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PR00413

Identifier
HADHALOGNASE  [View Relations]  [View Alignment]  
Accession
PR00413
No. of Motifs
7
Creation Date
07-AUG-1995  (UPDATE 19-JUN-1999)
Title
Haloacid dehalogenase/epoxide hydrolase family signature
Database References

PFAM; PF00702 Hydrolase
INTERPRO; IPR001454
UMBBD; e0006; e0021
Literature References
1. JANSSEN, D.B., PRIES, F. AND VAN DER PLOEG, J.R.
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 
iterative approach to database search.
J.MOL.BIOL. 244(1) 125-132 (1994).
 
3. BEETHAM, J.K., GRANT, D., ARAND, M., GARBARINO, J., KIYOSUE, T.,
PINOT, F., OESCH, F., BELKNAP, W.R., SHINOZAKI, K. AND HAMMOCK, B.D.
Gene evolution of epoxide hydrolases and recommended nomenclature.
DNA CELL BIOL. 14(1) 61-71 (1995).
 
4. MYERS, R.W., WRAY, J.W., FISH, S. AND ABELES, R.H.
Purification and characterization of an enzyme involved in oxidative 
carbon-carbon bond cleavage reactions in the methionine salvage pathway of
Klebsiella pneumoniae.
J.BIOL.CHEM. 268 24785-24791 (1993).

Documentation
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 [1]. 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 [2].  
 
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 [3]. The
N-terminal domain is similar to bacterial HADs; the C-terminal domain is 
similar to soluble plant EH, microsomal EH, and bacterial haloalkane 
dehalogenase.
 
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 [2]. 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 [4].
 
An update on SPTR37_9f identified a true set of 12 sequences, and 13
partial matches.
Summary Information
  12 codes involving  7 elements
1 codes involving 6 elements
0 codes involving 5 elements
0 codes involving 4 elements
1 codes involving 3 elements
10 codes involving 2 elements
Composite Feature Index
712121212121212
61011111
50000000
40000000
30001011
27004621
1234567
True Positives
DEH2_MORSP    HAD1_PSEPU    HAD1_PSESP    HAD2_PSEPU    
HAD2_PSESP HAD4_BURCE HAD_PSESP HAD_XANAU
HYES_HUMAN HYES_MOUSE HYES_RAT Q16764
True Positive Partials
Codes involving 6 elements
HAD_PSEFL
Codes involving 3 elements
O17860
Codes involving 2 elements
CBBY_RHOSH GPH_AQUAE GPH_ECOLI GPH_RHOSH
O01590 O26311 O50405 O58216
O59599 O83565
Sequence Titles
DEH2_MORSP  HALOACETATE DEHALOGENASE H-2 (EC 3.8.1.3) - MORAXELLA SP. 
HAD1_PSEPU 2-HALOALKANOIC ACID DEHALOGENASE (EC 3.8.1.2) (L-2-HALOACID DEHALOGENASE) (HALOCARBOXYLIC ACID HALIDOHYDROLASE) - PSEUDOMONAS PUTIDA.
HAD1_PSESP 2-HALOALKANOIC ACID DEHALOGENASE I (EC 3.8.1.2) (L-2-HALOACID DEHALOGENASE I) (HALOCARBOXYLIC ACID HALIDOHYDROLASE I) (DEHCI) - PSEUDOMONAS SP. (STRAIN CBS3).
HAD2_PSEPU 2-HALOALKANOIC ACID DEHALOGENASE H-109 (EC 3.8.1.2) (L-2-HALOACID DEHALOGENASE H-109) (HALOCARBOXYLIC ACID HALIDOHYDROLASE H-109) - PSEUDOMONAS PUTIDA.
HAD2_PSESP 2-HALOALKANOIC ACID DEHALOGENASE II (EC 3.8.1.2) (L-2-HALOACID DEHALOGENASE II) (HALOCARBOXYLIC ACID HALIDOHYDROLASE II) (DEHCII) - PSEUDOMONAS SP. (STRAIN CBS3).
HAD4_BURCE 2-HALOALKANOIC ACID DEHALOGENASE IVA (EC 3.8.1.2) (L-2-HALOACID DEHALOGENASE IVA) (HALOCARBOXYLIC ACID HALIDOHYDROLASE IVA) - BURKHOLDERIA CEPACIA (PSEUDOMONAS CEPACIA).
HAD_PSESP 2-HALOALKANOIC ACID DEHALOGENASE (EC 3.8.1.2) (L-2-HALOACID DEHALOGENASE) (HALOCARBOXYLIC ACID HALIDOHYDROLASE) (L-DEX) - PSEUDOMONAS SP. (STRAIN YL).
HAD_XANAU 2-HALOALKANOIC ACID DEHALOGENASE (EC 3.8.1.2) (L-2-HALOACID DEHALOGENASE) (HALOCARBOXYLIC ACID HALIDOHYDROLASE) - XANTHOBACTER AUTOTROPHICUS.
HYES_HUMAN SOLUBLE EPOXIDE HYDROLASE (SEH) (EC 3.3.2.3) (EPOXIDE HYDRATASE) (CYTOSOLIC EPOXIDE HYDROLASE) (CEH) - HOMO SAPIENS (HUMAN).
HYES_MOUSE SOLUBLE EPOXIDE HYDROLASE (SEH) (EC 3.3.2.3) (EPOXIDE HYDRATASE) (CYTOSOLIC EPOXIDE HYDROLASE) (CEH) - MUS MUSCULUS (MOUSE).
HYES_RAT SOLUBLE EPOXIDE HYDROLASE (SEH) (EC 3.3.2.3) (EPOXIDE HYDRATASE) (CYTOSOLIC EPOXIDE HYDROLASE) (CEH) - RATTUS NORVEGICUS (RAT).
Q16764 EPOXIDE HYDROLASE (EC 3.3.2.3) (EPOXIDE HYDRATASE) (ARENE-OXIDE HYDRATASE) - HOMO SAPIENS (HUMAN).

HAD_PSEFL 2-HALOALKANOIC ACID DEHALOGENASE (EC 3.8.1.2) (L-2-HALOACID DEHALOGENASE) (HALOCARBOXYLIC ACID HALIDOHYDROLASE) - PSEUDOMONAS FLUORESCENS.

O17860 F37H8.3 PROTEIN - CAENORHABDITIS ELEGANS.

CBBY_RHOSH CBBY PROTEIN - RHODOBACTER SPHAEROIDES (RHODOPSEUDOMONAS SPHAEROIDES).
GPH_AQUAE PHOSPHOGLYCOLATE PHOSPHATASE (EC 3.1.3.18) (PGP) - AQUIFEX AEOLICUS.
GPH_ECOLI PHOSPHOGLYCOLATE PHOSPHATASE (EC 3.1.3.18) (PGP) - ESCHERICHIA COLI.
GPH_RHOSH PHOSPHOGLYCOLATE PHOSPHATASE (EC 3.1.3.18) (PGP) - RHODOBACTER SPHAEROIDES (RHODOPSEUDOMONAS SPHAEROIDES).
O01590 SIMILAR TO ACYL-COA DEHYDROGENASES AND EPOXIDE HYDROLASES - CAENORHABDITIS ELEGANS.
O26311 CONSERVED PROTEIN - METHANOBACTERIUM THERMOAUTOTROPHICUM.
O50405 HYPOTHETICAL 23.7 KD PROTEIN - MYCOBACTERIUM TUBERCULOSIS.
O58216 232AA LONG HYPOTHETICAL PROTEIN - PYROCOCCUS HORIKOSHII.
O59599 217AA LONG HYPOTHETICAL PROTEIN - PYROCOCCUS HORIKOSHII.
O83565 PHOSPHOGLYCOLATE PHOSPHATASE (GPH-2) - TREPONEMA PALLIDUM.
Scan History
OWL25_3    2  1000 NSINGLE    
SPTR37_9f 2 50 NSINGLE
Initial Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
LRVAAFDLDGVL HYES_MOUSE 3 3 -
IEAIAFDMYGTL DEH2_MORSP 4 4 -
IRGVVFDLYGTL HAD2_PSESP 4 4 -
IRACVFDAYGTL HAD1_PSESP 4 4 -
IEGIVFDLYGTL JC2075 4 4 -
LRACVFDAYGTL S29096 5 5 -
IKGIAFDLYGTL S74078 4 4 -
IKAVVFDAYGTL XAADHLB 2 2 -
LRVAAFDLDGVL HYES_RAT 3 3 -
LRGAVFDLDGVL HYES_HUMAN 3 3 -

Motif 2 width=14
Element Seqn Id St Int Rpt
PERGTEISLMWRQK HAD2_PSESP 30 14 -
GGCAEELSSLWRQR HAD1_PSESP 30 14 -
KFPEGPTEQLMKGK HYES_RAT 44 29 -
EFPEGPTEQLMKGK HYES_MOUSE 44 29 -
PGQGEAISRLWRQK JC2075 30 14 -
GASAEALSMLWRQR S29096 31 14 -
PGRGREISALWRQK S74078 30 14 -
PGRGEYITQVWRQK XAADHLB 28 14 -
GGPEGATTRLMKGE HYES_HUMAN 44 29 -
PGKGKDISVLWRQK DEH2_MORSP 30 14 -

Motif 3 width=14
Element Seqn Id St Int Rpt
QLEYTWLSSLMGRY JC2075 44 0 -
QLEYSWTRTLMHQY S29096 45 0 -
QLEYTWLRSLMNRY S74078 44 0 -
QLEYSWLRALMGRY XAADHLB 42 0 -
QLEYSWTRTLMGRY HAD1_PSESP 44 0 -
QLEYSWLRSLMGQY HAD2_PSESP 44 0 -
QLEYAWLRCLMGQY DEH2_MORSP 44 0 -
ITLSQWIPLMEENC HYES_HUMAN 58 0 -
ITFSQWVPLMDESY HYES_MOUSE 58 0 -
ITFSQWVPLMDESC HYES_RAT 58 0 -

Motif 4 width=14
Element Seqn Id St Int Rpt
LKKKGFTTCIVTNN HYES_MOUSE 112 40 -
LKKKGFTTCIVTNN HYES_RAT 112 40 -
AELAPLKRAILSNG XAADHLB 103 47 -
LKRRGLKLAILSNG S74078 107 49 -
LKSAGYIVAILSNG S29096 108 49 -
LKASGLPMAIASNG JC2075 107 49 -
LKAAGFTTAILSNG HAD1_PSESP 107 49 -
LRSGAVPLAILSNG HAD2_PSESP 107 49 -
LRQRGMRLAILSNG DEH2_MORSP 107 49 -
LRKKGFTTAILTNT HYES_HUMAN 112 40 -

Motif 5 width=17
Element Seqn Id St Int Rpt
FDFLIESCQVGMIKPEP HYES_RAT 147 21 -
FDFLIESCQVGMIKPEP HYES_MOUSE 147 21 -
FDAVISVDAKRVFKPHP XAADHLB 134 17 -
FDHLLSVDPVQVYKPDN S74078 138 17 -
LDSCLSADDLKIYKPDP S29096 139 17 -
FDHLISVETVKVFKPDN JC2075 138 17 -
FDFLIESCQVGMVKPEP HYES_HUMAN 147 21 -
FEHLISVDSARAYKPHP DEH2_MORSP 138 17 -
FSHLISADEVSVSKPSP HAD2_PSESP 138 17 -
LDQCISVDEIKIYKPDP HAD1_PSESP 138 17 -

Motif 6 width=21
Element Seqn Id St Int Rpt
VYELAEQALGLDRSAILFVSS S74078 156 1 -
VYSLAEQTMAIPRDRLLFVSS JC2075 156 1 -
VYQFACDRLDVRPSEVCFVSS HAD1_PSESP 156 1 -
AYELAEKRLKVVRSKLLFVSS HAD2_PSESP 156 1 -
AYELGEEAFGISRESILFVSS DEH2_MORSP 156 1 -
IYKFLLDTLKASPSEVVFLDD HYES_HUMAN 165 1 -
IYNFLLDTLKAKPNEVVFLDD HYES_MOUSE 165 1 -
IYKFVLDTLKAKPNEVVFLDD HYES_RAT 165 1 -
SYALVEEVLGVTPAEVLFVSS XAADHLB 152 1 -
IYQFACDRLGVNPNEVCFVSS S29096 157 1 -

Motif 7 width=14
Element Seqn Id St Int Rpt
GARHFGFPVCWVNR JC2075 183 6 -
GAGKFGFNTVRINR S29096 184 6 -
PARDMGMVTILVRD HYES_RAT 192 6 -
PARDMGMVTILVHN HYES_MOUSE 192 6 -
PARDLGMVTILVQD HYES_HUMAN 192 6 -
GAKAFGYQVCWINR DEH2_MORSP 183 6 -
GARHFGFQVCWVNR HAD2_PSESP 183 6 -
GAGAFGFNTVRINR HAD1_PSESP 183 6 -
GARYFGFPTCWINR S74078 183 6 -
GAKNFGFSVARVAR XAADHLB 179 6 -
Final Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
IKGIAFDLYGTL HAD_PSESP 4 4 -
IEGIVFDLYGTL HAD2_PSEPU 4 4 -
IQGIVFDLYGTL HAD1_PSEPU 4 4 -
IRACVFDAYGTL HAD1_PSESP 4 4 -
IRGVVFDLYGTL HAD2_PSESP 4 4 -
IEAIAFDMYGTL DEH2_MORSP 4 4 -
LRACVFDAYGTL HAD4_BURCE 5 5 -
IKAVVFDAYGTL HAD_XANAU 2 2 -
LRGAVFDLDGVL HYES_HUMAN 3 3 -
LRAAVFDLDGVL Q16764 3 3 -
LRVAAFDLDGVL HYES_MOUSE 3 3 -
LRVAAFDLDGVL HYES_RAT 3 3 -

Motif 2 width=14
Element Seqn Id St Int Rpt
PGRGREISALWRQK HAD_PSESP 30 14 -
PGQGEAISRLWRQK HAD2_PSEPU 30 14 -
PGQGDAISRLWRQK HAD1_PSEPU 30 14 -
GGCAEELSSLWRQR HAD1_PSESP 30 14 -
PERGTEISLMWRQK HAD2_PSESP 30 14 -
PGKGKDISVLWRQK DEH2_MORSP 30 14 -
GASAEALSMLWRQR HAD4_BURCE 31 14 -
PGRGEYITQVWRQK HAD_XANAU 28 14 -
GGPEGATTRLMKGE HYES_HUMAN 44 29 -
GGPEGATTRLMKGE Q16764 44 29 -
EFPEGPTEQLMKGK HYES_MOUSE 44 29 -
KFPEGPTEQLMKGK HYES_RAT 44 29 -

Motif 3 width=14
Element Seqn Id St Int Rpt
QLEYTWLRSLMNRY HAD_PSESP 44 0 -
QLEYTWLSSLMGRY HAD2_PSEPU 44 0 -
QLEYTWLRSLMGRY HAD1_PSEPU 44 0 -
QLEYSWTRTLMGRY HAD1_PSESP 44 0 -
QLEYSWLRSLMGQY HAD2_PSESP 44 0 -
QLEYAWLRCLMGQY DEH2_MORSP 44 0 -
QLEYSWTRTLMHQY HAD4_BURCE 45 0 -
QLEYSWLRALMGRY HAD_XANAU 42 0 -
ITLSQWIPLMEENC HYES_HUMAN 58 0 -
ITLSQWIPLMEENC Q16764 58 0 -
ITFSQWVPLMDESY HYES_MOUSE 58 0 -
ITFSQWVPLMDESC HYES_RAT 58 0 -

Motif 4 width=14
Element Seqn Id St Int Rpt
LKRRGLKLAILSNG HAD_PSESP 107 49 -
LKASGLPMAIASNG HAD2_PSEPU 107 49 -
LKAAGLPLGIISNG HAD1_PSEPU 107 49 -
LKAAGFTTAILSNG HAD1_PSESP 107 49 -
LRSGAVPLAILSNG HAD2_PSESP 107 49 -
LRQRGMRLAILSNG DEH2_MORSP 107 49 -
LKSAGYIVAILSNG HAD4_BURCE 108 49 -
AELAPLKRAILSNG HAD_XANAU 103 47 -
LRKKGFTTAILTNT HYES_HUMAN 112 40 -
LRKKGFTTAILTNT Q16764 112 40 -
LKKKGFTTCIVTNN HYES_MOUSE 112 40 -
LKKKGFTTCIVTNN HYES_RAT 112 40 -

Motif 5 width=17
Element Seqn Id St Int Rpt
FDHLLSVDPVQVYKPDN HAD_PSESP 138 17 -
FDHLISVETVKVFKPDN HAD2_PSEPU 138 17 -
FDQLISVEDVQVFKPDS HAD1_PSEPU 138 17 -
LDQCISVDEIKIYKPDP HAD1_PSESP 138 17 -
FSHLISADEVSVSKPSP HAD2_PSESP 138 17 -
FEHLISVDSARAYKPHP DEH2_MORSP 138 17 -
LDSCLSADDLKIYKPDP HAD4_BURCE 139 17 -
FDAVISVDAKRVFKPHP HAD_XANAU 134 17 -
FDFLIESCQVGMVKPEP HYES_HUMAN 147 21 -
FDFLIESCQVGMVKPEP Q16764 147 21 -
FDFLIESCQVGMIKPEP HYES_MOUSE 147 21 -
FDFLIESCQVGMIKPEP HYES_RAT 147 21 -

Motif 6 width=21
Element Seqn Id St Int Rpt
VYELAEQALGLDRSAILFVSS HAD_PSESP 156 1 -
VYSLAEQTMAIPRDRLLFVSS HAD2_PSEPU 156 1 -
VYSLAEKRMGFPKENILFVSS HAD1_PSEPU 156 1 -
VYQFACDRLDVRPSEVCFVSS HAD1_PSESP 156 1 -
AYELAEKRLKVVRSKLLFVSS HAD2_PSESP 156 1 -
AYELGEEAFGISRESILFVSS DEH2_MORSP 156 1 -
IYQFACDRLGVNPNEVCFVSS HAD4_BURCE 157 1 -
SYALVEEVLGVTPAEVLFVSS HAD_XANAU 152 1 -
IYKFLLDTLKASPSEVVFLDD HYES_HUMAN 165 1 -
IYKFLLDTLKASPSEVVFLDD Q16764 165 1 -
IYNFLLDTLKAKPNEVVFLDD HYES_MOUSE 165 1 -
IYKFVLDTLKAKPNEVVFLDD HYES_RAT 165 1 -

Motif 7 width=14
Element Seqn Id St Int Rpt
GARYFGFPTCWINR HAD_PSESP 183 6 -
GARHFGFPVCWVNR HAD2_PSEPU 183 6 -
AASNFGFPVCWINR HAD1_PSEPU 183 6 -
GAGAFGFNTVRINR HAD1_PSESP 183 6 -
GARHFGFQVCWVNR HAD2_PSESP 183 6 -
GAKAFGYQVCWINR DEH2_MORSP 183 6 -
GAGKFGFNTVRINR HAD4_BURCE 184 6 -
GAKNFGFSVARVAR HAD_XANAU 179 6 -
PARDLGMVTILVQD HYES_HUMAN 192 6 -
PARDLGMVTILVQD Q16764 192 6 -
PARDMGMVTILVHN HYES_MOUSE 192 6 -
PARDMGMVTILVRD HYES_RAT 192 6 -