gatB

UniProt ID: Q88PC0
Organism: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
Review Status: DRAFT
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Gene Description

GatB is the ATP-dependent synthetase subunit of the GatABC tRNA-dependent amidotransferase in Pseudomonas putida KT2440. In the heterotrimer it activates the tRNA-bound glutamyl or aspartyl side chain for ammonia transfer, enabling formation of Gln-tRNA(Gln) or Asn-tRNA(Asn).

Existing Annotations Review

GO Term Evidence Action Reason
GO:0003824 catalytic activity
IEA
GO_REF:0000002
MARK AS OVER ANNOTATED
Summary: Generic catalytic activity is true but uninformative beside the two separately annotated GatABC synthase activities.
Reason: GO:0050566 and GO:0050567 already capture the Asn- and Gln-tRNA transamidation reactions specifically.
Supporting Evidence:
file:PSEPK/gatB/gatB-uniprot.txt
Reaction=L-glutamyl-tRNA(Gln) + L-glutamine + ATP + H2O
GO:0006412 translation
IEA
GO_REF:0000104
KEEP AS NON CORE
Summary: GatB supports translation, but its direct role is tRNA transamidation.
Reason: Translation is a downstream context broader than either GatABC charging reaction.
Supporting Evidence:
file:PSEPK/gatB/gatB-uniprot.txt
Allows the formation of correctly charged Asn-tRNA(Asn) or
GO:0016874 ligase activity
IEA
GO_REF:0000120
MARK AS OVER ANNOTATED
Summary: Generic ligase activity is correct but uninformative beside the two separately annotated GatABC synthase activities.
Reason: GO:0050566 and GO:0050567 already capture ATP-dependent ligation on the two tRNA-bound substrates.
Supporting Evidence:
file:PSEPK/gatB/gatB-uniprot.txt
Reaction=L-glutamyl-tRNA(Gln) + L-glutamine + ATP + H2O
GO:0016884 carbon-nitrogen ligase activity, with glutamine as amido-N-donor
IEA
GO_REF:0000002
MARK AS OVER ANNOTATED
Summary: The broad amido-N-donor ligase term is true but uninformative beside the two tRNA-specific activities.
Reason: GO:0050566 and GO:0050567 already capture the exact Asn-tRNA(Asn) and Gln-tRNA(Gln) products.
Supporting Evidence:
file:PSEPK/gatB/gatB-uniprot.txt
Reaction=L-glutamyl-tRNA(Gln) + L-glutamine + ATP + H2O
GO:0030956 glutamyl-tRNA(Gln) amidotransferase complex
IEA
GO_REF:0000104
ACCEPT
Summary: GatB is a required subunit of heterotrimeric GatABC.
Reason: UniProt explicitly specifies the A/B/C heterotrimer.
Supporting Evidence:
file:PSEPK/gatB/gatB-uniprot.txt
SUBUNIT: Heterotrimer of A, B and C subunits.
GO:0050566 asparaginyl-tRNA synthase (glutamine-hydrolyzing) activity
IEA
GO_REF:0000120
MARK AS OVER ANNOTATED
Summary: GatABC can form Asn-tRNA(Asn) by transamidating Asp-tRNA(Asn).
Reason: The reviewed entry includes the exact asparaginyl-tRNA synthase reaction, but GatB contributes to rather than independently enables the whole-complex activity.
Supporting Evidence:
file:PSEPK/gatB/gatB-uniprot.txt
Reaction=L-aspartyl-tRNA(Asn) + L-glutamine + ATP + H2O
GO:0050567 glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity
IEA
GO_REF:0000120
MARK AS OVER ANNOTATED
Summary: GatABC can form Gln-tRNA(Gln) by transamidating Glu-tRNA(Gln).
Reason: The reviewed entry includes the exact glutaminyl-tRNA synthase reaction, but GatB contributes to rather than independently enables the whole-complex activity.
Supporting Evidence:
file:PSEPK/gatB/gatB-uniprot.txt
Reaction=L-glutamyl-tRNA(Gln) + L-glutamine + ATP + H2O
GO:0070681 glutaminyl-tRNAGln biosynthesis via transamidation
IEA
GO_REF:0000120
UNDECIDED
Summary: GatABC has the reaction capacity, but this route is not established in KT2440.
Reason: The reaction requires Glu-tRNA(Gln), but KT2440 has direct GlnRS and no evidence establishes that its GltX supplies this misacylated precursor. The characterized Pseudomonas aeruginosa system instead uses discriminating GluRS and direct GlnRS.
Supporting Evidence:
file:PSEPK/gatB/gatB-uniprot.txt
Reaction=L-glutamyl-tRNA(Gln) + L-glutamine + ATP + H2O
PMID:14729703
GluRS is discriminating in the sense that it does not glutamylate tRNA(Gln)
GO:0043039 tRNA aminoacylation
ISS
PMID:14729703
Direct glutaminyl-tRNA biosynthesis and indirect asparaginyl...
NEW
Summary: GatB participates directly in indirect Asn-tRNA(Asn) formation from Asp-tRNA(Asn).
Reason: The KT2440 GatB record contains the exact asparaginyl-tRNA synthase reaction, and the corresponding ND-AspRS/GatABC route is experimentally established in Pseudomonas aeruginosa. This row originally proposed GO:0070680 asparaginyl-tRNAAsn biosynthesis via transamidation, which is obsolete in the GO release 2026-07-26. Its replaced_by, GO:0070981 L-asparagine biosynthetic process, is not used because the indirect route ends at Asn-tRNA(Asn), not free asparagine, so GO:0043039 tRNA aminoacylation (the is_a parent of the obsolete term) is asserted instead. The GOA descendant GO:0070681 (glutaminyl-tRNAGln biosynthesis via transamidation) does not make this row redundant: that row is UNDECIDED here because the Gln transamidation route is not established in KT2440, whereas this row rests on the Asn route.
Supporting Evidence:
file:PSEPK/gatB/gatB-uniprot.txt
Reaction=L-aspartyl-tRNA(Asn) + L-glutamine + ATP + H2O
PMID:14729703
The essential role of AdT in the formation of Asn-tRNA in P. aeruginosa

Core Functions

Activates Asp-tRNA(Asn) within GatABC for glutamine-dependent transamidation to Asn-tRNA(Asn), the required indirect Asn charging route in KT2440.

Supporting Evidence:
  • file:PSEPK/gatB/gatB-uniprot.txt
    Reaction=L-aspartyl-tRNA(Asn) + L-glutamine + ATP + H2O

References

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Notes

(gatB-notes.md)

gatB curation notes

  • Q88PC0 is the ATP-dependent GatB subunit of heterotrimeric GatABC
    [file:PSEPK/gatB/gatB-uniprot.txt, "SUBUNIT: Heterotrimer of A, B and C subunits."].
  • The reviewed record includes both Glu-tRNA(Gln) and Asp-tRNA(Asn)
    transamidation reactions [file:PSEPK/gatB/gatB-uniprot.txt,
    "Reaction=L-glutamyl-tRNA(Gln) + L-glutamine + ATP + H2O"].
  • The Asn-forming reaction is required in the PSEPK pathway because the genome
    has non-discriminating AspS but no canonical AsnRS; the corresponding route
    is experimentally established in Pseudomonas aeruginosa
    [PMID:14729703, "The essential role of AdT in the formation of Asn-tRNA in P. aeruginosa"].

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