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PR00409

Identifier
PHDIOXRDTASE  [View Relations]  [View Alignment]  
Accession
PR00409
No. of Motifs
8
Creation Date
20-OCT-1995  (UPDATE 30-JUN-1999)
Title
Phthalate dioxygenase reductase family signature
Database References

INTERPRO; IPR000951
UMBBD; e0117
PDB; 2PIA
SCOP; 2PIA
CATH; 2PIA
Literature References
1. HYDE, G.E., CRAWFORD, N.M. AND CAMPBELL, W.H.
The sequence of squash NADH:nitrate reductase and its relationship to the
sequences of other flavoprotein oxidoreductases. A family of flavoprotein
pyridine nucleotide cytochrome reductases.
J.BIOL.CHEM. 266 23542-23547 (1991).
 
2. KARPLUS, P.A. AND BRUNS, C.M.
Structure-function relations for ferredoxin reductase.
J.BIOENERG.BIOMEMBR. 26 89-99 (1994).
 
3. CORRELL, C.C., BATIE, C.J., BALLOU, D.P. AND LUDWIG, M.L.
Phthalate dioxygenase reductase: a modular structure for electron transfer
from pyridine nucleotides to [2Fe-2S].
SCIENCE 258 1604-1610 (1992).
 
4. BRUNEL F. AND DAVISON J.
Cloning and sequencing of Pseudomonas genes encoding vanillate demethylase.
J.BACTERIOL. 170 4924-4930 (1988).
 
5. CORRELL, C.C., LUDWIG, M.L., BRUNS, C.M. AND KARPLUS, P.A.
Structural prototypes for an extended family of flavoprotein reductases: 
comparison of phthalate dioxygenase reductase with ferredoxin reductase 
and ferredoxin. 
PROTEIN SCI. 2 2112-2133 (1993).

Documentation
Flavoprotein pyridine nucleotide cytochrome reductases [1] (FPNCR) catalyse
the interchange of reducing equivalents between one-electron carriers and
the two-electron-carrying nicotinamide dinucleotides. The enzymes include
ferredoxin:NADP+ reductases (FNR) [2]; plant and fungal NAD(P)H:nitrate
reductases [1]; NADH:cytochrome b5 reductases; NADPH:P450 reductases;
NADPH:sulfite reductases; nitric oxide synthases; phthalate dioxygenase
reductase [3]; and various other flavoproteins.
 
Phthalate dioxygenase reductase (PDR) is a member of family of
FPNCR/[2Fe-2S] ferredoxin fusion proteins, found in flavobacteria, that
participate in oxidative metabolism of a variety of substrates. Other
family members are vanillate demethylase reductase [4]; phenoxybenzoate
dioxygenase; and pentachlorophenol 4-monooxygenase. All of contain a
[2Fe-2S] ferredoxin domain fused to the C-terminus of an FPNCR domain. The
direction of electron flow is from flavin to the [2Fe-2S] center. By
contrast with most FPNCRs, PDR binds FMN instead of FAD.
 
The 3D-structure of PDR has been solved [3]. The overall fold of the FPNCR
module is similar to that of ferredoxin:NADP+ reductase [2]; the FMN-binding
domain (N-terminal) has the topology of an anti-parallel beta-barrel; and
the NAD(P)-binding domain (C-terminal) has the topology of a classical
pyridine dinucleotide-binding fold (i.e., a central parallel beta-sheet
flanked by 2 helices on each side).
 
PHDIOXRDTASE is an 8-element fingerprint that provides a signature for the
phthalate dioxygenase reductase family. The fingerprint was derived from
an initial alignment of 5 sequences: the motifs were drawn solely from the
FPNCR domain - motifs 1-5 encode the beta-barrel, and motifs 6-8 span the
NAD(H)-binding domain. Motif 1 corresponds to the first motif of the FPNCR
signature; motifs 3 and 4 are involved in binding the isoalloxazine ring
and the phosphate group of FMN, respectively (cf. FPNCR motifs 2 and 3);
motif 6 includes residues involved in binding the diphosphate group of the
pyridine nucleotide (cf. FPNCR motif 4); and motif 8 contains a conserved
Cys residue that may interact with NAD(H) and is necessary for efficient
electron transfer (cf. FPNCR motif 8) [5]. Two iterations on OWL26.2 were
required to reach convergence, at which point a true set comprising 6
sequences was identified. Several partial matches were also found.
 
An update on SPTR37_9f identified a true set of 8 sequences, and 9
partial matches.
Summary Information
   8 codes involving  8 elements
0 codes involving 7 elements
2 codes involving 6 elements
2 codes involving 5 elements
1 codes involving 4 elements
2 codes involving 3 elements
2 codes involving 2 elements
Composite Feature Index
888888888
700000000
601222212
501121212
400101101
301110201
200000202
12345678
True Positives
P95277        PDR_BURCE     POBB_PSEPS    Q47914        
VANB_ACICA VANB_PSEPU VANB_PSES9 VANB_PSESP
True Positive Partials
Codes involving 6 elements
O86996 O88034
Codes involving 5 elements
O86347 YEAX_ECOLI
Codes involving 4 elements
CBAB_ALCSP
Codes involving 3 elements
HMPA_ERWCH P94680
Codes involving 2 elements
HMPA_ECOLI HMPA_VIBPA
Sequence Titles
P95277      HYPOTHETICAL 93.4 KD PROTEIN - MYCOBACTERIUM TUBERCULOSIS. 
PDR_BURCE PHTHALATE DIOXYGENASE REDUCTASE (EC 1.-.-.-) (PDR) - BURKHOLDERIA CEPACIA (PSEUDOMONAS CEPACIA).
POBB_PSEPS PHENOXYBENZOATE DIOXYGENASE BETA SUBUNIT (EC 1.-.-.-) (4-CARBOXYDIPHENYL ETHER;PHENOXYBENZOATE DIOXYGENASE BETA SUBUNIT) - PSEUDOMONAS PSEUDOALCALIGENES.
Q47914 PENTACHLOROPHENOL 4-MONOOXYGENASE REDUCTASE - FLAVOBACTERIUM SP.
VANB_ACICA VANILLATE O-DEMETHYLASE OXIDOREDUCTASE (EC 1.14.13.-) (VANILLATE DEGRADATION FERREDOXIN-LIKE PROTEIN) - ACINETOBACTER CALCOACETICUS.
VANB_PSEPU VANILLATE O-DEMETHYLASE OXIDOREDUCTASE (EC 1.14.13.-) (VANILLATE DEGRADATION FERREDOXIN-LIKE PROTEIN) - PSEUDOMONAS PUTIDA.
VANB_PSES9 VANILLATE O-DEMETHYLASE OXIDOREDUCTASE (EC 1.14.13.-) (VANILLATE DEGRADATION FERREDOXIN-LIKE PROTEIN) - PSEUDOMONAS SP. (STRAIN ATCC 19151).
VANB_PSESP VANILLATE O-DEMETHYLASE OXIDOREDUCTASE (EC 1.14.13.-) (VANILLATE DEGRADATION FERREDOXIN-LIKE PROTEIN) - PSEUDOMONAS SP. (STRAIN HR199 / DSM 7063).

O86996 HYPOTHETICAL 41.4 KD PROTEIN - ACINETOBACTER LWOFFII K24.
O88034 IRON-SULFUR OXIDOREDUCTASE BETA SUBUNIT - STREPTOMYCES COELICOLOR.

O86347 HYPOTHETICAL 33.5 KD PROTEIN - MYCOBACTERIUM TUBERCULOSIS.
YEAX_ECOLI PUTATIVE DIOXYGENASE BETA SUBUNIT YEAX (EC 1.-.-.-) - ESCHERICHIA COLI.

CBAB_ALCSP 3-CHLOROBENZOATE-3,4-DIOXYGENASE REDUCTASE SUBUNIT (EC 1.14.-.-) - ALCALIGENES SP. (STRAIN BR60).

HMPA_ERWCH FLAVOHEMOPROTEIN (HEMOGLOBIN-LIKE PROTEIN) (FLAVOHEMOGLOBIN) (HEMOPROTEIN X) - ERWINIA CHRYSANTHEMI.
P94680 TOLUENESULFONATE METHYL-MONOOXYGENASE REDUCTASE COMPONENT - COMAMONAS TESTOSTERONI (PSEUDOMONAS TESTOSTERONI).

HMPA_ECOLI FLAVOHEMOPROTEIN (HEMOGLOBIN-LIKE PROTEIN) (FLAVOHEMOGLOBIN) (DIHYDROPTERIDINE REDUCTASE (EC 1.6.99.7)) (FERRISIDEROPHORE REDUCTASE B) (NITRIC OXIDE DIOXYGENASE) (NOD) - ESCHERICHIA COLI.
HMPA_VIBPA FLAVOHEMOPROTEIN (HEMOGLOBIN-LIKE PROTEIN) (FLAVOHEMOGLOBIN) - VIBRIO PARAHAEMOLYTICUS.
Scan History
OWL26_2    2  1000 NSINGLE    
SPTR37_9f 3 50 NSINGLE
Initial Motifs
Motif 1  width=11
Element Seqn Id St Int Rpt
GSPLPTFEAGA VANB_PSES9 26 26 -
GAPLPPFEAGA PDR_BURCE 33 33 -
GVILPEFTAGA FSU12290 32 32 -
GMLLPAFTAGA NM1PHT1 36 36 -
RDGLAPFDAGA S44172 34 34 -

Motif 2 width=13
Element Seqn Id St Int Rpt
AHLDLHLPGGLVR VANB_PSES9 36 -1 -
AHIDLRLPRGITR S44172 44 -1 -
AHIGVSLPNGIQR FSU12290 42 -1 -
AHLRVRVPNGSIR NM1PHT1 46 -1 -
ANLTVAVPNGSRR PDR_BURCE 43 -1 -

Motif 3 width=15
Element Seqn Id St Int Rpt
RPYSLCNAPGETHRY VANB_PSES9 48 -1 -
RSYSLVNPQGERDRY FSU12290 54 -1 -
RNYSLSNDPQERERY NM1PHT1 58 -1 -
RSYSLLNDPAERHRY S44172 56 -1 -
RTYSLCNESSERDRY PDR_BURCE 55 -1 -

Motif 4 width=15
Element Seqn Id St Int Rpt
SRGGSRAVHEQLRVG VANB_PSES9 72 9 -
GRGGSISFIDDTSEG PDR_BURCE 79 9 -
SRGGSRYLHEQLRVG FSU12290 78 9 -
GRGGSVSMADDIEAG NM1PHT1 82 9 -
SRGGSAWLHADARVG S44172 80 9 -

Motif 5 width=15
Element Seqn Id St Int Rpt
GDAVEVSLPRNEFPL PDR_BURCE 93 -1 -
GALIEVDGPSNHFAL S44172 94 -1 -
GDLLPVATPQNEFEL NM1PHT1 96 -1 -
GQRLSIVPPANNFAL FSU12290 92 -1 -
GQHLTTSAPRNLFPL VANB_PSES9 86 -1 -

Motif 6 width=20
Element Seqn Id St Int Rpt
VLFAGGIGITPIWSMIQRLR FSU12290 114 7 -
ILVAGGIGITPMLSMARQLR PDR_BURCE 115 7 -
LLFAGGIGITPILAMAQVLA VANB_PSES9 108 7 -
IFVAGGIGITPILSMMRHLK NM1PHT1 118 7 -
VFIAGGIGITPLWSMVQRLE S44172 116 7 -

Motif 7 width=10
Element Seqn Id St Int Rpt
WTLHYRARSR S44172 141 5 -
WELQDACRGK FSU12290 139 5 -
FKLYYCTRNP NM1PHT1 144 6 -
FELHYCVRSR VANB_PSES9 133 5 -
FRLYYLTRDP PDR_BURCE 141 6 -

Motif 8 width=9
Element Seqn Id St Int Rpt
IFYCCGPEA FSU12290 195 46 -
HLYVCGPGG VANB_PSES9 184 41 -
HVYCCGPQA PDR_BURCE 195 44 -
HFYCCGPVP S44172 192 41 -
HVYCCGPRP NM1PHT1 198 44 -
Final Motifs
Motif 1  width=11
Element Seqn Id St Int Rpt
GSPLPTFEAGA VANB_PSES9 26 26 -
DGSLLRFSAGA VANB_PSEPU 25 25 -
GGLLPPVEAGA VANB_PSESP 26 26 -
GSDLPAFDAGS VANB_ACICA 28 28 -
GMLLPAFTAGA POBB_PSEPS 36 36 -
RDGLAPFDAGA P95277 34 34 -
GVILPEFTAGA Q47914 32 32 -
GAPLPPFEAGA PDR_BURCE 33 33 -

Motif 2 width=13
Element Seqn Id St Int Rpt
AHLDLHLPGGLVR VANB_PSES9 36 -1 -
AHIDVHLPEGQVR VANB_PSEPU 35 -1 -
AHVDVHLPGGLIR VANB_PSESP 36 -1 -
SHIDVHLKNGLTR VANB_ACICA 38 -1 -
AHLRVRVPNGSIR POBB_PSEPS 46 -1 -
AHIDLRLPRGITR P95277 44 -1 -
AHIGVSLPNGIQR Q47914 42 -1 -
ANLTVAVPNGSRR PDR_BURCE 43 -1 -

Motif 3 width=15
Element Seqn Id St Int Rpt
RPYSLCNAPGETHRY VANB_PSES9 48 -1 -
RQYSLCNHPEERHRY VANB_PSEPU 47 -1 -
RQYSLWNQPGAQSHY VANB_PSESP 48 -1 -
RQYSLSNCCSEQHRY VANB_ACICA 50 -1 -
RNYSLSNDPQERERY POBB_PSEPS 58 -1 -
RSYSLLNDPAERHRY P95277 56 -1 -
RSYSLVNPQGERDRY Q47914 54 -1 -
RTYSLCNESSERDRY PDR_BURCE 55 -1 -

Motif 4 width=15
Element Seqn Id St Int Rpt
SRGGSRAVHEQLRVG VANB_PSES9 72 9 -
SRGGSRSLHEQIHNG VANB_PSEPU 71 9 -
SRGGSKAVHENLRVG VANB_PSESP 72 9 -
SRGGSRCIHQDYREG VANB_ACICA 74 9 -
GRGGSVSMADDIEAG POBB_PSEPS 82 9 -
SRGGSAWLHADARVG P95277 80 9 -
SRGGSRYLHEQLRVG Q47914 78 9 -
GRGGSISFIDDTSEG PDR_BURCE 79 9 -

Motif 5 width=15
Element Seqn Id St Int Rpt
GQHLTTSAPRNLFPL VANB_PSES9 86 -1 -
GARLRISAPRNLFPL VANB_PSEPU 85 -1 -
GMRVQISEPRNLFPL VANB_PSESP 86 -1 -
GDHLNIGTPRNLFEI VANB_ACICA 88 -1 -
GDLLPVATPQNEFEL POBB_PSEPS 96 -1 -
GALIEVDGPSNHFAL P95277 94 -1 -
GQRLSIVPPANNFAL Q47914 92 -1 -
GDAVEVSLPRNEFPL PDR_BURCE 93 -1 -

Motif 6 width=20
Element Seqn Id St Int Rpt
LLFAGGIGITPILAMAQVLA VANB_PSES9 108 7 -
LLFAGGIGITPILCMAEQLA VANB_PSEPU 107 7 -
LLFAGGIGITPILCMAQELA VANB_PSESP 108 7 -
VLFAGGIGITPILSMAYRLK VANB_ACICA 110 7 -
IFVAGGIGITPILSMMRHLK POBB_PSEPS 118 7 -
VFIAGGIGITPLWSMVQRLE P95277 116 7 -
VLFAGGIGITPIWSMIQRLR Q47914 114 7 -
ILVAGGIGITPMLSMARQLR PDR_BURCE 115 7 -

Motif 7 width=10
Element Seqn Id St Int Rpt
FELHYCVRSR VANB_PSES9 133 5 -
FELHYCARSS VANB_PSEPU 131 4 -
FELHYCARST VANB_PSESP 133 5 -
FELHYFVRSH VANB_ACICA 135 5 -
FKLYYCTRNP POBB_PSEPS 144 6 -
WTLHYRARSR P95277 141 5 -
WELQDACRGK Q47914 139 5 -
FRLYYLTRDP PDR_BURCE 141 6 -

Motif 8 width=9
Element Seqn Id St Int Rpt
HLYVCGPGG VANB_PSES9 184 41 -
HLYVCGPGG VANB_PSEPU 184 43 -
HLYVCGPGG VANB_PSESP 187 44 -
HLYVCGPAG VANB_ACICA 187 42 -
HVYCCGPRP POBB_PSEPS 198 44 -
HFYCCGPVP P95277 192 41 -
IFYCCGPEA Q47914 195 46 -
HVYCCGPQA PDR_BURCE 195 44 -