accession

Primary (citable) accession number: Q58819

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 15, 1998
Last sequence update:	November 1, 1996
Last modified:	May 1, 2013
This is version 89 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program