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Protein

ATP-dependent RNA helicase SrmB

Gene

srmB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

DEAD-box RNA helicase involved in the assembly of the 50S ribosomal subunit at low temperature. Exhibits RNA-stimulated ATP hydrolysis and RNA unwinding activity. Acts before DeaD.UniRule annotation3 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.UniRule annotation1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi48 – 55ATPUniRule annotation8

GO - Molecular functioni

  • ATP binding Source: UniProtKB-HAMAP
  • ATP-dependent RNA helicase activity Source: UniProtKB
  • poly(A) binding Source: UniProtKB
  • RNA-dependent ATPase activity Source: UniProtKB
  • RNA strand annealing activity Source: EcoCyc

GO - Biological processi

  • ribosomal large subunit assembly Source: EcoCyc
  • RNA secondary structure unwinding Source: GO_Central
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

Ribosome biogenesis

Keywords - Ligandi

ATP-binding, Nucleotide-binding, RNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG10975-MONOMER.
ECOL316407:JW2560-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
ATP-dependent RNA helicase SrmBUniRule annotation (EC:3.6.4.13UniRule annotation)
Gene namesi
Name:srmBUniRule annotation
Synonyms:rbaB, rhlA
Ordered Locus Names:b2576, JW2560
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10975. srmB.

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Cells lacking this gene grow very poorly at 20 degrees Celsius, show a severe deficit of free 50S ribosomal subunits and accumulate an abnormal large ribosomal subunit. Disruption also impairs the processing of both 23S and 16S rRNAs.2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000551091 – 444ATP-dependent RNA helicase SrmBAdd BLAST444

Proteomic databases

EPDiP21507.
PaxDbiP21507.
PRIDEiP21507.

Interactioni

Subunit structurei

Interacts with the 50S ribosomal subunit. Forms a complex with the 50S ribosomal proteins L4 and L24, and a region near the 5'-end of 23S rRNA.UniRule annotation1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
rlmNP369793EBI-546628,EBI-559071
rluBP377654EBI-546628,EBI-561550

Protein-protein interaction databases

BioGridi4263366. 200 interactors.
851393. 1 interactor.
DIPiDIP-10920N.
IntActiP21507. 33 interactors.
MINTiMINT-1225512.
STRINGi511145.b2576.

Structurei

Secondary structure

1444
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi223 – 231Combined sources9
Helixi232 – 243Combined sources12
Beta strandi250 – 254Combined sources5
Beta strandi256 – 258Combined sources3
Helixi259 – 272Combined sources14
Beta strandi276 – 278Combined sources3
Helixi284 – 294Combined sources11
Beta strandi301 – 304Combined sources4
Helixi307 – 309Combined sources3
Beta strandi319 – 324Combined sources6
Helixi329 – 335Combined sources7
Helixi336 – 338Combined sources3
Beta strandi342 – 344Combined sources3
Beta strandi347 – 353Combined sources7
Helixi354 – 356Combined sources3
Helixi357 – 366Combined sources10
Beta strandi367 – 369Combined sources3
Beta strandi377 – 379Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2YJTX-ray2.90D219-388[»]
ProteinModelPortaliP21507.
SMRiP21507.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini35 – 209Helicase ATP-bindingUniRule annotationAdd BLAST175
Domaini238 – 387Helicase C-terminalUniRule annotationAdd BLAST150

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi4 – 32Q motifAdd BLAST29
Motifi157 – 160DEAD box4

Domaini

The C-terminal extension is not essential for ribosome assembly, but is important for the formation or the stability of the complex.1 Publication

Sequence similaritiesi

Belongs to the DEAD box helicase family. SrmB subfamily.UniRule annotation
Contains 1 helicase ATP-binding domain.UniRule annotation
Contains 1 helicase C-terminal domain.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C1J. Bacteria.
COG0513. LUCA.
HOGENOMiHOG000268807.
InParanoidiP21507.
KOiK05590.
OMAiPMMDRVA.
PhylomeDBiP21507.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
HAMAPiMF_00967. DEAD_helicase_SrmB. 1 hit.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR028621. DEAD_helicase_SrmB.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR000629. RNA-helicase_DEAD-box_CS.
IPR014014. RNA_helicase_DEAD_Q_motif.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiPS00039. DEAD_ATP_HELICASE. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P21507-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTVTTFSELE LDESLLEALQ DKGFTRPTAI QAAAIPPALD GRDVLGSAPT
60 70 80 90 100
GTGKTAAYLL PALQHLLDFP RKKSGPPRIL ILTPTRELAM QVSDHARELA
110 120 130 140 150
KHTHLDIATI TGGVAYMNHA EVFSENQDIV VATTGRLLQY IKEENFDCRA
160 170 180 190 200
VETLILDEAD RMLDMGFAQD IEHIAGETRW RKQTLLFSAT LEGDAIQDFA
210 220 230 240 250
ERLLEDPVEV SANPSTRERK KIHQWYYRAD DLEHKTALLV HLLKQPEATR
260 270 280 290 300
SIVFVRKRER VHELANWLRE AGINNCYLEG EMVQGKRNEA IKRLTEGRVN
310 320 330 340 350
VLVATDVAAR GIDIPDVSHV FNFDMPRSGD TYLHRIGRTA RAGRKGTAIS
360 370 380 390 400
LVEAHDHLLL GKVGRYIEEP IKARVIDELR PKTRAPSEKQ TGKPSKKVLA
410 420 430 440
KRAEKKKAKE KEKPRVKKRH RDTKNIGKRR KPSGTGVPPQ TTEE
Length:444
Mass (Da):49,914
Last modified:May 1, 1991 - v1
Checksum:i1A459538A25807A7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X14152 Genomic DNA. Translation: CAA32364.1.
D13169 Genomic DNA. Translation: BAA02447.1.
D64044 Genomic DNA. Translation: BAA10922.1.
U00096 Genomic DNA. Translation: AAC75629.1.
AP009048 Genomic DNA. Translation: BAE76752.1.
PIRiG65035.
RefSeqiNP_417071.1. NC_000913.3.
WP_000219203.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75629; AAC75629; b2576.
BAE76752; BAE76752; BAE76752.
GeneIDi947055.
KEGGiecj:JW2560.
eco:b2576.
PATRICi32120551. VBIEscCol129921_2678.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X14152 Genomic DNA. Translation: CAA32364.1.
D13169 Genomic DNA. Translation: BAA02447.1.
D64044 Genomic DNA. Translation: BAA10922.1.
U00096 Genomic DNA. Translation: AAC75629.1.
AP009048 Genomic DNA. Translation: BAE76752.1.
PIRiG65035.
RefSeqiNP_417071.1. NC_000913.3.
WP_000219203.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2YJTX-ray2.90D219-388[»]
ProteinModelPortaliP21507.
SMRiP21507.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263366. 200 interactors.
851393. 1 interactor.
DIPiDIP-10920N.
IntActiP21507. 33 interactors.
MINTiMINT-1225512.
STRINGi511145.b2576.

Proteomic databases

EPDiP21507.
PaxDbiP21507.
PRIDEiP21507.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75629; AAC75629; b2576.
BAE76752; BAE76752; BAE76752.
GeneIDi947055.
KEGGiecj:JW2560.
eco:b2576.
PATRICi32120551. VBIEscCol129921_2678.

Organism-specific databases

EchoBASEiEB0968.
EcoGeneiEG10975. srmB.

Phylogenomic databases

eggNOGiENOG4105C1J. Bacteria.
COG0513. LUCA.
HOGENOMiHOG000268807.
InParanoidiP21507.
KOiK05590.
OMAiPMMDRVA.
PhylomeDBiP21507.

Enzyme and pathway databases

BioCyciEcoCyc:EG10975-MONOMER.
ECOL316407:JW2560-MONOMER.

Miscellaneous databases

PROiP21507.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
HAMAPiMF_00967. DEAD_helicase_SrmB. 1 hit.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR028621. DEAD_helicase_SrmB.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR000629. RNA-helicase_DEAD-box_CS.
IPR014014. RNA_helicase_DEAD_Q_motif.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiPS00039. DEAD_ATP_HELICASE. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSRMB_ECOLI
AccessioniPrimary (citable) accession number: P21507
Secondary accession number(s): Q2MAF4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 1991
Last sequence update: May 1, 1991
Last modified: November 2, 2016
This is version 145 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Overexpression suppresses a mutant defective in 50S ribosomal subunit assembly.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.