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Genetics and biochemistry of dehalogenating enzymes.
ANNU.REV.MICROBIOL. 48 163-191 (1994).
2. KOONIN, E.V. AND TATUSOV, R.L.
Computer analysis of bacterial haloacid dehalogenases defines a large
superfamily of hydrolases with diverse specificity. Application of an
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PINOT, F., OESCH, F., BELKNAP, W.R., SHINOZAKI, K. AND HAMMOCK, B.D.
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Microorganisms that can utilise halogenated compounds as growth substrates
produce enzymes that cleave carbon-halogen bonds and are commonly called
dehalogenases. The hydrolytic dehalogenases catalyse a nucleophilic
displacement reaction, with water as the sole co-substrate . They are
divided into haloalkane dehalogenases and haloacid dehalogenases (HAD).
HADs belong to a large superfamily of hydrolases with diverse substrate
specificity, which also includes epoxide hydrolases, phosphoglycolate
phosphatases, histidinol phosphate phosphatases, nitrophenyl phosphatases
and numerous putative (not yet characterised) proteins .
The epoxide hydrolases (EH) add water to epoxides, forming the corresponding
diol. On the basis of sequence similarity, it has been proposed that the
mammalian soluble EHs contain 2 evolutionarily distinct domains . The
N-terminal domain is similar to bacterial HADs; the C-terminal domain is
similar to soluble plant EH, microsomal EH, and bacterial haloalkane
HADHALOGNASE is a 7-element fingerprint that provides a signature for the
haloacid dehalogenase/epoxide hydrolase family. The fingerprint was derived
from an initial alignment of 10 sequences: the motifs were drawn from
conserved regions spanning virtually the full alignment length - motifs 1,
5 and 6 encode the putative catalytic triad, including the invariant Asp
Lys, and nucleophile (Ser or Asp) respectively, and overlap with motifs I,
II and III proposed in . Two iterations on OWL26.0 were required to
reach convergence, at which point a true set comprising 12 sequences was
identified. Several partial matches were also found: a hypothetical protein
(YIHX_ECOLI) matches motifs 4-7; phosphoglycolate phosphatase (PGPC_ALCEU
and PGPP_ALCEU) matches motifs 4, 5 and 7; and hypothetical protein YigB
(YIGB_ECOLI and ECOXERC3) matches motifs 5, 6 and 7. Among the sequences
matching 2 motifs, only U00148 (Klebsiella oxytoca E1 enzyme), matching
motifs 1 and 6, has been characterised functionally .
An update on SPTR37_9f identified a true set of 12 sequences, and 13