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Entry version 164 (16 Oct 2019)
Sequence version 1 (01 Feb 1995)
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Protein

Serine--tRNA ligase, mitochondrial

Gene

DIA4

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
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

Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec) (By similarity).By similarity

Miscellaneous

Present with 405 molecules/cell in log phase SD medium.1 Publication

<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 <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: selenocysteinyl-tRNA(Sec) biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes L-seryl-tRNA(Sec) from L-serine and tRNA(Sec).
Proteins known to be involved in this subpathway in this organism are:
  1. Serine--tRNA ligase, cytoplasmic (SES1), Serine--tRNA ligase, mitochondrial (DIA4)
This subpathway is part of the pathway selenocysteinyl-tRNA(Sec) biosynthesis, which is itself part of Aminoacyl-tRNA biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-seryl-tRNA(Sec) from L-serine and tRNA(Sec), the pathway selenocysteinyl-tRNA(Sec) biosynthesis and in Aminoacyl-tRNA biosynthesis.

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 sitei300ATP; via amide nitrogen and carbonyl oxygenBy similarity1
Binding sitei307SerineBy similarity1
Binding sitei407SerineBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi284 – 286ATPBy similarity3
Nucleotide bindingi371 – 374ATPBy similarity4

<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 functionAminoacyl-tRNA synthetase, Ligase
Biological processProtein biosynthesis
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
YEAST:G3O-31074-MONOMER

UniPathway: a resource for the exploration and annotation of metabolic pathways

More...
UniPathwayi
UPA00906;UER00895

<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:
Serine--tRNA ligase, mitochondrial (EC:6.1.1.11)
Alternative name(s):
Digs into agar protein 4
Seryl-tRNA synthetase
Short name:
SerRS
Seryl-tRNA(Ser/Sec) synthetase
<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:DIA4
Ordered Locus Names:YHR011W
<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>OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
<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 identifieri559292 [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 lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
<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
  • UP000002311 <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: Chromosome VIII

Organism-specific databases

Eukaryotic Pathogen Database Resources

More...
EuPathDBi
FungiDB:YHR011W

Saccharomyces Genome Database

More...
SGDi
S000001053 DIA4

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

Keywords - Cellular componenti

Mitochondrion

<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.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001222001 – 446Serine--tRNA ligase, mitochondrialAdd BLAST446

Proteomic databases

MaxQB - The MaxQuant DataBase

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MaxQBi
P38705

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
P38705

PRoteomics IDEntifications database

More...
PRIDEi
P38705

<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

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homodimer. The tRNA molecule binds across the dimer (By similarity).

By similarity

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...
BioGridi
36438, 119 interactors

Database of interacting proteins

More...
DIPi
DIP-5573N

Protein interaction database and analysis system

More...
IntActi
P38705, 5 interactors

Molecular INTeraction database

More...
MINTi
P38705

STRING: functional protein association networks

More...
STRINGi
4932.YHR011W

<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

3D structure databases

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

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SMRi
P38705

Database of comparative protein structure models

More...
ModBasei
Search...

<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>Regioni251 – 253Serine bindingBy similarity3

<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

Consists of two distinct domains, a catalytic core and a N-terminal extension that is involved in tRNA binding.By similarity

<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

Phylogenomic databases

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000035937

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P38705

KEGG Orthology (KO)

More...
KOi
K01875

Identification of Orthologs from Complete Genome Data

More...
OMAi
KHIRQNP

Family and domain databases

Conserved Domains Database

More...
CDDi
cd00770 SerRS_core, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR002314 aa-tRNA-synt_IIb
IPR006195 aa-tRNA-synth_II
IPR002317 Ser-tRNA-ligase_type_1
IPR033729 SerRS_core
IPR010978 tRNA-bd_arm

The PANTHER Classification System

More...
PANTHERi
PTHR11778 PTHR11778, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00587 tRNA-synt_2b, 1 hit

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF001529 Ser-tRNA-synth_IIa, 1 hit

Protein Motif fingerprint database; a protein domain database

More...
PRINTSi
PR00981 TRNASYNTHSER

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF46589 SSF46589, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00414 serS, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS50862 AA_TRNA_LIGASE_II, 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.

P38705-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MIIRRLFSIS NRSFFLKKPQ FDVKKIIEMI PQYQTSIQNR ELIEADSIIR
60 70 80 90 100
SLQLLGERYQ NIKEIDKVIA DIQIQRKSIE AQIKKDKTKI TEYSAALKAL
110 120 130 140 150
KEQYNDQNSK SSELKKKILE TCKSLPNTLD PTVPLDAPQI EQWINPLKTH
160 170 180 190 200
KTSEAQAHVD IMLKKNMLDL QTASNVTGMS WYYLLNDGAR LEQALVAYAL
210 220 230 240 250
KKANENGFSS CVPPSITKKE LIDACGFNPR DMNNERQIYA LQDTNLGLVA
260 270 280 290 300
TAEIPLAGLG ANKVLELNSG ECSKKLVGVS RCYRAEAGAR GKDTKGLYRV
310 320 330 340 350
HEFTKVELFC WSKPETSAKV LEEIKQFQIS VVEELGIPAK VLNMPSNDLG
360 370 380 390 400
NPAFKKYDIE AWMPGRGKFG EISSASNCTD FQSRRLNTKY RDDNTGKLEY
410 420 430 440
VHTLNGTAMA IPRVIVALVE NFYDPSTGKI SVPECLREFM NGQRYI
Length:446
Mass (Da):50,390
Last modified:February 1, 1995 - 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:i2C0AE2CB644E7C54
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
U10400 Genomic DNA Translation: AAB68940.1
AY558105 Genomic DNA Translation: AAS56431.1
BK006934 Genomic DNA Translation: DAA06700.1

Protein sequence database of the Protein Information Resource

More...
PIRi
S46786

NCBI Reference Sequences

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RefSeqi
NP_011875.1, NM_001179141.1

Genome annotation databases

Ensembl fungal genome annotation project

More...
EnsemblFungii
YHR011W_mRNA; YHR011W; YHR011W

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
856402

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
sce:YHR011W

<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
U10400 Genomic DNA Translation: AAB68940.1
AY558105 Genomic DNA Translation: AAS56431.1
BK006934 Genomic DNA Translation: DAA06700.1
PIRiS46786
RefSeqiNP_011875.1, NM_001179141.1

3D structure databases

SMRiP38705
ModBaseiSearch...

Protein-protein interaction databases

BioGridi36438, 119 interactors
DIPiDIP-5573N
IntActiP38705, 5 interactors
MINTiP38705
STRINGi4932.YHR011W

Proteomic databases

MaxQBiP38705
PaxDbiP38705
PRIDEiP38705

Genome annotation databases

EnsemblFungiiYHR011W_mRNA; YHR011W; YHR011W
GeneIDi856402
KEGGisce:YHR011W

Organism-specific databases

EuPathDBiFungiDB:YHR011W
SGDiS000001053 DIA4

Phylogenomic databases

HOGENOMiHOG000035937
InParanoidiP38705
KOiK01875
OMAiKHIRQNP

Enzyme and pathway databases

UniPathwayiUPA00906;UER00895
BioCyciYEAST:G3O-31074-MONOMER

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P38705

Family and domain databases

CDDicd00770 SerRS_core, 1 hit
InterProiView protein in InterPro
IPR002314 aa-tRNA-synt_IIb
IPR006195 aa-tRNA-synth_II
IPR002317 Ser-tRNA-ligase_type_1
IPR033729 SerRS_core
IPR010978 tRNA-bd_arm
PANTHERiPTHR11778 PTHR11778, 1 hit
PfamiView protein in Pfam
PF00587 tRNA-synt_2b, 1 hit
PIRSFiPIRSF001529 Ser-tRNA-synth_IIa, 1 hit
PRINTSiPR00981 TRNASYNTHSER
SUPFAMiSSF46589 SSF46589, 1 hit
TIGRFAMsiTIGR00414 serS, 1 hit
PROSITEiView protein in PROSITE
PS50862 AA_TRNA_LIGASE_II, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

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 nameiSYSM_YEAST
<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: P38705
Secondary accession number(s): D3DKV6
<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: February 1, 1995
Last sequence update: February 1, 1995
Last modified: October 16, 2019
This is version 164 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 programFungal 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

Complete proteome, Reference proteome

Documents

  1. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  2. Aminoacyl-tRNA synthetases
    List of aminoacyl-tRNA synthetase entries
  3. SIMILARITY comments
    Index of protein domains and families
  4. Yeast chromosome VIII
    Yeast (Saccharomyces cerevisiae) chromosome VIII: entries and gene names
  5. PATHWAY comments
    Index of metabolic and biosynthesis pathways
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