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Entry version 102 (29 Sep 2021)
Sequence version 1 (01 Oct 1993)
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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

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Repairs 3'-OH/5'-PO4 nicks in duplex RNA or RNA:DNA hybrid in which the broken 3'-OH strand is RNA (Probable) (PubMed:12611899, PubMed:24158792, PubMed:15494308, PubMed:16671895, PubMed:15851476).

The nick ligation reaction entails three nucleotidyl transfer steps (PubMed:24158792, PubMed:15851476).

In the first step, the RNA ligase reacts with ATP in the absence of nucleic acid to form a covalent ligase-AMP intermediate and release pyrophosphate (PubMed:24158792, PubMed:15851476).

In step 2, the ligase-AMP binds to the nicked duplex nucleic acid and transfers the adenylate to the 5'-PO4 terminus to form an adenylylated nicked intermediate (PubMed:24158792, PubMed:15851476).

In step 3, the RNA ligase directs the attack of the nick 3'-OH on the 5'-phosphoanhydride linkage, resulting in a repaired 3' - 5' phosphodiester and release of AMP (PubMed:24158792, PubMed:15851476).

UniRule annotation2 Publications5 Publications

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Mg2+UniRule annotation3 Publications, Mn2+UniRule annotation1 PublicationNote: Binds 2 magnesium ions that may perform the catalytic activity via a two-metal mechanism.UniRule annotation1 Publication

<p>This subsection of the 'Function' section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>pH dependencei

Optimum pH is 7.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei34AMPUniRule annotation2 Publications1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei35N6-AMP-lysine intermediateUniRule annotation1 Publication1
Binding sitei35AMP2 Publications1
Binding sitei36AMPUniRule annotation2 Publications1
Binding sitei40AMPUniRule annotation2 Publications1
Binding sitei55AMPUniRule annotation1 Publication1
Binding sitei99AMPUniRule annotation2 Publications1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi162Magnesium 2; via carbonyl oxygenUniRule annotation1 Publication1
Metal bindingi164Magnesium 2; via carbonyl oxygenUniRule annotation1 Publication1
Metal bindingi166Magnesium 2UniRule annotation1 Publication1
Metal bindingi204MagnesiumUniRule annotation1
Metal bindingi204Magnesium 11 Publication1
Metal bindingi206Magnesium 2UniRule annotation1 Publication1
Binding sitei225AMPUniRule annotation2 Publications1
Binding sitei227AMPUniRule annotation2 Publications1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

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

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
MetaCyc:MONOMER-19918

BRENDA Comprehensive Enzyme Information System

More...
BRENDAi
6.5.1.3, 732

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
RNA ligase 2UniRule annotation (EC:6.5.1.3UniRule annotation5 Publications)
Alternative name(s):
Rnl2UniRule annotation
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:Y10A
Synonyms:24.1
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEnterobacteria phage T4 (Bacteriophage T4)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri10665 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiVirusesDuplodnaviriaHeunggongviraeUroviricotaCaudoviricetesCaudoviralesMyoviridaeTevenvirinaeTequatrovirus
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section only exists in viral entries and indicates the host(s) either as a specific organism or taxonomic group of organisms that are susceptible to be infected by a virus.<p><a href='/help/virus_host' target='_top'>More...</a></p>Virus hostiEscherichia coli [TaxID: 562]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000009087 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Genome

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi34E → A or D: Complete loss of adenylyltransferase activity and RNA ligation. 1 Publication1
Mutagenesisi34E → Q: Almost complete loss of adenylyltransferase activity and RNA ligation. 1 Publication1
Mutagenesisi35K → A: Complete loss of RNA ligase activity in vitro. Complete loss of ligase-AMP formation and RNA-adenylate intermediate. 2 Publications1
Mutagenesisi37H → D: No effect on RNA ligase activity in vitro. 2 Publications1
Mutagenesisi39T → A: No effect on RNA ligase activity. 1 Publication1
Mutagenesisi40N → A: 85% loss of adenylyltransferase activity. 1 Publication1
Mutagenesisi40N → D: No effect on adenylyltransferase activity and RNA ligation. 1 Publication1
Mutagenesisi40N → Q: 80% loss of adenylyltransferase activity and RNA ligation. 1 Publication1
Mutagenesisi40N → R: Complete loss of adenylyltransferase activity and RNA ligation. 1 Publication1
Mutagenesisi55R → A or Q: Almost complete loss of adenylyltransferase activity and RNA ligation. 1 Publication1
Mutagenesisi65F → A: Strongly reduced RNA ligase activity. 1 Publication1
Mutagenesisi66F → A: Strongly reduced RNA ligase activity. 1 Publication1
Mutagenesisi99E → A, D or Q: Complete loss of adenylyltransferase activity and RNA ligation. 1 Publication1
Mutagenesisi119F → A: Complete loss of adenylyltransferase activity and RNA ligation. 1 Publication1
Mutagenesisi119F → L: Complete loss of adenylyltransferase activity. Partial loss of RNA ligation. 1 Publication1
Mutagenesisi120D → A or N: Complete loss of adenylyltransferase activity and RNA ligation. 1 Publication1
Mutagenesisi120D → E: 88% loss of adenylyltransferase activity. Partial loss of RNA ligation. 1 Publication1
Mutagenesisi189K → A: 30% loss of adenylyltransferase activity. No effect on RNA ligation. 1 Publication1
Mutagenesisi204E → A: Complete loss of RNA ligase activity in vitro. 1 Publication1
Mutagenesisi209K → A: Almost complete loss of adenylyltransferase activity. 1 Publication1
Mutagenesisi225K → A: Complete loss of RNA ligase activity in vitro. 1 Publication1
Mutagenesisi227K → A: Complete loss of RNA ligase activity in vitro. Almost complete loss of adenylyltransferase activity and RNA ligation. 2 Publications1
Mutagenesisi227K → R or Q: Complete loss of RNA ligase activity in vitro. Almost complete loss of adenylyltransferase activity. Partial loss of RNA ligation. 1 Publication1

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001651561 – 334RNA ligase 2Add BLAST334

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections ('Function', 'PTM / Processing', 'Pathology and Biotech') according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei218Interaction with RNAUniRule annotation1
Sitei314Interaction with RNAUniRule annotation1

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1334
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

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SMRi
P32277

Database of comparative protein structure models

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ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
P32277

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni1 – 234AdenylyltransferaseUniRule annotationAdd BLAST234

<p>This subsection of the 'Family and domains' section provides general information on the biological role of a domain. The term 'domain' is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

The adenylyltransferase domain in the N-terminus performs step 1 and step 3 reactions (PubMed:14962393). The C-terminus domain is required for step 2 of the ligation pathway (PubMed:14962393, PubMed:17018278).UniRule annotation2 Publications

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the RNA ligase 2 family.UniRule annotation

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
1.10.10.1810, 1 hit

HAMAP database of protein families

More...
HAMAPi
MF_04150, RNALIG2_T4, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR012647, RNA_lig_RNL2
IPR021122, RNA_ligase_dom_REL/Rnl2
IPR041948, Rnl1/2_C_sf
IPR040609, Rnl2_C
IPR044263, Rnl2_vir

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF09414, RNA_ligase, 1 hit
PF18043, T4_Rnl2_C, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR02307, RNA_lig_RNL2, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i1E272FBFCE02605A
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
X69459 Genomic DNA Translation: CAA49218.1
AF158101 Genomic DNA Translation: AAD42430.1

Protein sequence database of the Protein Information Resource

More...
PIRi
S28563

NCBI Reference Sequences

More...
RefSeqi
NP_049790.1, NC_000866.4

Genome annotation databases

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
1258563

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
vg:1258563

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

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

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
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[»]
SMRiP32277
ModBaseiSearch...
PDBe-KBiSearch...

Genome annotation databases

GeneIDi1258563
KEGGivg:1258563

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-19918
BRENDAi6.5.1.3, 732

Miscellaneous databases

EvolutionaryTraceiP32277

Family and domain databases

Gene3Di1.10.10.1810, 1 hit
HAMAPiMF_04150, RNALIG2_T4, 1 hit
InterProiView protein in InterPro
IPR012647, RNA_lig_RNL2
IPR021122, RNA_ligase_dom_REL/Rnl2
IPR041948, Rnl1/2_C_sf
IPR040609, Rnl2_C
IPR044263, Rnl2_vir
PfamiView protein in Pfam
PF09414, RNA_ligase, 1 hit
PF18043, T4_Rnl2_C, 1 hit
TIGRFAMsiTIGR02307, RNA_lig_RNL2, 1 hit

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiRLIG2_BPT4
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P32277
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: October 1, 1993
Last modified: September 29, 2021
This is version 102 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Reference proteome

Documents

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