HolD is the divergent psi accessory subunit of the Pseudomonas putida KT2440 clamp-loader system, encoded at PP_0696. It forms a complex with HolC/chi and is inferred to connect and stabilize the accessory assembly on the DnaX-containing loader. Purified KT2440 chiโpsi binds single-stranded DNA under low-salt conditions; experiments on homologous Pseudomonas complexes attribute this binding to the psi N-terminal region. The literature uses a corrected noncanonical start predicting a 261-residue native protein, whereas Q88Q02 retains an older 291-residue translation. The characterized fusion insert corresponds to database residues 32โ291 and does not establish a function for the upstream extension.
The protein sequence of this entry may not correspond to a single real gene product (for example, two neighbouring genes joined into one model, or a truncated model). Read the name, features and annotations of the entry with this in mind.
WRONG START SITE CONFIRMED GENOMIC SEQUENCEOTHER
The frozen Q88Q02 model contains 291 residues. The literature-selected TTG initiation codon at AE015451.2 position 809524 predicts 261 residues, corresponding to database positions 31โ291 with initiator methionine replacing the internal leucine at position 31. Independently mapping the published KT2440 primers identifies a 260-residue GST-fusion insert at database positions 32โ291, excluding the native initiator; the fusion was cleaved during purification. Thus the reviewed functional construct excludes the upstream 30-residue extension. CONFIRMED refers to the literature/model and construct-coordinate discrepancy, not newly demonstrated native N-terminal sequencing or exclusion of every possible alternative initiation product.
Segment reviewed: residues 32-291
Supported by:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003689 DNA clamp loader activity | ISS PMID:16210315 Discovery and characterization of the cryptic psi subunit of... | NEW | Summary: The divergent psi accessory subunit contributes to the multisubunit clamp loader. Reason: Primer mapping establishes PP_0696/Q88Q02 as the KT2440 holD locus used for chiโpsi expression in PMID21955458. The original Pseudomonas psi discovery/reconstitution (PMID16210315) assigns the chiโpsi accessory assembly to stimulation of the DnaX loader, and E. coli experiments (PMID17210572) dissect psi-dependent stabilization. This is a conserved contribution to complex activity, not complete clamp loading by isolated HolD. The full older291-residue translation was not tested: the mapped insert covers residues32โ291 and the corrected native261-residue start is documented. No seed MF exists and this proposal does not duplicate the separate ssDNA-binding function. Supporting Evidence: file:PSEPK/holC/holC-source-analysis/README.md The psi primers map PP_0696, AAN66321.1, Q88Q02, not neighboring PP_0978. PMID:21955458 The holC and holD genes of P. putida were amplified by PCR from genomic DNA of P. putida strain KT2440 PMID:16210315 aeruginosa chiPsi increased the specific activity of tau(3)deltadelta' 25-fold and enabled the holoenzyme to function under physiological salt conditions. PMID:17210572 The psi subunit is important for stabilizing an ATP-induced conformational state with high affinity for DNA |
| GO:0003697 single-stranded DNA binding | IDA PMID:21955458 Characterization of the ฯฯ subcomplex of Pseudomonas aerugin... | NEW | Summary: The KT2440 chiโpsi complex binds ssDNA in vitro, with psi assigned the DNA-engaging contribution. Reason: Sedimentation experiments directly show ssDNA binding by the purified KT2440 complex under low-salt conditions. Chimeric and N-terminal truncation experiments in the homologous P. aeruginosa system assign direct DNA engagement to psi. The contributes_to qualifier preserves the complex-level nature of the KT2440 measurement; isolated Q88Q02 was not assayed. Identity maps to the corrected-start expression construct, not the old upstream extension. The native significance and affinity at physiological ionic strength remain unresolved, so this capability is not presented as a separate established core role. It is not a duplicate of the ATP-driven clamp-loader contribution. Supporting Evidence: file:PSEPK/holC/holC-source-analysis/README.md The psi primers map PP_0696, AAN66321.1, Q88Q02, not neighboring PP_0978. PMID:21955458 The holC and holD genes of P. putida were amplified by PCR from genomic DNA of P. putida strain KT2440 PMID:21955458 P. putida (Ppu) ฯฯ, similarly to Paeฯฯ, increased the sedimentation coefficient of poly(dT), indicating ssDNA-binding |
| GO:0006261 DNA-templated DNA replication | IC PMID:21955458 Characterization of the ฯฯ subcomplex of Pseudomonas aerugin... | NEW | Summary: The psi accessory component contributes physical organization of the replicative clamp loader. Reason: HolD contributes physical assembly and stabilization of the chi-containing clamp-loader accessory unit rather than merely being necessary for growth. The KT2440 clone-to-locus mapping and direct chiโpsi complex characterization combine with characterized Pseudomonas clamp-loader reconstitution to support participation in DNA-templated DNA replication. The process uses parental DNA, matching GO:0006261 and the core function; RNA-templated replication is not the demonstrated context. Same-role loader accessory comparators support this annotation convention, not the experimental claim itself. This proposal was authored in PR6117 commit 47acac27a0 and is refined here under an explicit archived-proposal exception; it was inherited only by a later review-round snapshot, not from upstream GOA or main. No redundant ancestor proposal is retained, and no KT2440 knockout-essentiality, firing regulation or function of the untested upstream extension is asserted. Supporting Evidence: file:PSEPK/holC/holC-source-analysis/README.md The psi primers map PP_0696, AAN66321.1, Q88Q02, not neighboring PP_0978. PMID:21955458 The holC and holD genes of P. putida were amplified by PCR from genomic DNA of P. putida strain KT2440 PMID:16210315 aeruginosa chiPsi increased the specific activity of tau(3)deltadelta' 25-fold and enabled the holoenzyme to function under physiological salt conditions. |
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