Identifier | PHDIOXRDTASE  [View Relations]  [View Alignment]  
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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
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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).
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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.
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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
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Composite Feature Index | 8 | 8 | 8 | 8 | 8 | 8 | 8 | 8 | 8 | 7 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 6 | 0 | 1 | 2 | 2 | 2 | 2 | 1 | 2 | 5 | 0 | 1 | 1 | 2 | 1 | 2 | 1 | 2 | 4 | 0 | 0 | 1 | 0 | 1 | 1 | 0 | 1 | 3 | 0 | 1 | 1 | 1 | 0 | 2 | 0 | 1 | 2 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 2 | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 |
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True Positives | P95277 PDR_BURCE POBB_PSEPS Q47914 VANB_ACICA VANB_PSEPU VANB_PSES9 VANB_PSESP |
True Positive Partials | |
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.
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Scan History | OWL26_2 2 1000 NSINGLE SPTR37_9f 3 50 NSINGLE
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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 -
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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 -
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