parA

UniProt ID: P0A149
Organism: Pseudomonas putida KT2440
Review Status: DRAFT
Aliases:
PP_0002
📝 Provide Detailed Feedback

Gene Description

ParA (PP_0002) is the ATPase of the Pseudomonas putida ParABS chromosome-partitioning system, encoded immediately next to parB beside oriC. It is a 263-residue deviant Walker-type (ParA/MinD-family) P-loop ATPase related to B. subtilis Soj, with the KGGVGKT Walker A box at residues 11-17. It is 84% identical to P. aeruginosa ParA, whose purified protein hydrolyses ATP, dimerizes and binds ParB. In P. putida, parA mutants produce anucleate cells, mainly in minimal medium as cultures enter stationary phase. Together with ParB, ParA stabilises a plasmid carrying an oriC-region parS-like sequence in E. coli, showing that the P. putida proteins have partition activity of their own.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0016887 ATP hydrolysis activity
ISO
GO_REF:0000024 		NEW
Summary: ParA is a deviant Walker-type ATPase; ATP hydrolysis is measured on its P. aeruginosa ortholog.
Reason: The protein has no GO annotation in GOA at all. The 84%-identical P. aeruginosa ParA hydrolyses ATP as a purified protein, and the P. putida protein keeps the identical deviant Walker A box (KGGVGKT) at the same position. UniProt classes it with B. subtilis Soj (curated similarity). NCBI's SPARCLE architecture for this protein already asserts ATP binding and ATP hydrolysis activity. The P. aeruginosa source annotation is itself proposed (IDA) in the genes/PSEAE/parA review and is not yet in GOA, so this transfer depends on that row being accepted.
Supporting Evidence:
PMID:25139949
ParA-His6 demonstrated ATPase activity (Fig. 3) of ~1.2 pmol Pi released min−1 (pmol ParA)−1.
file:PSEPK/parA/parA-bioinformatics/RESULTS.md
ParA has the deviant Walker A box KGGVGKT at 11-17, the ATP-binding signature of the ParA/MinD family.
file:PSEPK/parA/parA-uniprot.txt
SIMILARITY: To B.subtilis soj.
GO:0007059 chromosome segregation
IMP
PMID:11832517
Chromosome loss from par mutants of Pseudomonas putida depen... 		NEW
Summary: P. putida parA mutants lose chromosomes, and ParAB partitions a parS plasmid.
Reason: Based on P. putida data only. The abstract reports that parA (and parB) mutations raise the frequency of anucleate cells in minimal medium at the transition to stationary phase. ParA together with ParB also stabilises a parS-carrying plasmid in E. coli. Only the abstracts are cached, so the allele structure is not visible here; because parA lies upstream of parB in the same operon, a parA mutation could act partly by a polar effect on parB. The plasmid assay supplies both proteins and does not separate them either. ParA passes the participation test as the partition ATPase that positions the ParB-parS complex.
Supporting Evidence:
PMID:11832517
However, in M9-minimal medium different parA and parB mutations gave between 5 and 10% anucleate cells during the transition from exponential phase to stationary phase.
PMID:11849535
One was inserted into an unstable mini-F and shown to stabilize it in E. coli in a ParAB-dependent manner.
GO:0005524 ATP binding
ISM
file:PSEPK/parA/parA-bioinformatics/RESULTS.md 		NEW
Summary: ParA carries the deviant Walker A ATP-binding box of the ParA/MinD family.
Reason: The deviant Walker A box KGGVGKT at residues 11-17 is the ATP-binding signature of the ParA/MinD family and is identical in the directly assayed P. aeruginosa ParA. NCBI's architecture already asserts this term. It is recorded separately from ATP hydrolysis activity because GO does not derive one from the other.
Supporting Evidence:
file:PSEPK/parA/parA-bioinformatics/RESULTS.md
ParA has the deviant Walker A box KGGVGKT at 11-17, the ATP-binding signature of the ParA/MinD family.

Core Functions

Deviant Walker-type ATPase of the ParABS system that, with ParB bound at the oriC-region parS sites, segregates replicated chromosome origins. The activity is inferred from the P. aeruginosa ortholog and the conserved Walker A box; the partition role is shown in P. putida.

Molecular Function:
ATP hydrolysis activity
Directly Involved In:
chromosome segregation
Supporting Evidence:
  • PMID:25139949
    ParA-His6 demonstrated ATPase activity (Fig. 3) of ~1.2 pmol Pi released min−1 (pmol ParA)−1.
  • PMID:11832517
    However, in M9-minimal medium different parA and parB mutations gave between 5 and 10% anucleate cells during the transition from exponential phase to stationary phase.

References

Loading supporting content…

Download this section (compressed HTML)

Suggested Questions for Experts

Q: Why are P. putida par mutants defective mainly when cells divide without ongoing replication (minimal medium, entry into stationary phase), when P. aeruginosa par mutants are defective during exponential growth?

Q: Is P. putida ParA ATPase stimulated by ParB and by non-specific DNA, as for SopA and P1 ParA?

Suggested Experiments

Experiment: Purify P. putida ParA and measure ATP hydrolysis alone and with ParB, parS DNA and non-specific DNA.

Hypothesis: P. putida ParA is a weak ATPase stimulated by ParB and DNA, like its orthologs.

Type: enzyme assay

External Prediction Reviews

These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.

NCBI PGAP External predictions

View prediction review YAML · parA-pgap-predictions-review.yaml · Review status: COMPLETE

NCBI PGAP names WP_003253182.1 "ParA family protein" from SPARCLE CDD architecture 11439703 (a single COG1192 ParA region) and passes on ATP binding and ATP hydrolysis activity. Both are correct. This is a case where CDD architecture GO fills a gap that UniProt/GOA leaves completely open: GOA has no annotation of any kind for this protein. UniProt keeps the Swiss-Prot entry as "Uncharacterized protein PP_0002", and its Pfam (AAA_31) and PANTHER (PTHR13696:SF52) matches bring no GO. The main review proposes ATP hydrolysis activity as the core function, on the basis of the 84%-identical P. aeruginosa ParA and the conserved Walker A box, and adds ATP binding as a separate row from the same motif. Neither pipeline provides the process: chromosome segregation is supported directly by P. putida parA mutants, but the ParA architecture carries no process term.

Source documents: genes/PSEPK/parA/parA-pgap-prediction-evidence/WP_003253182.1.gp · genes/PSEPK/parA/parA-pgap-prediction-evidence/pgap_models.yaml

Review score: 2 = concordant with evidence; 1 = uncertain; 0 = discordant with evidence. This is an assessment score, not a model probability.

GO:0005524 ATP binding GO_MF
COR — Correct novel prediction Review score: 2/2
Prediction method: NCBI PGAP · Version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record · PMID:33270901
Review rationale: Correct and not in GOA. ParA binds ATP through its deviant Walker A box (KGGVGKT, residues 11-17), conserved and identically placed in the characterized P. aeruginosa ortholog. The main review adds it as a NEW row (ISM). GO does not derive ATP binding from ATP hydrolysis activity, which sits in a separate branch, so the term carries information of its own.
Supporting Evidence:
GO:0016887 ATP hydrolysis activity GO_MF
COR — Correct novel prediction Review score: 2/2
Prediction method: NCBI PGAP · Version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record · PMID:33270901
Review rationale: Correct and not in GOA, which has no annotation for this protein. The 84%-identical P. aeruginosa ParA hydrolyses ATP as a purified protein. The main review proposes this term as the core molecular function (NEW, ISO).
Supporting Evidence:
  • PMID:25139949: "ParA-His6 demonstrated ATPase activity (Fig. 3) of ~1.2 pmol Pi released min−1 (pmol ParA)−1."

📚 Additional Documentation

Notes

(parA-notes.md)

Loading supporting content…

Download this section (compressed HTML)

Bioinformatics Results

(RESULTS.md)

Loading supporting content…

Download this section (compressed HTML)

📄 View Raw YAML

Loading supporting content…

Download this section (compressed HTML)