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Protein

RNA ligase 2

Gene

Y10A

Organism
Enterobacteria phage T4 (Bacteriophage T4)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes intramolecular and intermolecular RNA strand joining (in vitro). May play a role in the repair of nicked RNA molecules.2 Publications

Catalytic activityi

ATP + (ribonucleotide)(n)-3'-hydroxyl + 5'-phospho-(ribonucleotide)(m) = (ribonucleotide)(n+m) + AMP + diphosphate.2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei35N6-AMP-lysine intermediate1 Publication1
Binding sitei55ATP1 Publication1
Binding sitei99ATP1 Publication1
Binding sitei119ATPBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi6 – 8ATPBy similarity3
Nucleotide bindingi34 – 40ATP1 Publication7
Nucleotide bindingi225 – 227ATP1 Publication3

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionLigase
Biological processRNA repair
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

BRENDAi6.5.1.3. 732.

Names & Taxonomyi

Protein namesi
Recommended name:
RNA ligase 2 (EC:6.5.1.32 Publications)
Short name:
Rnl2
Gene namesi
Name:Y10A
Synonyms:24.1
OrganismiEnterobacteria phage T4 (Bacteriophage T4)
Taxonomic identifieri10665 [NCBI]
Taxonomic lineageiVirusesdsDNA viruses, no RNA stageCaudoviralesMyoviridaeTevenvirinaeT4virus
Virus hostiEscherichia coli [TaxID: 562]
Proteomesi
  • UP000009087 Componenti: Genome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi35K → A: Complete loss of RNA ligase activity in vitro. 1 Publication1
Mutagenesisi37H → D: No effect on RNA ligase activity in vitro. 1 Publication1
Mutagenesisi39T → A: No effect on RNA ligase activity. 1 Publication1
Mutagenesisi65F → A: Strongly reduced RNA ligase activity. 1 Publication1
Mutagenesisi66F → A: Strongly reduced RNA ligase activity. 1 Publication1
Mutagenesisi204E → A: Complete loss of RNA ligase activity in vitro. 1 Publication1
Mutagenesisi225K → A: Complete loss of RNA ligase activity in vitro. 1 Publication1
Mutagenesisi227K → A: Complete loss of RNA ligase activity in vitro. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001651561 – 334RNA ligase 2Add BLAST334

Interactioni

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei218Interaction with RNA1
Sitei314Interaction with RNA1

Structurei

Secondary structure

1334
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi14 – 23Combined sources10
Beta strandi30 – 34Combined sources5
Beta strandi38 – 48Combined sources11
Beta strandi50 – 54Combined sources5
Turni66 – 68Combined sources3
Helixi69 – 74Combined sources6
Helixi76 – 89Combined sources14
Beta strandi91 – 102Combined sources12
Turni103 – 105Combined sources3
Beta strandi106 – 108Combined sources3
Beta strandi115 – 125Combined sources11
Beta strandi130 – 132Combined sources3
Helixi135 – 145Combined sources11
Beta strandi148 – 150Combined sources3
Beta strandi152 – 156Combined sources5
Helixi158 – 161Combined sources4
Helixi172 – 182Combined sources11
Helixi184 – 189Combined sources6
Beta strandi198 – 200Combined sources3
Beta strandi205 – 212Combined sources8
Beta strandi224 – 227Combined sources4
Helixi229 – 231Combined sources3
Helixi249 – 258Combined sources10
Helixi259 – 261Combined sources3
Helixi264 – 272Combined sources9
Helixi282 – 299Combined sources18
Beta strandi305 – 308Combined sources4
Helixi310 – 323Combined sources14
Turni324 – 327Combined sources4
Turni329 – 331Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1S68X-ray1.90A1-249[»]
2HVQX-ray2.40A1-334[»]
2HVRX-ray2.45A/B1-334[»]
2HVSX-ray2.50A/B1-334[»]
ProteinModelPortaliP32277.
SMRiP32277.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP32277.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 234AdenylyltransferaseAdd BLAST234

Sequence similaritiesi

Belongs to the RNA ligase 2 family.Curated

Phylogenomic databases

KOiK18962.
OrthoDBiVOG090000FL.

Family and domain databases

InterProiView protein in InterPro
IPR012647. RNA_lig_RNL2.
IPR021122. RNA_ligase_dom_REL/Rnl2.
PfamiView protein in Pfam
PF09414. RNA_ligase. 1 hit.
TIGRFAMsiTIGR02307. RNA_lig_RNL2. 1 hit.

Sequencei

Sequence statusi: Complete.

P32277-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFKKYSSLEN HYNSKFIEKL YSLGLTGGEW VAREKIHGTN FSLIIERDKV
60 70 80 90 100
TCAKRTGPIL PAEDFFGYEI ILKNYADSIK AVQDIMETSA VVSYQVFGEF
110 120 130 140 150
AGPGIQKNVD YCDKDFYVFD IIVTTESGDV TYVDDYMMES FCNTFKFKMA
160 170 180 190 200
PLLGRGKFEE LIKLPNDLDS VVQDYNFTVD HAGLVDANKC VWNAEAKGEV
210 220 230 240 250
FTAEGYVLKP CYPSWLRNGN RVAIKCKNSK FSEKKKSDKP IKAKVELSEA
260 270 280 290 300
DNKLVGILAC YVTLNRVNNV ISKIGEIGPK DFGKVMGLTV QDILEETSRE
310 320 330
GITLTQADNP SLIKKELVKM VQDVLRPAWI ELVS
Length:334
Mass (Da):37,627
Last modified:October 1, 1993 - v1
Checksum:i1E272FBFCE02605A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X69459 Genomic DNA. Translation: CAA49218.1.
AF158101 Genomic DNA. Translation: AAD42430.1.
PIRiS28563.
RefSeqiNP_049790.1. NC_000866.4.

Genome annotation databases

GeneIDi1258563.
KEGGivg:1258563.

Entry informationi

Entry nameiRLIG2_BPT4
AccessioniPrimary (citable) accession number: P32277
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: October 1, 1993
Last modified: February 15, 2017
This is version 88 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families