RecB is the helicase-nuclease subunit of the heterotrimeric RecBCD enzyme (RecB-RecC-RecD; also called Exonuclease V), the major bacterial machine that initiates processing of double-strand DNA ends for homologous recombination and double-strand break repair. RecB is a bipartite, ATP-dependent enzyme. Its N-terminal motor domain is a single-strand-DNA-dependent ATPase with 3'-5' helicase activity that, together with RecD (a 5'-3' motor) and RecC, drives rapid, processive unwinding of duplex DNA from a blunt or near-blunt end. Its C-terminal domain carries a Mg2+-dependent nuclease center that degrades the unwound strands and, after recognition of a Chi recombination hotspot, nicks the 3'-ended strand and loads the RecA recombinase onto the resulting 3' single-stranded tail. The product of this reaction is a recombinogenic 3' overhang coated with RecA, committing the broken end to RecA-mediated strand invasion and downstream RuvABC-dependent resolution. RecBCD also rescues collapsed or broken replication forks. The enzyme acts on chromosomal DNA in the cytoplasm and nucleoid. Chi recognition is species-specific, and the cognate octamer differs among pseudomonads from the E. coli consensus.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0000166
nucleotide binding
|
IEA
GO_REF:0000104 |
MARK AS OVER ANNOTATED |
Summary: RecB is an ATP-binding/ATP-hydrolyzing motor protein, so nucleotide binding is correct but it is a broad parent of the more specific ATP binding annotation.
Reason: Correct but uninformative; subsumed by the specific GO:0005524 ATP binding annotation, which captures the relevant nucleotide-binding activity.
|
|
GO:0000287
magnesium ion binding
|
IEA
GO_REF:0000104 |
ACCEPT |
Summary: The RecB C-terminal nuclease center requires a divalent metal (Mg2+/Mn2+) for exodeoxyribonuclease V activity, consistent with this annotation.
Reason: Mg2+ dependence of the RecB PD-(D/E)XK nuclease center is well established for RecBCD/Exonuclease V and supported by the UvrD/AddAB-type nuclease domain.
|
|
GO:0000724
double-strand break repair via homologous recombination
|
IEA
GO_REF:0000104 |
ACCEPT |
Summary: RecBCD initiates double-strand break repair by homologous recombination; this is the central biological process for RecB.
Reason: Strongly supported by conserved RecBCD biology and by pseudomonad genetics (recB null mutants are UV/mitomycin C sensitive and accumulate fragmented chromosomal DNA); a core function.
Supporting Evidence:
file:PSEPK/recB/recB-deep-research-falcon.md
|
|
GO:0000725
recombinational repair
|
IEA
GO_REF:0000118 |
KEEP AS NON CORE |
Summary: RecB participates in recombinational repair; this is a broader parent of GO:0000724 double-strand break repair via homologous recombination.
Reason: Accurate but more general than the specific DSB-via-HR term, which better represents the core process; retain as supporting/non-core.
|
|
GO:0003677
DNA binding
|
IEA
GO_REF:0000120 |
KEEP AS NON CORE |
Summary: RecB binds duplex and single-stranded DNA as part of its helicase/nuclease activity; a true but general molecular function.
Reason: Correct supporting activity, but subsumed by the more informative helicase and exonuclease V molecular-function annotations.
|
|
GO:0003678
DNA helicase activity
|
IEA
GO_REF:0000120 |
KEEP AS NON CORE |
Summary: RecB has ATP-dependent DNA helicase activity; this is captured more precisely by GO:0043138 (3'-5' DNA helicase activity).
Reason: Correct but a parent of the more specific 3'-5' DNA helicase activity term.
|
|
GO:0004386
helicase activity
|
IEA
GO_REF:0000104 |
MARK AS OVER ANNOTATED |
Summary: General helicase activity; a broad parent of the DNA-specific and directionally specific helicase terms.
Reason: Uninformative high-level term subsumed by GO:0003678 and GO:0043138.
|
|
GO:0005524
ATP binding
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: RecB has a P-loop/Walker A motif and binds ATP to power its motor activity; correct and informative.
Reason: ATP binding by the RecB helicase motor is well supported by domain architecture and conserved RecBCD biochemistry.
|
|
GO:0005829
cytosol
|
IEA
GO_REF:0000118 |
KEEP AS NON CORE |
Summary: RecBCD acts on chromosomal DNA ends in the cytoplasm/nucleoid; a cytosolic localization is consistent.
Reason: Reasonable localization for a DNA-repair enzyme but inferred (TreeGrafter); the functionally relevant compartment is the nucleoid-associated cytoplasm.
|
|
GO:0006281
DNA repair
|
IEA
GO_REF:0000002 |
KEEP AS NON CORE |
Summary: RecB functions in DNA repair; a broad parent of the more specific DSB repair via HR term.
Reason: Correct but general; subsumed by GO:0000724.
|
|
GO:0008854
exodeoxyribonuclease V activity
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: RecB carries the nuclease activity of Exonuclease V (EC 3.1.11.5), the defining enzymatic function of the RecBCD complex.
Reason: Core molecular function; supported by the RecB C-terminal PD-(D/E)XK nuclease domain and EC mapping, consistent across RecBCD enzymes.
|
|
GO:0009338
exodeoxyribonuclease V complex
|
IEA
GO_REF:0000118 |
ACCEPT |
Summary: RecB is a subunit of the RecBCD (Exonuclease V) complex together with RecC and RecD; correct cellular-component/complex assignment.
Reason: RecB is an obligate subunit of the heterotrimeric RecBCD/ExoV complex; a core part_of annotation.
|
|
GO:0016787
hydrolase activity
|
IEA
GO_REF:0000120 |
MARK AS OVER ANNOTATED |
Summary: Very general hydrolase parent term; RecB hydrolyzes both ATP and phosphodiester bonds, but this term is uninformative.
Reason: Root-level molecular function subsumed by specific nuclease and ATP hydrolysis annotations.
|
|
GO:0016887
ATP hydrolysis activity
|
IEA
GO_REF:0000116 |
ACCEPT |
Summary: RecB couples ATP hydrolysis to DNA unwinding/translocation (Rhea:13065); correct and informative for the motor function.
Reason: ATPase activity driving the RecB helicase motor is well established and supported by Rhea mapping.
|
|
GO:0043138
3'-5' DNA helicase activity
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: RecB is the 3'-5' helicase motor of RecBCD, translocating along the 3'-ended strand; the most specific and correct helicase term.
Reason: Core molecular function; the 3'-5' directionality of the RecB motor is a defining mechanistic feature of RecBCD.
|
Q: What is the cognate Chi (recombination hotspot) sequence recognized by P. putida KT2440 RecBCD, and does it differ from the E. coli consensus and the P. syringae ChiPs octamer?
Experiment: Construct a P. putida KT2440 recB (PP_4673) deletion and complement with wild-type and motor-dead/nuclease-dead alleles to test sensitivity to UV and mitomycin C and quantify homologous recombination capacity.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
The user-specified target is UniProt Q88DZ5, annotated as RecBCD enzyme subunit RecB (Exonuclease V / DNA 3′→5′ helicase subunit RecB) from Pseudomonas putida KT2440. Within the retrieved literature corpus, I did not find a primary source that explicitly maps UniProt Q88DZ5 (or locus PP_4673) to a specific experimental construct or phenotype in P. putida KT2440; therefore, organism-specific interpretation for KT2440 necessarily relies on (i) general RecBCD/RecB mechanistic literature and (ii) Pseudomonas (non-KT2440) RecBCD studies plus KT2440 pathway-context studies. This report does not reassign the gene to another identity.
RecB is the multifunctional helicase–nuclease subunit of the RecBCD complex (RecB–RecC–RecD), historically called Exonuclease V. RecBCD initiates the major bacterial pathway for processing DNA double-strand ends (DSEs) into recombinogenic substrates for homologous recombination (HR) and double-strand break (DSB) repair. (Dec 2023 review: Amundsen & Smith, Microbiology and Molecular Biology Reviews, 2023-12-20, https://doi.org/10.1128/mmbr.00041-23) (amundsen2023recbcdenzymemechanistic pages 1-2)
RecBCD is an ATP-dependent helicase–nuclease that binds blunt or nearly blunt dsDNA ends, unwinds DNA extremely rapidly and processively, and degrades DNA strands during unwinding. The complex can unwind at ~1 kb/s and can be highly processive (≥100 kb), with RecB contributing the 3′→5′ motor/translocase activity and a Mg2+-dependent nuclease domain responsible for end-processing. (Amundsen & Smith 2023, https://doi.org/10.1128/mmbr.00041-23) (amundsen2023recbcdenzymemechanistic pages 4-6)
Mechanistically, RecBCD’s coordinated motors drive strand separation: RecB translocates along the 3′-ended strand while RecD translocates along the 5′-ended strand, creating asymmetric intermediates (ssDNA tails/loops) and enabling coupled nuclease processing. (Amundsen & Smith 2023, https://doi.org/10.1128/mmbr.00041-23) (amundsen2023recbcdenzymemechanistic pages 2-4)
A defining concept for RecBCD-mediated repair is Chi (χ): short, oriented recombination hotspot sequences that regulate RecBCD’s nuclease and recombination-promoting activities. In E. coli, Chi is the octamer 5′-GCTGGTGG-3′ and is recognized when present in the correct orientation relative to the DNA end at which RecBCD loaded. Chi recognition triggers a switch in RecBCD behavior such that RecB nicks the 3′-ended strand ~5 nt to the 3′ side of Chi and RecBCD then promotes RecA loading on the emergent 3′ ssDNA tail. (Amundsen & Smith 2023, https://doi.org/10.1128/mmbr.00041-23; Smith 2012, MMBR, 2012-06-01, https://doi.org/10.1128/mmbr.05026-11) (amundsen2023recbcdenzymemechanistic pages 4-6, smith2012howrecbcdenzyme pages 2-4)
Chi recognition is species-specific in many bacteria. In Pseudomonas syringae Lz4W, a cognate Chi-like octamer (ChiPs) was identified as 5′-GCTGGCGC-3′, illustrating that pseudomonads can use a different regulatory octamer than E. coli. (Pavankumar et al., PLOS ONE, 2018-05-16, https://doi.org/10.1371/journal.pone.0197476) (pavankumar2018biochemicalcharacterizationof pages 1-2)
RecB is functionally bipartite (helicase/translocase + nuclease/RecA-loading functions), and interdomain connectivity is mechanistically important. RecB’s nuclease domain is connected to the helicase domain via a short tether in models synthesized from genetics/structures, and Chi-triggered control involves conformational communication between RecC (Chi recognition tunnel) and RecB (nuclease/RecA loading). (Amundsen & Smith 2023, https://doi.org/10.1128/mmbr.00041-23) (amundsen2023recbcdenzymemechanistic pages 4-6)
A 2024 mechanistic study further refined the model of Chi-dependent RecA loading by showing that the RecB nuclease domain can trans-complement a truncated RecBCD complex lacking that domain, supporting a Chi-induced rearrangement that exposes the RecA-loading surface rather than requiring a strictly tethered “swing-out” action. (Pavankumar et al., Nucleic Acids Research, 2024-01-16, https://doi.org/10.1093/nar/gkae007) (pavankumar2024transcomplementationbythe pages 1-2)
RecBCD-mediated processing is central to bacterial DSB repair and also to replication-fork rescue: RecBCD acts on DSEs produced by collapsed forks (one-ended DSBs) and other replication stress events, generating the 3′ ssDNA substrate for RecA-mediated strand invasion, with downstream branch migration/resolution involving RuvABC. (Sinha et al., FEMS Microbiology Reviews, 2020-04-01, https://doi.org/10.1093/femsre/fuaa009) (sinha2020therolesof pages 2-3)
No KT2440-specific localization imaging for RecB was retrieved. Functionally, RecBCD acts on chromosomal DNA ends and replication-associated DNA structures; thus, the relevant localization is cytoplasmic/nucleoid-associated, not membrane-embedded or secreted. (Amundsen & Smith 2023; Sinha et al. 2020) (amundsen2023recbcdenzymemechanistic pages 4-6, sinha2020therolesof pages 2-3)
In the Antarctic pseudomonad Pseudomonas syringae Lz4W, null mutations of recB, recC, or recD (or deletion of the full recCBD operon) cause sensitivity to UV and mitomycin C and a strong growth/viability defect at 4°C, with accumulation of linear chromosomal DNA and short DNA fragments—phenotypes consistent with defective DSB processing/repair. (Pavankumar et al., PLOS ONE, 2010-02-17, https://doi.org/10.1371/journal.pone.0009412) (pavankumar2010allthreesubunits pages 1-2, pavankumar2010allthreesubunits pages 4-7)
Crucially, targeted active-site mutants separated RecB functions:
- ATPase/helicase motor mutants in RecB (RecB K28Q/K29Q in that study’s notation) and RecD (RecD K229Q) were defective in DNA repair phenotypes and cold growth, indicating ATP-dependent motor functions are essential in vivo. (pavankumar2010allthreesubunits pages 1-2, pavankumar2010allthreesubunits pages 7-8)
- By contrast, a RecB nuclease-center mutant (D1118A) was highly deficient for exonuclease activity yet could still support UV/MMC resistance and near-wild-type low-temperature growth in that system, implying that under some conditions the nuclease contribution is less critical than the ATP-dependent unwinding/translocation functions. (pavankumar2010allthreesubunits pages 7-8)
Complementation data also support conservation of core RecBCD function: plasmid-borne E. coli recBCD could complement defects of a P. syringae ΔrecCBD strain. (pavankumar2010allthreesubunits pages 1-2)
Biochemical characterization of RecBCD from P. syringae Lz4W identified the species-specific Chi-like octamer 5′-GCTGGCGC-3′ (ChiPs) and noted functional differences relative to E. coli RecBCD (e.g., RecD indispensability for specific Chi-like fragment production). (Pavankumar et al., PLOS ONE, 2018-05-16, https://doi.org/10.1371/journal.pone.0197476) (pavankumar2018biochemicalcharacterizationof pages 1-2)
This matters for P. putida KT2440 annotation: even if RecB is homologous, the exact Chi sequence and switching kinetics may differ across pseudomonads and should not be assumed to match E. coli without direct evidence.
A high-citation study in Environmental Microbiology examined the “proviral load” of P. putida KT2440 and created a prophage-free derivative (Δall-Φ). In UV assays, KT2440 was reported to be extraordinarily UV sensitive relative to E. coli (30 J/m² leaving E. coli “virtually intact” but reducing KT2440 survival by >4 orders of magnitude), and deleting all prophages increased UV tolerance—especially at 15–30 J/m². (Martínez-García et al., Environmental Microbiology, 2015-06-01, https://doi.org/10.1111/1462-2920.12492) (martinez‐garcia2015freeingpseudomonasputida pages 7-10)
Importantly for functional annotation: the same work reports that measures of RecA-mediated homologous recombination showed no significant difference between wild type KT2440 and Δall-Φ, and spontaneous mutation rates (rifampicin resistance) were comparable, suggesting that increased DNA-damage tolerance in Δall-Φ is not due to a global increase in HR capacity but likely due to eliminating SOS-triggered lethal prophage induction. (martinez‐garcia2015freeingpseudomonasputida pages 7-10, martinez‐garcia2015freeingpseudomonasputida pages 10-12)
Although this study mentions directed recA and recB mutants in its experimental framing, the retrieved text segments did not provide direct, quantitative recB-mutant phenotype readouts. Therefore, it provides pathway context for DNA damage and SOS induction in KT2440, but not a direct functional dissection of PP_4673/Q88DZ5.
A 2023 MMBR review consolidated structural/genetic/biochemical evidence that RecBCD is an exceptionally fast and processive helicase–nuclease and emphasized RecB’s tethered nuclease domain and Chi-dependent switching that yields a nick near Chi and subsequent RecA loading. (Amundsen & Smith, 2023-12-20, https://doi.org/10.1128/mmbr.00041-23) (amundsen2023recbcdenzymemechanistic pages 4-6, amundsen2023recbcdenzymemechanistic pages 1-2)
A 2024 paper in Nucleic Acids Research tested the long-discussed model that Chi recognition undocks the RecB nuclease domain to reveal a RecA-loading interface. Reconstitution experiments showed that a severed RecB nuclease domain can still functionally enable RecA loading when paired with a truncated RecBCD lacking that domain, supporting a Chi-induced rearrangement mechanism in which the RecA-loading surface is exposed by conformational change rather than a purely tether-constrained “swing-out.” (Pavankumar et al., 2024-01-16, https://doi.org/10.1093/nar/gkae007) (pavankumar2024transcomplementationbythe pages 1-2)
While not an assay of KT2440 RecB function per se, modern Pseudomonas genome engineering often contends with host nucleases that degrade linear DNA substrates; RecBCD is frequently a key factor in this context.
A 2023 study demonstrating improved CRISPR/Cas9 editing in E. coli and Pseudomonas showed that DSB repair outcomes in bacterial genome editing can occur independently of RecA and RecBCD under certain engineered conditions (SSB-mediated effects), illustrating how host DSB-repair factors are relevant design variables in applied editing workflows. (Chai et al., Microorganisms, 2023-03-30, https://doi.org/10.3390/microorganisms11040850) (pavankumar2018biochemicalcharacterizationof pages 1-2)
KT2440 is also an active platform for recombineering-based engineering (e.g., integration/deletion of large genomic regions), underscoring the practical importance of understanding DNA repair and end-processing systems in this chassis even when individual studies do not isolate recB phenotypes. (Martínez-García et al. 2015 discusses extensive phenotyping under >1000 conditions and DNA-damage assays in KT2440 backgrounds.) (martinez‐garcia2015freeingpseudomonasputida pages 7-10)
Highly cited authoritative reviews describe RecBCD as the entry point to DSB repair by HR, combining end binding, unwinding, regulated nucleolysis, and RecA loading controlled by Chi sequences. (Smith 2012, https://doi.org/10.1128/mmbr.05026-11; Sinha et al. 2020, https://doi.org/10.1093/femsre/fuaa009; Amundsen & Smith 2023, https://doi.org/10.1128/mmbr.00041-23) (smith2012howrecbcdenzyme pages 2-4, sinha2020therolesof pages 2-3, amundsen2023recbcdenzymemechanistic pages 4-6)
The Pseudomonas syringae genetic dissection provides an expert-relevant nuance: in that organism’s cold-stress context, ATP-dependent motor function of RecB/RecD is essential, while the RecB nuclease center can be partially bypassed/compensated (e.g., by RecJ), highlighting that in vivo criticality of RecB subfunctions can vary with physiology and redundant pathways. (Pavankumar et al. 2010, https://doi.org/10.1371/journal.pone.0009412) (pavankumar2010allthreesubunits pages 7-8, pavankumar2010allthreesubunits pages 8-9)
RecB is repeatedly described as a low-copy DNA repair protein, on the order of only a few molecules per cell in E. coli. A synthesis review cites ~5 RecB molecules/cell, and a later single-cell study measured ~3.9 ± 0.6 molecules/cell (with recB mRNA mean ~0.62 molecules/cell). While these values are not from P. putida, they underscore that RecB is tightly regulated due to its potent DNA-processing activity. (Vincent & Uphoff, Biochemical Society Transactions, 2020-03-23, https://doi.org/10.1042/bst20190364; Kalita et al., eLife, 2025-08-21, https://doi.org/10.7554/elife.94918) (vincent2020bacterialphenotypicheterogeneity pages 2-4, kalita2025anhfqdependentposttranscriptional pages 2-3)
| Category | Summary |
|---|---|
| Identity/Complex | UniProt Q88DZ5 is annotated as RecBCD enzyme subunit RecB from Pseudomonas putida KT2440; available mechanistic literature supports RecB as the helicase–nuclease subunit of the heterotrimeric RecBCD complex (RecB/RecC/RecD), also called Exonuclease V, with RecB carrying helicase/ATPase and nuclease-linked functions (amundsen2023recbcdenzymemechanistic pages 4-6, amundsen2023recbcdenzymemechanistic pages 1-2, amundsen2023recbcdenzymemechanistic pages 2-4). |
| Enzymatic activities | RecB contributes ATP-dependent 3′→5′ translocation/helicase activity, while its C-terminal nuclease domain cleaves DNA in a Mg2+-dependent manner; after Chi recognition, RecBCD nicks the 3′-ended strand and promotes RecA loading onto the resulting 3′ ssDNA tail (amundsen2023recbcdenzymemechanistic pages 4-6, sinha2020therolesof pages 2-3, pavankumar2024transcomplementationbythe pages 1-2, smith2012howrecbcdenzyme pages 2-4). |
| Substrates | RecBCD acts primarily on blunt or nearly blunt dsDNA ends, including two-ended DSBs and one-ended broken replication forks; during processing it unwinds duplex DNA and degrades emerging ssDNA to short oligonucleotides, ultimately generating recombinogenic 3′-tailed DNA (amundsen2023recbcdenzymemechanistic pages 4-6, pavankumar2018biochemicalcharacterizationof pages 1-2, sinha2020therolesof pages 2-3, amundsen2023recbcdenzymemechanistic pages 2-4). |
| Chi regulation | Canonical E. coli Chi is 5′-GCTGGTGG-3′ and triggers a switch from degradative to recombination-promoting processing; in Pseudomonas syringae Lz4W the cognate octamer is ChiPs 5′-GCTGGCGC-3′, showing that Chi recognition is species-specific within pseudomonads (amundsen2023recbcdenzymemechanistic pages 4-6, pavankumar2018biochemicalcharacterizationof pages 1-2, amundsen2023recbcdenzymemechanistic pages 8-11, smith2012howrecbcdenzyme pages 2-4). |
| Pathway role | RecB functions in the major bacterial homologous recombination pathway for DSB repair, replication-fork rescue, and genome maintenance by helping RecBCD create a 3′ overhang and load RecA, followed by downstream RuvABC-mediated branch migration/resolution (pavankumar2018biochemicalcharacterizationof pages 1-2, sinha2020therolesof pages 2-3, amundsen2023recbcdenzymemechanistic pages 1-2, amundsen2023recbcdenzymemechanistic pages 2-4). |
| Localization | No direct localization study for Q88DZ5 in KT2440 was retrieved, but RecBCD acts on chromosomal DNA ends and stalled/broken replication forks; this supports a cytoplasmic, nucleoid-associated functional location rather than membrane or extracellular localization (amundsen2023recbcdenzymemechanistic pages 4-6, sinha2020therolesof pages 2-3, amundsen2023recbcdenzymemechanistic pages 2-4). |
| Pseudomonas-specific evidence | In P. syringae Lz4W, recB/recC/recD mutants are UV- and mitomycin C-sensitive, fail to grow at 4°C, and accumulate linear/fragmented chromosomal DNA; RecB and RecD ATPase/helicase activities are essential in vivo, whereas RecB nuclease activity is partly dispensable and can be compensated by RecJ in some contexts (pavankumar2010allthreesubunits pages 1-2, pavankumar2010allthreesubunits pages 7-8, pavankumar2010allthreesubunits pages 8-9, pavankumar2010allthreesubunits pages 10-13). |
| KT2440-specific evidence | Direct experimental evidence for PP_4673/Q88DZ5 in P. putida KT2440 is limited in the retrieved corpus. KT2440 studies instead show that DNA-damage tolerance and SOS-linked phenotypes can be assayed genetically in this strain, and that prophage-free KT2440 is more UV-tolerant without detectable change in RecA-mediated homologous recombination; these data provide pathway context but not a direct recB functional test (martinez‐garcia2015freeingpseudomonasputida pages 7-10, martinez‐garcia2015freeingpseudomonasputida pages 12-15, martinez‐garcia2015freeingpseudomonasputida pages 10-12). |
| Recent (2023-2024) advances | Recent work refined RecB-centered mechanism: a 2023 review synthesized mutant/structural evidence for RecB tethering, Chi-triggered conformational control, and inter-subunit signaling; a 2024 study showed the RecB nuclease domain can trans-complement truncated RecBCD, supporting a Chi-induced rearrangement that exposes the RecA-loading surface rather than a simple tethered “swing-out” model (amundsen2023recbcdenzymemechanistic pages 4-6, amundsen2023recbcdenzymemechanistic pages 1-2, pavankumar2024transcomplementationbythe pages 1-2). |
| Quantitative stats | RecBCD is among the fastest/processive bacterial helicase–nucleases, reported at ~1 kb/s and ≥100 kb processivity in recent review literature; older review values cite ~300 bp/s depending on assay conditions. In E. coli, RecB is low abundance (~5 molecules/cell in one synthesis; ~3.9 ± 0.6 molecules/cell in a later single-cell study), indicating tight expression control for this potentially DNA-destructive activity (amundsen2023recbcdenzymemechanistic pages 4-6, smith2012howrecbcdenzyme pages 2-4, kalita2025anhfqdependentposttranscriptional pages 2-3, vincent2020bacterialphenotypicheterogeneity pages 2-4). |
Table: This table summarizes the evidence-supported functional annotation of RecB/RecBCD for Pseudomonas putida KT2440, while clearly separating broad conserved RecBCD biology from the more limited KT2440-specific evidence. It is useful for identifying what can be stated confidently for Q88DZ5 and where inference relies on pseudomonad or model-organism studies.
References
(amundsen2023recbcdenzymemechanistic pages 1-2): Susan K. Amundsen and Gerald R. Smith. Recbcd enzyme: mechanistic insights from mutants of a complex helicase-nuclease. Microbiology and Molecular Biology Reviews, Dec 2023. URL: https://doi.org/10.1128/mmbr.00041-23, doi:10.1128/mmbr.00041-23. This article has 23 citations and is from a domain leading peer-reviewed journal.
(amundsen2023recbcdenzymemechanistic pages 4-6): Susan K. Amundsen and Gerald R. Smith. Recbcd enzyme: mechanistic insights from mutants of a complex helicase-nuclease. Microbiology and Molecular Biology Reviews, Dec 2023. URL: https://doi.org/10.1128/mmbr.00041-23, doi:10.1128/mmbr.00041-23. This article has 23 citations and is from a domain leading peer-reviewed journal.
(amundsen2023recbcdenzymemechanistic pages 2-4): Susan K. Amundsen and Gerald R. Smith. Recbcd enzyme: mechanistic insights from mutants of a complex helicase-nuclease. Microbiology and Molecular Biology Reviews, Dec 2023. URL: https://doi.org/10.1128/mmbr.00041-23, doi:10.1128/mmbr.00041-23. This article has 23 citations and is from a domain leading peer-reviewed journal.
(smith2012howrecbcdenzyme pages 2-4): Gerald R. Smith. How recbcd enzyme and chi promote dna break repair and recombination: a molecular biologist's view. Microbiology and Molecular Biology Reviews, 76:217-228, Jun 2012. URL: https://doi.org/10.1128/mmbr.05026-11, doi:10.1128/mmbr.05026-11. This article has 219 citations and is from a domain leading peer-reviewed journal.
(pavankumar2018biochemicalcharacterizationof pages 1-2): Theetha L. Pavankumar, Anurag K. Sinha, and Malay K. Ray. Biochemical characterization of recbcd enzyme from an antarctic pseudomonas species and identification of its cognate chi (χ) sequence. PLOS ONE, 13:e0197476, May 2018. URL: https://doi.org/10.1371/journal.pone.0197476, doi:10.1371/journal.pone.0197476. This article has 15 citations and is from a peer-reviewed journal.
(pavankumar2024transcomplementationbythe pages 1-2): Theetha L Pavankumar, C Jason Wong, Yun Ka Wong, Maria Spies, and Stephen C Kowalczykowski. Trans-complementation by the recb nuclease domain of recbcd enzyme reveals new insight into reca loading upon χ recognition. Nucleic Acids Research, 52:2578-2589, Jan 2024. URL: https://doi.org/10.1093/nar/gkae007, doi:10.1093/nar/gkae007. This article has 10 citations and is from a highest quality peer-reviewed journal.
(sinha2020therolesof pages 2-3): Anurag Kumar Sinha, Christophe Possoz, and David R F Leach. The roles of bacterial dna double-strand break repair proteins in chromosomal dna replication. FEMS Microbiology Reviews, 44:351-368, Apr 2020. URL: https://doi.org/10.1093/femsre/fuaa009, doi:10.1093/femsre/fuaa009. This article has 46 citations and is from a domain leading peer-reviewed journal.
(pavankumar2010allthreesubunits pages 1-2): Theetha L. Pavankumar, Anurag K. Sinha, and Malay K. Ray. All three subunits of recbcd enzyme are essential for dna repair and low-temperature growth in the antarctic pseudomonas syringae lz4w. PLoS ONE, 5:e9412, Feb 2010. URL: https://doi.org/10.1371/journal.pone.0009412, doi:10.1371/journal.pone.0009412. This article has 31 citations and is from a peer-reviewed journal.
(pavankumar2010allthreesubunits pages 4-7): Theetha L. Pavankumar, Anurag K. Sinha, and Malay K. Ray. All three subunits of recbcd enzyme are essential for dna repair and low-temperature growth in the antarctic pseudomonas syringae lz4w. PLoS ONE, 5:e9412, Feb 2010. URL: https://doi.org/10.1371/journal.pone.0009412, doi:10.1371/journal.pone.0009412. This article has 31 citations and is from a peer-reviewed journal.
(pavankumar2010allthreesubunits pages 7-8): Theetha L. Pavankumar, Anurag K. Sinha, and Malay K. Ray. All three subunits of recbcd enzyme are essential for dna repair and low-temperature growth in the antarctic pseudomonas syringae lz4w. PLoS ONE, 5:e9412, Feb 2010. URL: https://doi.org/10.1371/journal.pone.0009412, doi:10.1371/journal.pone.0009412. This article has 31 citations and is from a peer-reviewed journal.
(martinez‐garcia2015freeingpseudomonasputida pages 7-10): Esteban Martínez‐García, Tatjana Jatsenko, Maia Kivisaar, and Víctor de Lorenzo. Freeing pseudomonas putida kt2440 of its proviral load strengthens endurance to environmental stresses. Environmental microbiology, 17 1:76-90, Jun 2015. URL: https://doi.org/10.1111/1462-2920.12492, doi:10.1111/1462-2920.12492. This article has 94 citations and is from a domain leading peer-reviewed journal.
(martinez‐garcia2015freeingpseudomonasputida pages 10-12): Esteban Martínez‐García, Tatjana Jatsenko, Maia Kivisaar, and Víctor de Lorenzo. Freeing pseudomonas putida kt2440 of its proviral load strengthens endurance to environmental stresses. Environmental microbiology, 17 1:76-90, Jun 2015. URL: https://doi.org/10.1111/1462-2920.12492, doi:10.1111/1462-2920.12492. This article has 94 citations and is from a domain leading peer-reviewed journal.
(pavankumar2010allthreesubunits pages 8-9): Theetha L. Pavankumar, Anurag K. Sinha, and Malay K. Ray. All three subunits of recbcd enzyme are essential for dna repair and low-temperature growth in the antarctic pseudomonas syringae lz4w. PLoS ONE, 5:e9412, Feb 2010. URL: https://doi.org/10.1371/journal.pone.0009412, doi:10.1371/journal.pone.0009412. This article has 31 citations and is from a peer-reviewed journal.
(vincent2020bacterialphenotypicheterogeneity pages 2-4): Maxence S. Vincent and Stephan Uphoff. Bacterial phenotypic heterogeneity in dna repair and mutagenesis. Biochemical Society Transactions, 48:451-462, Mar 2020. URL: https://doi.org/10.1042/bst20190364, doi:10.1042/bst20190364. This article has 43 citations and is from a peer-reviewed journal.
(kalita2025anhfqdependentposttranscriptional pages 2-3): Irina Kalita, Ira Alexandra Iosub, Lorna McLaren, Louise Goossens, Sander Granneman, and Meriem El Karoui. An hfq-dependent post-transcriptional mechanism fine tunes recb expression in escherichia coli. eLife, Aug 2025. URL: https://doi.org/10.7554/elife.94918, doi:10.7554/elife.94918. This article has 6 citations and is from a domain leading peer-reviewed journal.
(amundsen2023recbcdenzymemechanistic pages 8-11): Susan K. Amundsen and Gerald R. Smith. Recbcd enzyme: mechanistic insights from mutants of a complex helicase-nuclease. Microbiology and Molecular Biology Reviews, Dec 2023. URL: https://doi.org/10.1128/mmbr.00041-23, doi:10.1128/mmbr.00041-23. This article has 23 citations and is from a domain leading peer-reviewed journal.
(pavankumar2010allthreesubunits pages 10-13): Theetha L. Pavankumar, Anurag K. Sinha, and Malay K. Ray. All three subunits of recbcd enzyme are essential for dna repair and low-temperature growth in the antarctic pseudomonas syringae lz4w. PLoS ONE, 5:e9412, Feb 2010. URL: https://doi.org/10.1371/journal.pone.0009412, doi:10.1371/journal.pone.0009412. This article has 31 citations and is from a peer-reviewed journal.
(martinez‐garcia2015freeingpseudomonasputida pages 12-15): Esteban Martínez‐García, Tatjana Jatsenko, Maia Kivisaar, and Víctor de Lorenzo. Freeing pseudomonas putida kt2440 of its proviral load strengthens endurance to environmental stresses. Environmental microbiology, 17 1:76-90, Jun 2015. URL: https://doi.org/10.1111/1462-2920.12492, doi:10.1111/1462-2920.12492. This article has 94 citations and is from a domain leading peer-reviewed journal.
id: Q88DZ5
gene_symbol: recB
product_type: PROTEIN
status: DRAFT
taxon:
id: NCBITaxon:160488
label: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
description: >-
RecB is the helicase-nuclease subunit of the heterotrimeric RecBCD enzyme
(RecB-RecC-RecD; also called Exonuclease V), the major bacterial machine that
initiates processing of double-strand DNA ends for homologous recombination
and double-strand break repair. RecB is a bipartite, ATP-dependent enzyme. Its
N-terminal motor domain is a single-strand-DNA-dependent ATPase with 3'-5'
helicase activity that, together with RecD (a 5'-3' motor) and RecC, drives
rapid, processive unwinding of duplex DNA from a blunt or near-blunt end. Its
C-terminal domain carries a Mg2+-dependent nuclease center that degrades the
unwound strands and, after recognition of a Chi recombination hotspot, nicks
the 3'-ended strand and loads the RecA recombinase onto the resulting 3'
single-stranded tail. The product of this reaction is a recombinogenic 3'
overhang coated with RecA, committing the broken end to RecA-mediated strand
invasion and downstream RuvABC-dependent resolution. RecBCD also rescues
collapsed or broken replication forks. The enzyme acts on chromosomal DNA in
the cytoplasm and nucleoid. Chi recognition is species-specific, and the
cognate octamer differs among pseudomonads from the E. coli consensus.
existing_annotations:
- term:
id: GO:0000166
label: nucleotide binding
evidence_type: IEA
original_reference_id: GO_REF:0000104
qualifier: enables
review:
summary: RecB is an ATP-binding/ATP-hydrolyzing motor protein, so nucleotide binding is correct but it is a broad parent of the more specific ATP binding annotation.
action: MARK_AS_OVER_ANNOTATED
reason: Correct but uninformative; subsumed by the specific GO:0005524 ATP binding annotation, which captures the relevant nucleotide-binding activity.
- term:
id: GO:0000287
label: magnesium ion binding
evidence_type: IEA
original_reference_id: GO_REF:0000104
qualifier: enables
review:
summary: The RecB C-terminal nuclease center requires a divalent metal (Mg2+/Mn2+) for exodeoxyribonuclease V activity, consistent with this annotation.
action: ACCEPT
reason: Mg2+ dependence of the RecB PD-(D/E)XK nuclease center is well established for RecBCD/Exonuclease V and supported by the UvrD/AddAB-type nuclease domain.
- term:
id: GO:0000724
label: double-strand break repair via homologous recombination
evidence_type: IEA
original_reference_id: GO_REF:0000104
qualifier: involved_in
review:
summary: RecBCD initiates double-strand break repair by homologous recombination; this is the central biological process for RecB.
action: ACCEPT
reason: Strongly supported by conserved RecBCD biology and by pseudomonad genetics (recB null mutants are UV/mitomycin C sensitive and accumulate fragmented chromosomal DNA); a core function.
supported_by:
- reference_id: file:PSEPK/recB/recB-deep-research-falcon.md
- term:
id: GO:0000725
label: recombinational repair
evidence_type: IEA
original_reference_id: GO_REF:0000118
qualifier: involved_in
review:
summary: RecB participates in recombinational repair; this is a broader parent of GO:0000724 double-strand break repair via homologous recombination.
action: KEEP_AS_NON_CORE
reason: Accurate but more general than the specific DSB-via-HR term, which better represents the core process; retain as supporting/non-core.
- term:
id: GO:0003677
label: DNA binding
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: enables
review:
summary: RecB binds duplex and single-stranded DNA as part of its helicase/nuclease activity; a true but general molecular function.
action: KEEP_AS_NON_CORE
reason: Correct supporting activity, but subsumed by the more informative helicase and exonuclease V molecular-function annotations.
- term:
id: GO:0003678
label: DNA helicase activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: enables
review:
summary: RecB has ATP-dependent DNA helicase activity; this is captured more precisely by GO:0043138 (3'-5' DNA helicase activity).
action: KEEP_AS_NON_CORE
reason: Correct but a parent of the more specific 3'-5' DNA helicase activity term.
- term:
id: GO:0004386
label: helicase activity
evidence_type: IEA
original_reference_id: GO_REF:0000104
qualifier: enables
review:
summary: General helicase activity; a broad parent of the DNA-specific and directionally specific helicase terms.
action: MARK_AS_OVER_ANNOTATED
reason: Uninformative high-level term subsumed by GO:0003678 and GO:0043138.
- term:
id: GO:0005524
label: ATP binding
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: enables
review:
summary: RecB has a P-loop/Walker A motif and binds ATP to power its motor activity; correct and informative.
action: ACCEPT
reason: ATP binding by the RecB helicase motor is well supported by domain architecture and conserved RecBCD biochemistry.
- term:
id: GO:0005829
label: cytosol
evidence_type: IEA
original_reference_id: GO_REF:0000118
qualifier: located_in
review:
summary: RecBCD acts on chromosomal DNA ends in the cytoplasm/nucleoid; a cytosolic localization is consistent.
action: KEEP_AS_NON_CORE
reason: Reasonable localization for a DNA-repair enzyme but inferred (TreeGrafter); the functionally relevant compartment is the nucleoid-associated cytoplasm.
- term:
id: GO:0006281
label: DNA repair
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: involved_in
review:
summary: RecB functions in DNA repair; a broad parent of the more specific DSB repair via HR term.
action: KEEP_AS_NON_CORE
reason: Correct but general; subsumed by GO:0000724.
- term:
id: GO:0008854
label: exodeoxyribonuclease V activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: enables
review:
summary: RecB carries the nuclease activity of Exonuclease V (EC 3.1.11.5), the defining enzymatic function of the RecBCD complex.
action: ACCEPT
reason: Core molecular function; supported by the RecB C-terminal PD-(D/E)XK nuclease domain and EC mapping, consistent across RecBCD enzymes.
- term:
id: GO:0009338
label: exodeoxyribonuclease V complex
evidence_type: IEA
original_reference_id: GO_REF:0000118
qualifier: part_of
review:
summary: RecB is a subunit of the RecBCD (Exonuclease V) complex together with RecC and RecD; correct cellular-component/complex assignment.
action: ACCEPT
reason: RecB is an obligate subunit of the heterotrimeric RecBCD/ExoV complex; a core part_of annotation.
- term:
id: GO:0016787
label: hydrolase activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: enables
review:
summary: Very general hydrolase parent term; RecB hydrolyzes both ATP and phosphodiester bonds, but this term is uninformative.
action: MARK_AS_OVER_ANNOTATED
reason: Root-level molecular function subsumed by specific nuclease and ATP hydrolysis annotations.
- term:
id: GO:0016887
label: ATP hydrolysis activity
evidence_type: IEA
original_reference_id: GO_REF:0000116
qualifier: enables
review:
summary: RecB couples ATP hydrolysis to DNA unwinding/translocation (Rhea:13065); correct and informative for the motor function.
action: ACCEPT
reason: ATPase activity driving the RecB helicase motor is well established and supported by Rhea mapping.
- term:
id: GO:0043138
label: 3'-5' DNA helicase activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: enables
review:
summary: RecB is the 3'-5' helicase motor of RecBCD, translocating along the 3'-ended strand; the most specific and correct helicase term.
action: ACCEPT
reason: Core molecular function; the 3'-5' directionality of the RecB motor is a defining mechanistic feature of RecBCD.
core_functions:
- description: ATP-dependent 3'-5' DNA helicase/translocase motor of the RecBCD complex that unwinds duplex DNA from a double-strand end.
supported_by:
- reference_id: PMID:38047637
molecular_function:
id: GO:0043138
label: 3'-5' DNA helicase activity
directly_involved_in:
- id: GO:0000724
label: double-strand break repair via homologous recombination
- description: Mg2+-dependent exodeoxyribonuclease V (Exonuclease V) nuclease that degrades unwound DNA strands and, upon Chi recognition, nicks the 3'-ended strand and loads RecA, generating a recombinogenic 3' single-stranded overhang.
supported_by:
- reference_id: PMID:38047637
molecular_function:
id: GO:0008854
label: exodeoxyribonuclease V activity
directly_involved_in:
- id: GO:0000724
label: double-strand break repair via homologous recombination
- description: Functions as an obligate subunit of the heterotrimeric RecBCD (Exonuclease V) complex.
supported_by:
- reference_id: PMID:20195537
in_complex:
id: GO:0009338
label: exodeoxyribonuclease V complex
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO terms
findings: []
- id: GO_REF:0000104
title: Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features
findings: []
- id: GO_REF:0000116
title: Automatic Gene Ontology annotation based on Rhea mapping
findings: []
- id: GO_REF:0000118
title: TreeGrafter-generated GO annotations
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
- id: file:PSEPK/recB/recB-deep-research-falcon.md
title: Deep research report (Falcon/Edison) on P. putida KT2440 recB (Q88DZ5)
findings:
- statement: Conserved RecBCD biology supports RecB as the ATP-dependent helicase-nuclease subunit that processes dsDNA ends into recombinogenic 3' ssDNA and loads RecA; pseudomonad genetics (P. syringae recB mutants UV/MMC-sensitive, accumulate fragmented DNA) corroborate the DSB-repair role. No KT2440-specific recB mutant phenotype was recovered, so organism-specific claims are inferred.
reference_section_type: RESULTS
- id: PMID:38047637
title: 'RecBCD enzyme: mechanistic insights from mutants of a complex helicase-nuclease'
findings:
- statement: RecBCD is a fast, processive ATP-dependent helicase-nuclease; RecB contributes the 3'-5' motor and a tethered Mg2+-dependent nuclease domain, and Chi recognition switches the enzyme to nick near Chi and load RecA.
reference_section_type: ABSTRACT
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Citation-integrity fix: this reference was originally entered as PMID:38000388,
which actually resolves to an unrelated RNA paper ("Co-transcriptional folding
of the glmS ribozyme enables a rapid response to metabolite", Nucleic Acids Res
2024) and was a wrong identifier. The intended source is Amundsen & Smith 2023
MMBR review "RecBCD enzyme: mechanistic insights from mutants of a complex
helicase-nuclease" (doi:10.1128/mmbr.00041-23). The correct PMID was recovered
from the DOI via doi_to_pmid and confirmed against PubMed (PMID:38047637 ->
matching title/DOI), on-topic for RecB helicase/nuclease/RecA-loading mechanism.
The replacement PMID:38047637 is VERIFIED on-topic.
- id: PMID:20195537
title: All three subunits of RecBCD enzyme are essential for DNA repair and low-temperature growth in the Antarctic Pseudomonas syringae Lz4W
findings:
- statement: In a pseudomonad, recB/recC/recD null mutants are UV- and mitomycin C-sensitive and accumulate linear/fragmented chromosomal DNA; RecB ATPase/helicase activity is essential in vivo while the nuclease center is partly dispensable.
reference_section_type: ABSTRACT
reference_review:
relevance: HIGH
correctness: UNVERIFIED
review_notes: Pavankumar et al. 2010 PLoS ONE; closest Pseudomonas genetic evidence for RecBCD function. PMID from deep-research summary, not independently PubMed-verified.
suggested_questions:
- question: What is the cognate Chi (recombination hotspot) sequence recognized by P. putida KT2440 RecBCD, and does it differ from the E. coli consensus and the P. syringae ChiPs octamer?
suggested_experiments:
- description: Construct a P. putida KT2440 recB (PP_4673) deletion and complement with wild-type and motor-dead/nuclease-dead alleles to test sensitivity to UV and mitomycin C and quantify homologous recombination capacity.