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UniProtKB - P25808 (SPB4_YEAST)

Entry version 179 (11 Dec 2019)
Sequence version 1 (01 May 1992)
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Protein

ATP-dependent rRNA helicase SPB4

Gene

SPB4

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

ATP-binding RNA helicase involved in the biogenesis of 60S ribosomal subunits (PubMed:2408148, PubMed:25579579). Binds 90S pre-ribosomal particles and dissociates from pre-60S ribosomal particles after processing of 27SB pre-rRNA (PubMed:21825077). Required for the normal formation of 18S rRNA through the processing of pre-rRNAs at sites A0, A1 and A2, and the normal formation of 25S and 5.8S rRNAs through the processing of pre-rRNAs at sites C1 and C2 (PubMed:9769101). Also required for recruitment of NOG2 to pre-ribosomes (PubMed:22735702).5 Publications

Miscellaneous

Present with 5740 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

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 bindingi51 – 58ATPPROSITE-ProRule annotation8

<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

  • ATP binding Source: UniProtKB-KW
  • RNA binding Source: GO_Central
  • RNA helicase activity Source: SGD
Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<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 functionHelicase, Hydrolase, RNA-binding
Biological processRibosome biogenesis, rRNA processing
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		YEAST:G3O-30452-MONOMER

<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:
ATP-dependent rRNA helicase SPB4Curated (EC:3.6.4.131 Publication)
Alternative name(s):
Suppressor of PAB1 protein 41 Publication
<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:SPB41 Publication
Ordered Locus Names:YFL002CImported
<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 lineageiEukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›
<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 VI

Organism-specific databases

Eukaryotic Pathogen Database Resources

More...EuPathDBi		FungiDB:YFL002C

Saccharomyces Genome Database

More...SGDi		S000001894 SPB4

<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

Nucleus

<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>Mutagenesisi360R → G: Leads to accumulation of 35S and 27SB pre-rRNAs and a net 40S ribosomal subunit defect. 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.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000550651 – 606ATP-dependent rRNA helicase SPB4Add BLAST606

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei254PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQB - The MaxQuant DataBase

More...MaxQBi		P25808

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

More...PaxDbi		P25808

PRoteomics IDEntifications database

More...PRIDEi		P25808

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...iPTMneti		P25808

<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

Component of pre-60S ribosomal complexes.

4 Publications

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...BioGridi		31147, 676 interactors

Database of interacting proteins

More...DIPi		DIP-5423N

Protein interaction database and analysis system

More...IntActi		P25808, 36 interactors

Molecular INTeraction database

More...MINTi		P25808

STRING: functional protein association networks

More...STRINGi		4932.YFL002C

Miscellaneous databases

RNAct, Protein-RNA interaction predictions for model organisms.

More...RNActi		P25808 protein

<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

More...SMRi		P25808

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

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini38 – 224Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST187
Domaini248 – 404Helicase C-terminalPROSITE-ProRule annotationAdd BLAST157

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and domains’ section denotes the positions of regions of coiled coil within the protein.<p><a href='/help/coiled' target='_top'>More...</a></p>Coiled coili539 – 582Sequence analysisAdd BLAST44

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a short (usually not more than 20 amino acids) conserved sequence motif of biological significance.<p><a href='/help/motif' target='_top'>More...</a></p>Motifi7 – 35Q motifCuratedAdd BLAST29
Motifi172 – 175DEAD boxCurated4

<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 Q motif is unique to and characteristic of the DEAD box family of RNA helicases and controls ATP binding and hydrolysis.Curated

<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 DEAD box helicase family. DDX55/SPB4 subfamily.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		HOG000268803

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P25808

KEGG Orthology (KO)

More...KOi		K14809

Identification of Orthologs from Complete Genome Data

More...OMAi		RRHKETP

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR011545 DEAD/DEAH_box_helicase_dom
IPR025313 DUF4217
IPR014001 Helicase_ATP-bd
IPR001650 Helicase_C
IPR027417 P-loop_NTPase
IPR000629 RNA-helicase_DEAD-box_CS
IPR014014 RNA_helicase_DEAD_Q_motif

Pfam protein domain database

More...Pfami		View protein in Pfam
PF00270 DEAD, 1 hit
PF13959 DUF4217, 1 hit
PF00271 Helicase_C, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00487 DEXDc, 1 hit
SM01178 DUF4217, 1 hit
SM00490 HELICc, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF52540 SSF52540, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS00039 DEAD_ATP_HELICASE, 1 hit
PS51192 HELICASE_ATP_BIND_1, 1 hit
PS51194 HELICASE_CTER, 1 hit
PS51195 Q_MOTIF, 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.

P25808-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSKSLEWDNL GFSLLPWIRT GLDVMGFETM TPVQASTIPM LAGNKDVVVD 
        60         70         80         90        100
SVTGSGKTAA FVIPVLEKVV KEEANTSKFK KAHFHSLIIA PTRELSRQIE 
       110        120        130        140        150
SVVLSFLEHY PSDLFPIKCQ LLVGTNEATV RDDVSNFLRN RPQILIGTPG 
       160        170        180        190        200
RVLDFLQMPA VKTSACSMVV MDEADRLLDM SFIKDTEKIL RLLPKQRRTG 
       210        220        230        240        250
LFSATMRSAG SDIFKTGLRN PVRITVNSKN QAPSSLKLNY CVVNPAEKLQ 
       260        270        280        290        300
LLVSILNNYK FKKCIVYFPT CVSVSYFYSF IQYLGKRNIL VNEVEIFSLH 
       310        320        330        340        350
GKLQTSARTK TLTAFTDSLS NSVLFTTDVA ARGIDIPDVD LVIQLDPPTN 
       360        370        380        390        400
TDMFMHRCGR TGRANRVGKA ITFLNEGREE DFIPFMQVKN VELEELDLEV 
       410        420        430        440        450
KGITTNFYED FRNWILEDRD RFDKGVKAYV AFIKYYSNHS ATSIFRLQSL 
       460        470        480        490        500
DYVGIAKLYG LFRLPRMPEI TKYLATEKQE GIFPGNWLVD PPVNMDEYKY 
       510        520        530        540        550
KDKKREKERQ ETLKNISLIN DKKKLKSELK KKNLAWSDKT LTKERKLERK 
       560        570        580        590        600
EKMSLKRKAI EEELKAEELD ENAEEERIKE DWKEIVLQNK RKKVSSKAIQ 

GNFDDL
Length:606
Mass (Da):69,422
Last modified:May 1, 1992 - 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:iB2EC8B8B5E34AA10
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
X16147 Genomic DNA Translation: CAA34272.1
D50617 Genomic DNA Translation: BAA09238.1
BK006940 Genomic DNA Translation: DAA12439.1

Protein sequence database of the Protein Information Resource

More...PIRi		S14942

NCBI Reference Sequences

More...RefSeqi		NP_116654.1, NM_001179964.1

Genome annotation databases

Ensembl fungal genome annotation project

More...EnsemblFungii		YFL002C_mRNA; YFL002C; YFL002C

Database of genes from NCBI RefSeq genomes

More...GeneIDi		850549

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		sce:YFL002C

<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
X16147 Genomic DNA Translation: CAA34272.1
D50617 Genomic DNA Translation: BAA09238.1
BK006940 Genomic DNA Translation: DAA12439.1
PIRiS14942
RefSeqiNP_116654.1, NM_001179964.1

3D structure databases

SMRiP25808
ModBaseiSearch...

Protein-protein interaction databases

BioGridi31147, 676 interactors
DIPiDIP-5423N
IntActiP25808, 36 interactors
MINTiP25808
STRINGi4932.YFL002C

PTM databases

iPTMnetiP25808

Proteomic databases

MaxQBiP25808
PaxDbiP25808
PRIDEiP25808

Genome annotation databases

EnsemblFungiiYFL002C_mRNA; YFL002C; YFL002C
GeneIDi850549
KEGGisce:YFL002C

Organism-specific databases

EuPathDBiFungiDB:YFL002C
SGDiS000001894 SPB4

Phylogenomic databases

HOGENOMiHOG000268803
InParanoidiP25808
KOiK14809
OMAiRRHKETP

Enzyme and pathway databases

BioCyciYEAST:G3O-30452-MONOMER

Miscellaneous databases

Protein Ontology

More...PROi		PR:P25808
RNActiP25808 protein

Family and domain databases

InterProiView protein in InterPro
IPR011545 DEAD/DEAH_box_helicase_dom
IPR025313 DUF4217
IPR014001 Helicase_ATP-bd
IPR001650 Helicase_C
IPR027417 P-loop_NTPase
IPR000629 RNA-helicase_DEAD-box_CS
IPR014014 RNA_helicase_DEAD_Q_motif
PfamiView protein in Pfam
PF00270 DEAD, 1 hit
PF13959 DUF4217, 1 hit
PF00271 Helicase_C, 1 hit
SMARTiView protein in SMART
SM00487 DEXDc, 1 hit
SM01178 DUF4217, 1 hit
SM00490 HELICc, 1 hit
SUPFAMiSSF52540 SSF52540, 1 hit
PROSITEiView protein in PROSITE
PS00039 DEAD_ATP_HELICASE, 1 hit
PS51192 HELICASE_ATP_BIND_1, 1 hit
PS51194 HELICASE_CTER, 1 hit
PS51195 Q_MOTIF, 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 nameiSPB4_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: P25808
Secondary accession number(s): D6VTM9
<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: May 1, 1992
Last sequence update: May 1, 1992
Last modified: December 11, 2019
This is version 179 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

Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome VI
    Yeast (Saccharomyces cerevisiae) chromosome VI: entries and gene names
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