edd encodes the IlvD/Edd-family 6-phosphogluconate dehydratase that catalyzes dehydration of 6-phospho-D-gluconate to 2-keto-3-deoxy-6-phosphogluconate (KDPG; EC 4.2.1.12). In Pseudomonas putida KT2440 this reaction is the committed Entner-Doudoroff (ED) pathway step downstream of 6-phosphogluconate production from glucose, gluconate, or 2-ketogluconate. The protein is a predicted soluble cytosolic enzyme with an essential [4Fe-4S] cofactor and is part of the metabolic architecture that makes KT2440 rely strongly on ED catabolism during sugar utilization.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0003824
catalytic activity
|
IEA
GO_REF:0000002 |
MARK AS OVER ANNOTATED |
Summary: This parent term is technically correct for an enzyme, but it adds no useful specificity once the more precise phosphogluconate dehydratase activity annotation is present.
Reason: GO:0003824 is fully subsumed by GO:0004456 for this gene product and is therefore not informative as a separate functional statement.
|
|
GO:0004456
phosphogluconate dehydratase activity
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: This is the specific core molecular function of Edd. UniProt assigns the EC 4.2.1.12 activity and describes dehydration of 6-phospho-D-gluconate to 2-dehydro-3-deoxy-6-phospho-D-gluconate, and species-specific studies on KT2440 place PP_1010/Edd at this ED-pathway step.
Reason: The term captures the exact catalytic activity of the protein and is the most informative GO molecular-function term in the current annotation set.
Supporting Evidence:
file:PSEPK/edd/edd-uniprot.txt
Catalyzes the dehydration of 6-phospho-D-gluconate to 2-dehydro-3-deoxy-6-phospho-D-gluconate.
|
|
GO:0005829
cytosol
|
IEA
GO_REF:0000118 |
KEEP AS NON CORE |
Summary: This localization is plausible for a soluble central-metabolism enzyme acting on cytosolic 6-phosphogluconate and KDPG. It is reasonable to keep, but it is less informative than the catalytic and pathway terms for defining the gene's core evolved role.
Reason: Cytosolic localization is compatible with the known organization of sugar catabolism in KT2440, but the main biological value of this review is the enzyme activity and ED-pathway assignment.
|
|
GO:0009255
Entner-Doudoroff pathway through 6-phosphogluconate
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: This is the correct pathway-level annotation. In KT2440, 6-phosphogluconate enters the ED route by conversion to KDPG through Edd, and edd mutants are explicitly included in experimental analyses of glucose catabolism.
Reason: The term accurately captures the pathway context of the specific Edd reaction and is directly consistent with the established glucose catabolic network of P. putida KT2440.
Supporting Evidence:
file:PSEPK/edd/edd-deep-research-falcon.md
The ED pathway is not a peripheral option; it is a major organizing principle of glucose catabolism...This supports the GO process term `Entner-Doudoroff pathway through 6-phosphogluconate` as the right pathway annotation.
|
|
GO:0016836
hydro-lyase activity
|
IEA
GO_REF:0000120 |
MARK AS OVER ANNOTATED |
Summary: This mechanistic parent term is not wrong, but it is considerably less informative than the child term phosphogluconate dehydratase activity.
Reason: The child term GO:0004456 already captures the relevant hydro-lyase chemistry for this protein with appropriate substrate specificity.
|
|
GO:0051539
4 iron, 4 sulfur cluster binding
|
IEA
GO_REF:0000104 |
KEEP AS NON CORE |
Summary: Edd-family dehydratases typically require a [4Fe-4S] cluster, and the UniProt entry predicts the cofactor plus ligand residues for this protein. The annotation is therefore plausible, but it is best treated as a mechanistic supporting feature rather than the primary core function.
Reason: Cofactor binding is important for catalysis, but the more central biological statement for this gene is its phosphogluconate dehydratase activity in the ED pathway.
|
Q: How strongly is Edd activity modulated at the protein or metabolite level during oxidative stress, beyond the pathway-level phenotypes already known for KT2440?
Suggested experts: Pablo I. Nikel, Victor de Lorenzo
Q: Does the predicted [4Fe-4S] cluster of PP_1010 show unusual stability or repair dynamics during oxidative stress compared with other IlvD-family dehydratases?
Suggested experts: Pablo I. Nikel
Experiment: Purify PP_1010 and measure conversion of 6-phosphogluconate to KDPG in vitro with and without Fe-S cluster reconstitution.
Hypothesis: PP_1010 is a bona fide [4Fe-4S]-dependent phosphogluconate dehydratase whose catalytic activity depends on intact Fe-S loading.
Experiment: Compare wild type, delta-edd, and complemented strains for growth, flux redistribution, and intracellular NADPH/NADP+ balance during glucose growth with and without oxidant challenge.
Hypothesis: Loss of edd will block normal ED flux and exacerbate the redox defects that accompany oxidative stress in KT2440.
Experiment: Quantify Edd protein abundance and enzyme activity after shifts from succinate to glucose, gluconate, or 2-ketogluconate.
Hypothesis: Edd activity will increase when KT2440 is routed into hexose catabolism even if transcriptional changes are modest.
The KT2440 edd locus corresponds to UniProt Q88P43 / locus tag PP_1010 and
encodes phosphogluconate dehydratase (EC 4.2.1.12), an IlvD/Edd-family enzyme
that converts 6-phospho-D-gluconate to 2-keto-3-deoxy-6-phosphogluconate
(KDPG). The UniProt record explicitly assigns the Entner-Doudoroff (ED)
pathway, predicts an Fe-S cofactor, and places the protein in the
IlvD/Edd family. [file:PSEPK/edd/edd-uniprot.txt, "RecName:
Full=Phosphogluconate dehydratase"; "EC=4.2.1.12"; "Pathway: Carbohydrate
metabolism; Entner-Doudoroff pathway"; "Belongs to the IlvD/Edd family"]
The clearest functional conclusion is that edd encodes the specific ED-pathway
dehydratase rather than a generic lyase/catalytic activity. UniProt gives the
reaction directly, and KT2440 metabolic studies use edd (PP1010,
6-phosphogluconate dehydratase) as the defined gene product when measuring
glucose-catabolic flux and enzyme activity. [file:PSEPK/edd/edd-uniprot.txt,
"Catalyzes the dehydration of 6-phospho-D-gluconate to
2-dehydro-3-deoxy-6-phospho-D-gluconate"] [PMID:26350459 Pseudomonas putida
KT2440 strain metabolizes glucose through a cycle formed by enzymes of the
Entner-Doudoroff, Embden-Meyerhof-Parnas, and pentose phosphate pathways, "edd
(PP1010, 6-phosphogluconate dehydratase)", "Specific (Sp) enzymatic activities
of Edd"]
An earlier KT2440 paper describes the same biochemical step in the glucose
network: 6-phosphogluconate enters the ED branch by conversion to KDPG through
Edd. [PMID:20971912 Compartmentalized Glucose Metabolism in Pseudomonas putida
Is Controlled by the PtxS Repressor, "6PG...enters the Entner-Doudoroff route,
where it is first converted into 2-keto-3-deoxy-6-phosphogluconate (KDPG) by
the Edd enzyme"]
In P. putida KT2440 the ED pathway is not a peripheral option; it is a major
organizing principle of glucose catabolism. Studies of central carbon
metabolism, including mutant analysis of edd, show that glucose is processed
through a cyclic architecture that mixes ED, pentose-phosphate, and partial EMP
reactions. [PMID:24951791 The functional structure of central carbon metabolism
in Pseudomonas putida KT2440] [PMID:26350459 Pseudomonas putida KT2440 strain
metabolizes glucose through a cycle formed by enzymes of the Entner-Doudoroff,
Embden-Meyerhof-Parnas, and pentose phosphate pathways]
This supports the GO process term Entner-Doudoroff pathway through
6-phosphogluconate as the right pathway annotation. Broader parent terms such
as catalytic activity or hydro-lyase activity are true but less informative
than the specific dehydratase function.
The UniProt entry predicts a bound [4Fe-4S] cluster and specific binding
residues, which is consistent with known IlvD/Edd-family dehydratase chemistry.
This makes 4 iron, 4 sulfur cluster binding a plausible mechanistic
annotation, but it is secondary to the specific catalytic function in the review
hierarchy. [file:PSEPK/edd/edd-uniprot.txt, "Name=[4Fe-4S] cluster"; "Binds 1
[4Fe-4S] cluster"; "BINDING 154"; "BINDING 221"]
No direct localization experiment for PP_1010 was identified in the reviewed
KT2440 literature, but the enzyme is most plausibly cytosolic because it acts on
soluble ED intermediates within the bacterial central-carbon-metabolism network.
That makes cytosol reasonable to keep as a non-core localization statement.
The ED pathway is a key contributor to KT2440 physiology beyond simple glucose
catabolism. Oxidative-stress work shows that ED metabolism is essential for sugar
catabolism and contributes strongly to NADPH/redox robustness. This does not
establish a special moonlighting role for Edd, but it strengthens the case that
the ED-pathway annotation is biologically meaningful in this organism.
[PMID:23301697 The Entner-Doudoroff pathway empowers Pseudomonas putida KT2440
with a high tolerance to oxidative stress, "Glucose catabolism of Pseudomonas
putida is carried out exclusively through the Entner-Doudoroff (ED) pathway";
"ED was essential for sugar catabolism"; "required for counteracting oxidative
stress"]
GO:0004456 phosphogluconate dehydratase activity as the core MF.GO:0009255 Entner-Doudoroff pathway through 6-phosphogluconate asGO:0003824 catalytic activity and GO:0016836 hydro-lyase activityGO:0051539 4 iron, 4 sulfur cluster binding and GO:0005829 cytosolUniProt Q88P43 identifies edd / PP_1010 in Pseudomonas putida KT2440 as
phosphogluconate dehydratase (EC 4.2.1.12) of the IlvD/Edd family and states
that it catalyzes dehydration of 6-phospho-D-gluconate to
2-dehydro-3-deoxy-6-phospho-D-gluconate. [file:PSEPK/edd/edd-uniprot.txt,
"RecName: Full=Phosphogluconate dehydratase"; "Catalyzes the dehydration of
6-phospho-D-gluconate to 2-dehydro-3-deoxy-6-phospho-D-gluconate"; "Belongs to
the IlvD/Edd family"]
UniProt also predicts a bound [4Fe-4S] cluster with specific ligand residues,
supporting the cofactor-binding annotation as mechanistically plausible rather
than the primary biological function. [file:PSEPK/edd/edd-uniprot.txt,
"Name=[4Fe-4S] cluster"; "Binds 1 [4Fe-4S] cluster"; "BINDING 154";
"BINDING 221"]
A KT2440 glucose-metabolism review/experimental study describes 6PG entering
the ED route by conversion to KDPG through Edd and includes edd (PP1010,
6-phosphogluconate dehydratase) among the glucose-catabolic mutants and
enzyme assays. [PMID:26350459 Pseudomonas putida KT2440 strain metabolizes
glucose through a cycle formed by enzymes of the Entner-Doudoroff,
Embden-Meyerhof-Parnas, and pentose phosphate pathways, "6PG...is first
converted into 2-keto-3-deoxy-6-phosphogluconate (KDPG) by the Edd enzyme";
"edd (PP1010, 6-phosphogluconate dehydratase)"; "Specific (Sp) enzymatic
activities of Edd"]
Earlier KT2440 work on compartmentalized glucose metabolism likewise describes
Edd as the enzyme that converts 6PG to KDPG in the ED branch of the network.
[PMID:20971912 Compartmentalized Glucose Metabolism in Pseudomonas putida Is
Controlled by the PtxS Repressor, "6PG...enters the Entner-Doudoroff route,
where it is first converted into 2-keto-3-deoxy-6-phosphogluconate (KDPG) by
the Edd enzyme"]
KT2440 relies strongly on ED catabolism rather than a canonical EMP glycolytic
route; pathway-level studies connect this organization to redox balance and
oxidative-stress tolerance. This supports retaining the ED-process annotation,
but it does not justify broad extra pathway over-annotation beyond the specific
ED-through-6PG term already present. [PMID:23301697 The Entner-Doudoroff
pathway empowers Pseudomonas putida KT2440 with a high tolerance to oxidative
stress, "Glucose catabolism of Pseudomonas putida is carried out exclusively
through the Entner-Doudoroff (ED) pathway"; "ED was essential for sugar
catabolism"; "required for counteracting oxidative stress"]
Working curation judgement:
GO:0004456 phosphogluconate dehydratase activity should be core/accepted.GO:0009255 Entner-Doudoroff pathway through 6-phosphogluconate should beGO:0003824 catalytic activity and GO:0016836 hydro-lyase activity areGO:0005829 cytosol and GO:0051539 4 iron, 4 sulfur cluster binding areid: Q88P43
gene_symbol: edd
product_type: PROTEIN
status: DRAFT
taxon:
id: NCBITaxon:160488
label: Pseudomonas putida KT2440
aliases:
- PP_1010
description: edd encodes the IlvD/Edd-family 6-phosphogluconate dehydratase that catalyzes
dehydration of 6-phospho-D-gluconate to 2-keto-3-deoxy-6-phosphogluconate (KDPG;
EC 4.2.1.12). In Pseudomonas putida KT2440 this reaction is the committed Entner-Doudoroff
(ED) pathway step downstream of 6-phosphogluconate production from glucose, gluconate,
or 2-ketogluconate. The protein is a predicted soluble cytosolic enzyme with an
essential [4Fe-4S] cofactor and is part of the metabolic architecture that makes
KT2440 rely strongly on ED catabolism during sugar utilization.
existing_annotations:
- term:
id: GO:0003824
label: catalytic activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: This parent term is technically correct for an enzyme, but it adds no
useful specificity once the more precise phosphogluconate dehydratase activity
annotation is present.
action: MARK_AS_OVER_ANNOTATED
reason: GO:0003824 is fully subsumed by GO:0004456 for this gene product and is
therefore not informative as a separate functional statement.
- term:
id: GO:0004456
label: phosphogluconate dehydratase activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: This is the specific core molecular function of Edd. UniProt assigns
the EC 4.2.1.12 activity and describes dehydration of 6-phospho-D-gluconate
to 2-dehydro-3-deoxy-6-phospho-D-gluconate, and species-specific studies on
KT2440 place PP_1010/Edd at this ED-pathway step.
action: ACCEPT
reason: The term captures the exact catalytic activity of the protein and is the
most informative GO molecular-function term in the current annotation set.
supported_by:
- reference_id: file:PSEPK/edd/edd-uniprot.txt
supporting_text: Catalyzes the dehydration of 6-phospho-D-gluconate to 2-dehydro-3-deoxy-6-phospho-D-gluconate.
- term:
id: GO:0005829
label: cytosol
evidence_type: IEA
original_reference_id: GO_REF:0000118
review:
summary: This localization is plausible for a soluble central-metabolism enzyme
acting on cytosolic 6-phosphogluconate and KDPG. It is reasonable to keep, but
it is less informative than the catalytic and pathway terms for defining the
gene's core evolved role.
action: KEEP_AS_NON_CORE
reason: Cytosolic localization is compatible with the known organization of sugar
catabolism in KT2440, but the main biological value of this review is the enzyme
activity and ED-pathway assignment.
- term:
id: GO:0009255
label: Entner-Doudoroff pathway through 6-phosphogluconate
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: This is the correct pathway-level annotation. In KT2440, 6-phosphogluconate
enters the ED route by conversion to KDPG through Edd, and edd mutants are explicitly
included in experimental analyses of glucose catabolism.
action: ACCEPT
reason: The term accurately captures the pathway context of the specific Edd reaction
and is directly consistent with the established glucose catabolic network of
P. putida KT2440.
supported_by:
- reference_id: file:PSEPK/edd/edd-deep-research-falcon.md
supporting_text: The ED pathway is not a peripheral option; it is a major organizing
principle of glucose catabolism...This supports the GO process term `Entner-Doudoroff
pathway through 6-phosphogluconate` as the right pathway annotation.
- term:
id: GO:0016836
label: hydro-lyase activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: This mechanistic parent term is not wrong, but it is considerably less
informative than the child term phosphogluconate dehydratase activity.
action: MARK_AS_OVER_ANNOTATED
reason: The child term GO:0004456 already captures the relevant hydro-lyase chemistry
for this protein with appropriate substrate specificity.
- term:
id: GO:0051539
label: 4 iron, 4 sulfur cluster binding
evidence_type: IEA
original_reference_id: GO_REF:0000104
review:
summary: Edd-family dehydratases typically require a [4Fe-4S] cluster, and the
UniProt entry predicts the cofactor plus ligand residues for this protein. The
annotation is therefore plausible, but it is best treated as a mechanistic supporting
feature rather than the primary core function.
action: KEEP_AS_NON_CORE
reason: Cofactor binding is important for catalysis, but the more central biological
statement for this gene is its phosphogluconate dehydratase activity in the
ED pathway.
core_functions:
- description: Edd catalyzes the committed Entner-Doudoroff-pathway conversion of
6-phospho-D-gluconate to 2-keto-3-deoxy-6-phosphogluconate in the cytosol of P.
putida KT2440. This IlvD/Edd-family enzyme is predicted to use a [4Fe-4S] cofactor
and is part of the sugar-catabolic architecture that channels glucose-derived
carbon through the ED route in this organism.
molecular_function:
id: GO:0004456
label: phosphogluconate dehydratase activity
directly_involved_in:
- id: GO:0009255
label: Entner-Doudoroff pathway through 6-phosphogluconate
supported_by:
- reference_id: file:PSEPK/edd/edd-uniprot.txt
supporting_text: 'Catalyzes the dehydration of 6-phospho-D-gluconate to 2-dehydro-3-deoxy-6-phospho-D-gluconate...Pathway:
Carbohydrate metabolism; Entner-Doudoroff pathway.'
- reference_id: file:PSEPK/edd/edd-deep-research-falcon.md
supporting_text: The KT2440 `edd` locus corresponds to UniProt Q88P43 / locus
tag `PP_1010` and encodes phosphogluconate dehydratase...The ED pathway is
not a peripheral option; it is a major organizing principle of glucose catabolism.
references:
- id: file:PSEPK/edd/edd-uniprot.txt
title: UniProt entry for edd phosphogluconate dehydratase
findings:
- statement: UniProt assigns EC 4.2.1.12 and describes Edd as an IlvD/Edd-family
phosphogluconate dehydratase in the Entner-Doudoroff pathway.
- id: file:PSEPK/edd/edd-deep-research-falcon.md
title: Deep research summary for edd in Pseudomonas putida KT2440
findings: []
- 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:0000118
title: TreeGrafter-generated GO annotations
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods.
findings: []
- id: PMID:12534463
title: Complete genome sequence and comparative analysis of the metabolically versatile
Pseudomonas putida KT2440
findings: []
- id: PMID:24951791
title: The functional structure of central carbon metabolism in Pseudomonas putida
KT2440
findings: []
- id: PMID:26350459
title: Pseudomonas putida KT2440 strain metabolizes glucose through a cycle formed
by enzymes of the Entner-Doudoroff, Embden-Meyerhof-Parnas, and pentose phosphate
pathways
findings: []
- id: PMID:23301697
title: The Entner-Doudoroff pathway empowers Pseudomonas putida KT2440 with a high
tolerance to oxidative stress
findings: []
proposed_new_terms: []
suggested_questions:
- question: How strongly is Edd activity modulated at the protein or metabolite level
during oxidative stress, beyond the pathway-level phenotypes already known for
KT2440?
experts:
- Pablo I. Nikel
- Victor de Lorenzo
- question: Does the predicted [4Fe-4S] cluster of PP_1010 show unusual stability
or repair dynamics during oxidative stress compared with other IlvD-family dehydratases?
experts:
- Pablo I. Nikel
suggested_experiments:
- description: Purify PP_1010 and measure conversion of 6-phosphogluconate to KDPG
in vitro with and without Fe-S cluster reconstitution.
hypothesis: PP_1010 is a bona fide [4Fe-4S]-dependent phosphogluconate dehydratase
whose catalytic activity depends on intact Fe-S loading.
- description: Compare wild type, delta-edd, and complemented strains for growth,
flux redistribution, and intracellular NADPH/NADP+ balance during glucose growth
with and without oxidant challenge.
hypothesis: Loss of edd will block normal ED flux and exacerbate the redox defects
that accompany oxidative stress in KT2440.
- description: Quantify Edd protein abundance and enzyme activity after shifts from
succinate to glucose, gluconate, or 2-ketogluconate.
hypothesis: Edd activity will increase when KT2440 is routed into hexose catabolism
even if transcriptional changes are modest.