P0DTT0 · BIPA_ECOLI
- ProteinLarge ribosomal subunit assembly factor BipA
- GenebipA
- StatusUniProtKB reviewed (Swiss-Prot)
- Organism
- Amino acids607 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
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).
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
- GTP + H2O = GDP + H+ + phosphate
Features
Showing features for binding site.
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | cytosol | |
Cellular Component | ribonucleoprotein complex | |
Molecular Function | GTP binding | |
Molecular Function | GTPase activity | |
Molecular Function | guanosine tetraphosphate binding | |
Molecular Function | protein folding chaperone | |
Molecular Function | ribosome binding | |
Molecular Function | rRNA binding | |
Molecular Function | tRNA binding | |
Biological Process | response to cold | |
Biological Process | response to heat | |
Biological Process | ribosomal large subunit assembly | |
Biological Process | translation |
Keywords
- Molecular function
- Biological process
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameLarge ribosomal subunit assembly factor BipA
- EC number
- Alternative names
Gene names
Organism names
- Organism
- Strains
- Taxonomic lineageBacteria > Pseudomonadota > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Escherichia
Accessions
- Primary accessionP0DTT0
- Secondary accessions
Proteomes
Subcellular Location
UniProt Annotation
GO Annotation
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
- Cellular component
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)
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.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Mutagenesis | 128 | No GTPase activity, does not restore normal ribosomes to a bipA deletion, does not associate with ribosomes, retains its ability to help proteins refold. | ||||
Sequence: N → D | ||||||
Mutagenesis | 164 | No change in growth at 20 degrees Celsius. | ||||
Sequence: Y → P | ||||||
Mutagenesis | 472 | No change in growth at 20 degrees Celsius. | ||||
Sequence: Y → P | ||||||
Mutagenesis | 519 | No change in growth at 20 degrees Celsius. | ||||
Sequence: Y → P |
PTM/Processing
Features
Showing features for chain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000091550 | 1-607 | Large ribosomal subunit assembly factor BipA | |||
Sequence: MIEKLRNIAIIAHVDHGKTTLVDKLLQQSGTFDSRAETQERVMDSNDLEKERGITILAKNTAIKWNDYRINIVDTPGHADFGGEVERVMSMVDSVLLVVDAFDGPMPQTRFVTKKAFAYGLKPIVVINKVDRPGARPDWVVDQVFDLFVNLDATDEQLDFPIVYASALNGIAGLDHEDMAEDMTPLYQAIVDHVPAPDVDLDGPFQMQISQLDYNSYVGVIGIGRIKRGKVKPNQQVTIIDSEGKTRNAKVGKVLGHLGLERIETDLAEAGDIVAITGLGELNISDTVCDTQNVEALPALSVDEPTVSMFFCVNTSPFCGKEGKFVTSRQILDRLNKELVHNVALRVEETEDADAFRVSGRGELHLSVLIENMRREGFELAVSRPKVIFREIDGRKQEPYENVTLDVEEQHQGSVMQALGERKGDLKNMNPDGKGRVRLDYVIPSRGLIGFRSEFMTMTSGTGLLYSTFSHYDDVRPGEVGQRQNGVLISNGQGKAVAFALFGLQDRGKLFLGHGAEVYEGQIIGIHSRSNDLTVNCLTGKKLTNMRASGTDEAVVLVPPIRMTLEQALEFIDDDELVEVTPTSIRIRKRHLTENDRRRANRAPKDD |
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).
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).
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
Type | Entry 1 | Entry 2 | Number of experiments | Intact | |
---|---|---|---|---|---|
BINARY | P0DTT0 | rlmL P75864 | 3 | EBI-562154, EBI-547718 | |
BINARY | P0DTT0 | ybeY P0A898 | 2 | EBI-562154, EBI-560240 | |
BINARY | P0DTT0 | yigZ P27862 | 2 | EBI-562154, EBI-561235 |
Protein-protein interaction databases
Structure
Family & Domains
Features
Showing features for region, domain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Region | 1-202 | Domain I (or G domain), required for chaperone activity | ||||
Sequence: MIEKLRNIAIIAHVDHGKTTLVDKLLQQSGTFDSRAETQERVMDSNDLEKERGITILAKNTAIKWNDYRINIVDTPGHADFGGEVERVMSMVDSVLLVVDAFDGPMPQTRFVTKKAFAYGLKPIVVINKVDRPGARPDWVVDQVFDLFVNLDATDEQLDFPIVYASALNGIAGLDHEDMAEDMTPLYQAIVDHVPAPDVDLD | ||||||
Domain | 3-198 | tr-type G | ||||
Sequence: EKLRNIAIIAHVDHGKTTLVDKLLQQSGTFDSRAETQERVMDSNDLEKERGITILAKNTAIKWNDYRINIVDTPGHADFGGEVERVMSMVDSVLLVVDAFDGPMPQTRFVTKKAFAYGLKPIVVINKVDRPGARPDWVVDQVFDLFVNLDATDEQLDFPIVYASALNGIAGLDHEDMAEDMTPLYQAIVDHVPAPD | ||||||
Region | 203-320 | Domain II (or beta barrel domain) | ||||
Sequence: GPFQMQISQLDYNSYVGVIGIGRIKRGKVKPNQQVTIIDSEGKTRNAKVGKVLGHLGLERIETDLAEAGDIVAITGLGELNISDTVCDTQNVEALPALSVDEPTVSMFFCVNTSPFCG | ||||||
Region | 303-385 | Domain III | ||||
Sequence: DEPTVSMFFCVNTSPFCGKEGKFVTSRQILDRLNKELVHNVALRVEETEDADAFRVSGRGELHLSVLIENMRREGFELAVSRP | ||||||
Region | 386-482 | Domain V | ||||
Sequence: KVIFREIDGRKQEPYENVTLDVEEQHQGSVMQALGERKGDLKNMNPDGKGRVRLDYVIPSRGLIGFRSEFMTMTSGTGLLYSTFSHYDDVRPGEVGQ | ||||||
Region | 483-607 | C-terminal domain (CTD), binds A-site tRNA | ||||
Sequence: RQNGVLISNGQGKAVAFALFGLQDRGKLFLGHGAEVYEGQIIGIHSRSNDLTVNCLTGKKLTNMRASGTDEAVVLVPPIRMTLEQALEFIDDDELVEVTPTSIRIRKRHLTENDRRRANRAPKDD |
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).
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
Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. BipA subfamily.
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length607
- Mass (Da)67,355
- Last updated2020-02-26 v1
- Checksum3B4DE3A514F95FFB
Features
Showing features for sequence conflict.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Sequence conflict | 592-607 | in Ref. 1; AAB03005 | ||||
Sequence: Missing |
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
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 |