aroD (P05194, Escherichia coli K-12) review notes

Provenance of this notes file

Provider deep research was unavailable for this review (no deep-research provider key in
the session), so no aroD-deep-research-*.md file exists. These notes were compiled by the
reviewer from the cached publications in publications/, the UniProt record
(aroD-uniprot.txt) and one UniProt REST query recorded below.

Family: PANTHER PTHR43699 (3-DEHYDROQUINATE DEHYDRATASE), subfamily PTHR43699:SF1;
InterPro IPR050146 / IPR001381 (type I DHQase), Pfam PF01487, NCBIfam TIGR01093, HAMAP MF_00214.
No PTHR43699 family review exists yet (being written separately).

Function

• Type I 3-dehydroquinase; catalyses step 3 of the shikimate (chorismate) pathway,
  3-dehydroquinate = 3-dehydroshikimate + H2O (EC 4.2.1.10, RHEA:21096).
  [UniProt P05194 CC FUNCTION "Catalyzes the cis-dehydration of 3-dehydroquinate (DHQ) and introduces the first double bond of the aromatic ring to yield 3-dehydroshikimate."]
• Purified enzyme: PMID:2950851
  Catalytic properties PMID:2950851.
• Kinetics: Km 17-18 uM for 3-dehydroquinate, kcat 142 s-1 (UniProt BIOPHYSICOCHEMICAL PROPERTIES, from PMID:2950851 and PMID:7592767).
• Mechanism: Schiff base (imine) with Lys-170; His-143 is the general base.
  PMID:7592767
  PMID:7592767
  The H143A mutant accumulates the product Schiff base: PMID:7592767
  The type I enzyme performs a syn elimination PMID:7592767
• Quaternary structure: dimer.
  PMID:2950851
• Historical: Mitsuhashi and Davis (1954) first described the E. coli 5-dehydroquinase
  activity converting 5-dehydroquinic acid to 5-dehydroshikimic acid (PMID:13198937; only
  the citation/title is cached, no abstract).

Localization

• Soluble cytosolic enzyme. E. coli proteome fractionation studies (PMID:15911532,
  PMID:18304323) assigned proteins to the cytosolic fraction; aroD is not named in the
  cached text (gene-level data are in the supplementary tables, which are not cached), so
  these rows rest on the EcoCyc curators' reading of the supplements.
  PMID:18304323

3,4-dihydroxybenzoate (protocatechuate) biosynthesis rows

GOA carries GO:0046279 3,4-dihydroxybenzoate biosynthetic process on aroD by IDA (UniProt,
PMID:13198937 and PMID:7592767), IBA (PTN000472499) and IEA (ARBA). The cited papers
measure the dehydration of 3-dehydroquinate to 3-dehydroshikimate, not formation of
3,4-dihydroxybenzoate. 3-Dehydroshikimate is converted to protocatechuate only by a
3-dehydroshikimate dehydratase (EC 4.2.1.118; AroZ/QuiC/AsbF), which acts in quinate
catabolism (Pseudomonas, Acinetobacter, Neurospora) or petrobactin synthesis (Bacillus
anthracis).

Reviewer check (UniProt REST, 2026-11-11):
query=ec:4.2.1.118 AND organism_id:83333 returned no entries, i.e. no E. coli K-12
protein carries EC 4.2.1.118. The reviewed EC 4.2.1.118 entries returned by
query=ec:4.2.1.118 AND reviewed:true were asbF (Bacillus anthracis), quiC1
(Pseudomonas putida KT2440, Pseudomonas aeruginosa PAO1), qa-4 (Neurospora crassa) and
quiC (Acinetobacter baylyi ADP1). E. coli K-12 therefore has no known route from
3-dehydroshikimate to protocatechuate, and the GO:0046279 rows describe a process the
organism does not carry out; the enzyme's product is used for chorismate biosynthesis.
The term likely reflects the organism-independent observation that 3-dehydroshikimate is
the protocatechuate precursor in organisms that have AroZ. Judged an over-annotation
(MARK_AS_OVER_ANNOTATED) rather than REMOVE, because DHQase does supply the direct precursor
when such a route exists (e.g. engineered E. coli expressing a heterologous AroZ).

Pathway

• UniProt PATHWAY: chorismate biosynthesis, step 3/7 (HAMAP MF_00214). Reviewer check
  (UniProt REST, 2026-11-11): query=ec:4.2.1.10 AND organism_id:83333 returned only
  P05194 (aroD), so AroD is the only annotated 3-dehydroquinase of E. coli K-12 (no type II
  aroQ paralog), and chorismate and hence
  aromatic amino acid, folate, ubiquinone, menaquinone and enterobactin precursors depend
  on it.