P0DTT0 · BIPA_ECOLI

  • Protein
    Large ribosomal subunit assembly factor BipA
  • Gene
    bipA
  • Status
    UniProtKB reviewed (Swiss-Prot)
  • Amino acids
  • Protein existence
    Evidence at protein level
  • Annotation score
    5/5

Function

function

A 50S ribosomal subunit assembly protein with GTPase and nucleotide-independent chaperone activity, required for 50S subunit assembly at low temperatures, may also play a role in translation (PubMed:30305394).
Genetic and deletion evidence suggests this is involved in ribosome assembly at low temperatures; it may also affect translation (Probable) (PubMed:25777676, PubMed:30305394).
Involved in incorporation of ribosomal protein uL6 into precursor 44S ribosomal particles at low temperatures. Also has chaperone activity which does not require nucleotides (PubMed:30305394).
Binds GDP, ppGpp and GDPCP (a nonhydrolyzable GTP analog) with similar affinity; the conformation of the protein does not significantly change upon nucleotide binding (PubMed:26163516, PubMed:26283392).
Interacts with ribosomes (PubMed:26283392, Ref.12). Binds the 70S ribosome between the 30S and 50S subunits, in a similar position as ribosome-bound EF-G; it contacts a number of ribosomal proteins, both rRNAs and the A-site tRNA. Ribosome binding alters its conformation (PubMed:26283392).
Genetically its function does not overlap LepA, and it acts in a different pathway during ribosome assembly than does RNA helicase DeaD (PubMed:25777676).
GTPase that affects interactions between enteropathogenic E.coli (EPEC) and epithelial cells (PubMed:9622352).
Probably regulates expression of proteins required for (at least) K5 polysaccharide production (Probable) (PubMed:10781541).
Deletion mutants of bipA are suppressed by an rluC deletion, which no longer modifies uracils 955, 2504 and 2580 to pseudouridine in 23S rRNA; there are 5 other pseudouridine synthases in E.coli, only rluC suppresses this phenotype. Mutating 23S rRNA so the 3 uracils are other nucleotides also suppresses the bipA deletion; pseudouridine-2504 is required for ribosome assembly and translational accuracy (PubMed:18820021, PubMed:25777676).

Catalytic activity

Features

Showing features for binding site.

TypeIDPosition(s)Description
Binding site15-20GTP (UniProtKB | ChEBI)
Binding site128-131GTP (UniProtKB | ChEBI)
Binding site166-168GTP (UniProtKB | ChEBI)

GO annotations

AspectTerm
Cellular Componentcytosol
Cellular Componentribonucleoprotein complex
Molecular FunctionGTP binding
Molecular FunctionGTPase activity
Molecular Functionguanosine tetraphosphate binding
Molecular Functionprotein folding chaperone
Molecular Functionribosome binding
Molecular FunctionrRNA binding
Molecular FunctiontRNA binding
Biological Processresponse to cold
Biological Processresponse to heat
Biological Processribosomal large subunit assembly
Biological Processtranslation

Keywords

Enzyme and pathway databases

Names & Taxonomy

Protein names

  • Recommended name
    Large ribosomal subunit assembly factor BipA
  • EC number
  • Alternative names
    • 50S ribosomal subunit assembly factor BipA
    • GTP-binding protein BipA/TypA
    • Ribosome assembly factor BipA
    • Ribosome-dependent GTPase BipA
    • Tyrosine phosphorylated protein A

Gene names

    • Name
      bipA
    • Synonyms
      o591
      , typA, yihK
    • Ordered locus names
      b3871, JW5571

Organism names

  • Taxonomic identifier
  • Strains
    • K12 / MG1655 / ATCC 47076
    • K12 / W3110 / ATCC 27325 / DSM 5911
    • K12 / EMG2
  • Taxonomic lineage
    Bacteria > Pseudomonadota > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Escherichia

Accessions

  • Primary accession
    P0DTT0
  • Secondary accessions
    • P32132
    • Q2M8G8
    • Q6BEY2

Proteomes

Subcellular Location

Cytoplasm
Note: Associates with 70S ribosomes and 30S and 50S subunits in the presence of GMPPNP (a nonhydrolyzable GTP analog) at both 20 and 37 degrees Celsius; no change in ribosome association is seen in the presence of ppGpp or when the stringent response is triggered.

Keywords

Phenotypes & Variants

Disruption phenotype

Decreased extracellular K5 polysaccharide production at 37 degrees Celsius, increased extracellular K5 polysaccharide production at 20 degrees Celsius (PubMed:10781541).
Cold-sensitive growth (20 degrees Celsius); cells have a long lag phase and double more slowly (PubMed:11683274, PubMed:18820021).
Decreased capsule synthesis. Cold sensitive growth and decreased capsule synthesis are suppressed by an rluC deletion (PubMed:18820021).
Cold-sensitive growth (20 degrees Celsius); a single bipA deletion has a disturbed ribosome profile at low temperature, with more 30S than 50S subunits, accumulation of a precursor-23S rRNA and precursor 50S subunit and decreased 70S ribosomes (PubMed:25777676, PubMed:30305394).
These ribosome phenotypes are suppressed in an rluC deletion. A double bipA-deaD deletion has a more severe growth and ribosome phenotype than either single deletion (PubMed:25777676).
At 20 degrees Celsius the single deletion is missing ribosomal protein uL6 and has decreased amounts of bL9 and uL18 and makes less capsule. It has decreased motility at both 20 and 37 degrees Celsius (PubMed:30305394).
Cold-sensitive growth (18 degrees Celsius); 2-fold more Uup is expressed at 37 degrees Celsius, 10-fold more Uup at 18 degrees Celsius. A double bipA-uup deletion does not grow at 18 degrees Celsius (Ref.12)

Features

Showing features for mutagenesis.

TypeIDPosition(s)Description
Mutagenesis128No GTPase activity, does not restore normal ribosomes to a bipA deletion, does not associate with ribosomes, retains its ability to help proteins refold.
Mutagenesis164No change in growth at 20 degrees Celsius.
Mutagenesis472No change in growth at 20 degrees Celsius.
Mutagenesis519No change in growth at 20 degrees Celsius.

PTM/Processing

Features

Showing features for chain.

TypeIDPosition(s)Description
ChainPRO_00000915501-607Large ribosomal subunit assembly factor BipA

Post-translational modification

Very poorly to not phosphorylated on tyrosine (PubMed:30305394, PubMed:9622352, PubMed:9642082).
Phosphorylation in vitro is strongly activated by proteins present in pathogenic strain E2348/69 / EPEC / MAR001 but not non-pathogenic strain K12 / DH5 alpha. Phosphorylation in vitro increases GTPase activity (PubMed:9622352).
Mutation of 3 conserved Tyr residues (Tyr-164; Ty5-47 or Tyr-591) to Phe alone or in all combinations has no effect on the ability of the protein to restore growth to a deletion mutant, suggesting Tyr-phosphorylation is not important in non-EPEC strains (PubMed:30305394).

Proteomic databases

Expression

Induction

Induced about 2-fold at 18 degrees Celsius (at protein level) (Ref.12). Basally expressed at 37 degrees Celsius, 3.5-fold induced after shift to 20 degrees Celsius, maximal expression is seen at 2 hours (at protein level). No increase in expression when cells are grown at 43 degrees Celsius or when engineered to produce increased levels of the stress second messenger ppGpp. Expression at low temperatures is activated by CRP (PubMed:30305394).

Interaction

Subunit

Monomer (PubMed:26163516, PubMed:26283392).
Binds between the 30S and 50S ribosomal subunits, in a similar position as ribosome-bound EF-G; it contacts proteins bL12 (L7/12), uL11, uS2, 16S and 23S rRNA and the A-site tRNA. Binding to the ribosome alters its conformation (PubMed:26283392).

Binary interactions

TypeEntry 1Entry 2Number of experimentsIntact
BINARY P0DTT0rlmL P758643EBI-562154, EBI-547718
BINARY P0DTT0ybeY P0A8982EBI-562154, EBI-560240
BINARY P0DTT0yigZ P278622EBI-562154, EBI-561235

Protein-protein interaction databases

Family & Domains

Features

Showing features for region, domain.

TypeIDPosition(s)Description
Region1-202Domain I (or G domain), required for chaperone activity
Domain3-198tr-type G
Region203-320Domain II (or beta barrel domain)
Region303-385Domain III
Region386-482Domain V
Region483-607C-terminal domain (CTD), binds A-site tRNA

Domain

Crystallizes with 2 superdomains; the first comprises domains I (residues 1-202, also called the G domain) and II (203-302, also called the beta barrel domain), while the second is composed of domains III (303-385), V (386-482) and a BipA-specific C-terminal domain (CTD, 483-607). Domains I-V are homologous to domains in EF-G and LepA; although the domains are similar, their relative arrangement is different (PubMed:26163516, PubMed:26283392).
The structure of isolated superdomain 2 is more compact in the presence of Mg2+ than in the intact protein (PubMed:26163516).
Upon ribosome binding the second superdomain shifts and the CTD assumes a more compact conformation. The CTD binds to the A-site tRNA (PubMed:26283392).
Chaperone activity resides in domain I; truncated proteins of 49-607 and 149-607 have no chaperone activity (PubMed:30305394).

Sequence similarities

Phylogenomic databases

Family and domain databases

Sequence

  • Sequence status
    Complete
  • Length
    607
  • Mass (Da)
    67,355
  • Last updated
    2020-02-26 v1
  • Checksum
    3B4DE3A514F95FFB
MIEKLRNIAIIAHVDHGKTTLVDKLLQQSGTFDSRAETQERVMDSNDLEKERGITILAKNTAIKWNDYRINIVDTPGHADFGGEVERVMSMVDSVLLVVDAFDGPMPQTRFVTKKAFAYGLKPIVVINKVDRPGARPDWVVDQVFDLFVNLDATDEQLDFPIVYASALNGIAGLDHEDMAEDMTPLYQAIVDHVPAPDVDLDGPFQMQISQLDYNSYVGVIGIGRIKRGKVKPNQQVTIIDSEGKTRNAKVGKVLGHLGLERIETDLAEAGDIVAITGLGELNISDTVCDTQNVEALPALSVDEPTVSMFFCVNTSPFCGKEGKFVTSRQILDRLNKELVHNVALRVEETEDADAFRVSGRGELHLSVLIENMRREGFELAVSRPKVIFREIDGRKQEPYENVTLDVEEQHQGSVMQALGERKGDLKNMNPDGKGRVRLDYVIPSRGLIGFRSEFMTMTSGTGLLYSTFSHYDDVRPGEVGQRQNGVLISNGQGKAVAFALFGLQDRGKLFLGHGAEVYEGQIIGIHSRSNDLTVNCLTGKKLTNMRASGTDEAVVLVPPIRMTLEQALEFIDDDELVEVTPTSIRIRKRHLTENDRRRANRAPKDD

Features

Showing features for sequence conflict.

TypeIDPosition(s)Description
Sequence conflict592-607in Ref. 1; AAB03005

Keywords

Sequence databases

Nucleotide SequenceProtein SequenceMolecule TypeStatus
L19201
EMBL· GenBank· DDBJ
AAB03005.1
EMBL· GenBank· DDBJ
Genomic DNA
U00096
EMBL· GenBank· DDBJ
AAT48232.1
EMBL· GenBank· DDBJ
Genomic DNA
AP009048
EMBL· GenBank· DDBJ
BAE77438.1
EMBL· GenBank· DDBJ
Genomic DNA

Genome annotation databases

Similar Proteins

Disclaimer

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