Organism: Pseudomonas putida KT2440 (strain ATCC 47054 / DSM 6125 / NCIMB 11950)
Locus: PP_2800 · Gene product: Diaminobutyrate–2-oxoglutarate transaminase (putative)
Protein: 417 aa, ~45.25 kDa · UniProt: Q88J49 (unreviewed, TrEMBL) · RefSeq: WP_010953709.1
EC / KO: EC 2.6.1.76 / KEGG K00836
PP_2800 encodes a soluble, cytoplasmic, pyridoxal-5′-phosphate (PLP)-dependent class-III (ω-)aminotransferase of the DAT/EctB family (diaminobutyrate–2-oxoglutarate transaminase, EC 2.6.1.76). Enzymes of this family catalyze the reversible transfer of an amino group between the distal (ω) position of a C4 amino-acid semialdehyde and 2-oxoglutarate/glutamate, interconverting L-aspartate-β-semialdehyde + L-glutamate ⇌ L-2,4-diaminobutyrate (DABA) + 2-oxoglutarate. This assignment is based on sequence homology and conserved-domain signatures only — there is no direct experimental characterization of the PP_2800 protein. Importantly, although the DAT/EctB reaction is the canonical first, rate-limiting step of ectoine biosynthesis, P. putida KT2440 lacks the downstream ectoine genes (ectA, ectC, ectD) and therefore cannot make ectoine. The genome encodes two K00836 paralogs (PP_2800 and PP_4223, ~51 % identical) that are functionally partitioned: PP_4223 lies inside the pyoverdine (ferribactin-synthase) NRPS cluster and is the parsimonious supplier of L-2,4-diaminobutyrate (L-Dab) for the pyoverdine siderophore, whereas PP_2800 sits in a separate GABA/diamine metabolism cluster. Thus the physiological role of PP_2800 is best interpreted as cytoplasmic metabolism/interconversion of C4 amino compounds (aspartate-β-semialdehyde/DABA-, and possibly GABA-type ω-amino substrates), rather than siderophore or compatible-solute synthesis.
Domain/family evidence (bioinformatic). UniProt and InterPro assign PP_2800 to:
- Pfam PF00202 Aminotran_3 (class-III aminotransferase); PROSITE PS00600 (class-III PLP AA-transferase active-site motif).
- TIGRFAM TIGR00709 "dat" and NCBIfam NF006733 / PRK09264, both specific to 2,4-diaminobutyrate:2-oxoglutarate 4-aminotransferases.
- PANTHER PTHR43552:SF2 "diaminobutyrate–2-oxoglutarate transaminase."
- InterPro: IPR004637 (Dat), IPR005814/IPR049704 (Aminotrans_3), IPR015421/15424 (PLP-dependent transferase, major/fold).
- eggNOG COG0160 (4-aminobutyrate aminotransferase and related aminotransferases).
- Cofactor: pyridoxal-5′-phosphate (GO:0030170, PLP binding).
Confidence level in UniProt is PE 3 "Inferred from homology" — i.e., predicted, not experimentally verified for this protein.
The catalyzed reaction (from characterized family members). The founding biochemical study of the Acinetobacter baumannii Dat enzyme purified the protein and demonstrated the reversible reaction "L-2,4-diaminobutyric acid + 2-ketoglutaric acid ⇌ L-glutamic acid + L-aspartic beta-semialdehyde" (Ikai & Yamamoto, 1997, PMID 9260954). Recent structural/biochemical work on EctB confirms the physiological direction "converts aspartate-β-semialdehyde (ASA) to DABA" and that this is "the rate-limiting step of ectoine biosynthesis" (Skogvold et al., 2026, PMID 41652856).
Substrate specificity. DABA aminotransferases are ω-transaminases that aminate the distal ω-position of their substrate. Structural work on Chromohalobacter salexigens EctB provided "the first description of two binding pockets in the active site that may account for the catalytic character of DABA aminotransferases" (Hillier et al., 2020, PMID 32112674), explaining the characteristic dual-substrate specificity (one pocket for the amino donor/glutamate, one for the C4 amino-acceptor). Consistent with broad specificity, the Marinobacter EctB showed "activity was highest using DABA and GABA as substrates" (PMID 41652856). Such promiscuity means the exact in-vivo substrate of PP_2800 cannot be fixed from homology alone.
PP_2800 is predicted to be a cytoplasmic (cytosolic) soluble enzyme. This is inferred from: (i) it is a PLP-dependent central-metabolism aminotransferase, a class that is universally cytosolic; (ii) the sequence begins MNKIETFERL… with no Sec/Tat signal peptide and no transmembrane segment; and (iii) characterized homologs (EctB, Dat) are soluble oligomeric proteins purified from the cytosol. Family members assemble as homotetramers built from two functional dimers, with a "gating loop" from the neighboring monomer helping to shape each active site (PMID 32112674).
Canonical pathway (in ectoine producers). DABA aminotransferase (EctB) performs the first committed step of ectoine biosynthesis: ASA → DABA; DABA is then N-acetylated by EctA and cyclized by EctC (ectoine synthase) to ectoine, optionally hydroxylated by EctD to 5-hydroxyectoine (PMID 32112674; PMID 38960226). The same Dat reaction also feeds, together with a DABA decarboxylase (Ddc), the 1,3-diaminopropane pathway in Acinetobacter and Haemophilus (PMID 9260954; PMID 9514614), and can participate in promiscuous routes such as a "β-alanine biosynthetic pathway consisting of promiscuous metabolic enzymes … including 2,4-diaminobutyrate aminotransferase (Dat) and 2,4-diaminobutyrate decarboxylase (Ddc)" (Perchat et al., 2022, PMID 35623386).
Why the canonical roles do not apply directly to KT2440. A KEGG genome-wide orthology check shows P. putida KT2440 encodes the DABA-aminotransferase ortholog K00836 as two paralogs (PP_2800 and PP_4223) but has no ectA (K06718), no ectC (K06720), and no ectD (K10674). The ectoine pathway is therefore genetically incomplete, and PP_2800 cannot support ectoine synthesis. No DABA decarboxylase (ddc) is present adjacent to PP_2800 either, arguing against a dedicated 1,3-diaminopropane operon at this locus.
Genomic-neighborhood evidence. PP_2800 sits (complement strand, ~3.190–3.192 Mb) within a tight cluster of C4-amino/ω-amino-compound metabolism genes:
| Locus | Product | KO / EC |
|---|---|---|
| PP_2799 | 4-aminobutyrate(GABA)–pyruvate transaminase (class III) | K16871 / 2.6.1.96 |
| PP_2800 | DABA–2-oxoglutarate transaminase | K00836 / 2.6.1.76 |
| PP_2801 | 4-aminobutyraldehyde dehydrogenase | K00137 / 1.2.1.19 |
| PP_2802 | amino-acid permease | – |
| PP_2806 | TetR-family transcriptional regulator | – |
The co-occurrence of a GABA aminotransferase, an aminobutyraldehyde dehydrogenase (an enzyme of putrescine/polyamine→GABA catabolism), an amino-acid permease and a local TetR regulator indicates a locus dedicated to uptake and catabolic interconversion of 4-carbon amino compounds (GABA/polyamine-derived intermediates). Given the broad ω-transaminase specificity of the family, the most defensible interpretation is that PP_2800 supplies transamination of aspartate-β-semialdehyde/DABA (and possibly related ω-amino substrates such as GABA) feeding cytoplasmic amino-acid/polyamine metabolism, rather than a compatible-solute pathway.
P. putida KT2440 carries two K00836 DABA-aminotransferase paralogs, PP_2800 and PP_4223, which share 50.9 % amino-acid identity (global alignment, 201/395 aligned positions) and both retain the conserved class-III catalytic-lysine motif (PP_2800 …ICDEIQAGCGRTGD…TCAK…; PP_4223 …IVDEIQSGFARTGR…TLSK…). Crucially, their genomic contexts differ completely:
This partition means the siderophore role attributed to the orthology should be assigned primarily to PP_4223, whereas PP_2800 most likely serves general cytoplasmic amino-acid/diamine (C4 ω-amino) metabolism. The two enzymes may retain overlapping DABA-transaminase activity (potential partial redundancy), but their distinct genomic niches argue for distinct primary roles.
Orthology test (decisive). P. aeruginosa PAO1 carries a single K00836 gene, PA2413 = PvdH ("diaminobutyrate--2-oxoglutarate aminotransferase"), located within its pyoverdine locus and experimentally required to supply L-Dab for pyoverdine. Global pairwise identity shows PP_4223 is 85.7 % identical to PvdH (382/446), i.e. its clear ortholog, while PP_2800 is only 54.4 % identical to PvdH (211/388). This confirms with high confidence that the pyoverdine DABA-transaminase function in P. putida is carried by PP_4223 (the PvdH ortholog), and PP_2800 is a lineage-specific duplication whose primary role lies outside siderophore biosynthesis, consistent with its GABA/diamine-cluster context.