The enzymes which catalyze the reversible phosphorolysis of pyrimidine nucleosides are involved in the degradation of these compounds and in their utilization as carbon and energy sources, or in the rescue of pyrimidine bases for nucleotide synthesis. Sinorhizobium medicae (strain WSM419) (taxid: 366394) EC: 2EC: .EC: 4EC: .EC: 2EC: .EC: 4
Catalyzes the reversible phosphorolysis of thymidine. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis.
Score = 75.1 bits (183), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 40/68 (58%), Positives = 49/68 (72%), Gaps = 4/68 (5%)
Query: 13 AMLMAMFINGLTNEETIALTKSMVDSGETLSWGPEG---IVVDKHSTGGVGDKVSIPLVP 69
AMLMA+ + G+ EET LT+++ SG+ L W PE +VDKHSTGGVGDKVS+ L P
Sbjct: 73 AMLMAIRLRGMDLEETSVLTQALAQSGQQLEW-PEAWRQQLVDKHSTGGVGDKVSLVLAP 131
Query: 70 ALAACGLK 77
ALAACG K
Sbjct: 132 ALAACGCK 139
Catalyzes the reversible phosphorolysis of thymidine. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis.
The enzymes which catalyze the reversible phosphorolysis of pyrimidine nucleosides are involved in the degradation of these compounds and in their utilization as carbon and energy sources, or in the rescue of pyrimidine bases for nucleotide synthesis.
Catalyzes the reversible phosphorolysis of thymidine. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis.
Score = 70.1 bits (170), Expect = 3e-12, Method: Composition-based stats.
Identities = 37/78 (47%), Positives = 52/78 (66%), Gaps = 2/78 (2%)
Query: 1 MVTQSDTNNVPRAMLMAMFINGLTNEETIALTKSMVDSGETLSWGPE--GIVVDKHSTGG 58
+V +S + A+LMA++ NGL + E LTK+M+DSG+ + PE I++DKHSTGG
Sbjct: 28 LVNKSIPDYQISALLMAIWFNGLDDNELYFLTKAMIDSGKIYKFHPEYKKILIDKHSTGG 87
Query: 59 VGDKVSIPLVPALAACGL 76
+GDKVSI L P L + L
Sbjct: 88 IGDKVSIALRPILVSFDL 105
The enzymes which catalyze the reversible phosphorolysis of pyrimidine nucleosides are involved in the degradation of these compounds and in their utilization as carbon and energy sources, or in the rescue of pyrimidine bases for nucleotide synthesis.
The enzymes which catalyze the reversible phosphorolysis of pyrimidine nucleosides are involved in the degradation of these compounds and in their utilization as carbon and energy sources, or in the rescue of pyrimidine bases for nucleotide synthesis.
The enzymes which catalyze the reversible phosphorolysis of pyrimidine nucleosides are involved in the degradation of these compounds and in their utilization as carbon and energy sources, or in the rescue of pyrimidine bases for nucleotide synthesis.
Score = 68.6 bits (166), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 34/64 (53%), Positives = 44/64 (68%), Gaps = 1/64 (1%)
Query: 13 AMLMAMFINGLTNEETIALTKSMVDSGETLSWGPEGI-VVDKHSTGGVGDKVSIPLVPAL 71
A MA + +G+ +E +ALT +M DSG+ L W G +VDKHSTGGVGD VS+ L P +
Sbjct: 42 AFAMATWFSGMNRDECVALTLAMRDSGDILDWSEFGRPIVDKHSTGGVGDNVSLMLAPIV 101
Query: 72 AACG 75
AACG
Sbjct: 102 AACG 105
The enzymes which catalyze the reversible phosphorolysis of pyrimidine nucleosides are involved in the degradation of these compounds and in their utilization as carbon and energy sources, or in the rescue of pyrimidine bases for nucleotide synthesis.
Score = 67.8 bits (164), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 34/66 (51%), Positives = 46/66 (69%), Gaps = 3/66 (4%)
Query: 13 AMLMAMFINGLTNEETIALTKSMVDSGETLSWGPE---GIVVDKHSTGGVGDKVSIPLVP 69
A+ MA++ G++ +E ALT +M DSG+ L W + G V+DKHSTGGVGD VS+ L P
Sbjct: 41 ALAMAIYFRGMSAQEKTALTVAMRDSGDVLDWRQDNLNGPVLDKHSTGGVGDVVSLMLGP 100
Query: 70 ALAACG 75
+AACG
Sbjct: 101 IVAACG 106
The enzymes which catalyze the reversible phosphorolysis of pyrimidine nucleosides are involved in the degradation of these compounds and in their utilization as carbon and energy sources, or in the rescue of pyrimidine bases for nucleotide synthesis.
In general, members of this protein family are designated pyrimidine-nucleoside phosphorylase, enzyme family EC 2.4.2.2, as in Bacillus subtilis, and more narrowly as the enzyme family EC 2.4.2.4, thymidine phosphorylase (alternate name: pyrimidine phosphorylase), as in Escherichia coli. The set of proteins encompassed by this model is designated subfamily rather than equivalog for this reason; the protein name from this model should be used when TIGR02643 does not score above trusted cutoff [Purines, pyrimidines, nucleosides, and nucleotides, Other]. Length = 405
>gnl|CDD|223291 COG0213, DeoA, Thymidine phosphorylase [Nucleotide transport and metabolism]
Score = 79.0 bits (195), Expect = 4e-19
Identities = 37/67 (55%), Positives = 45/67 (67%), Gaps = 3/67 (4%)
Query: 13 AMLMAMFINGLTNEETIALTKSMVDSGETLSWGPE---GIVVDKHSTGGVGDKVSIPLVP 69
A MA+F NG+ +E +ALT +M DSG+ L W G VVDKHSTGGVGD VS+ L P
Sbjct: 40 AFAMAVFFNGMNRDERVALTLAMRDSGDVLDWRSLDLNGPVVDKHSTGGVGDVVSLMLGP 99
Query: 70 ALAACGL 76
+AACG
Sbjct: 100 IVAACGG 106
Thymidine phosphorylase (alternate name: pyrimidine phosphorylase), EC 2.4.2.4, is the designation for the enzyme of E. coli and other Proteobacteria involved in (deoxy)nucleotide degradation. It often occurs in an operon with a deoxyribose-phosphate aldolase, phosphopentomutase and a purine nucleoside phosphorylase. In many other lineages, the corresponding enzyme is designated pyrimidine-nucleoside phosphorylase (EC 2.4.2.2); the naming convention imposed by this model represents standard literature practice [Purines, pyrimidines, nucleosides, and nucleotides, Other]. Length = 437
This enzyme family is found, so far, strictly in the Archaea, and only in those with a type III Rubisco enzyme. Most of the members previously were annotated as thymidine phosphorylase, or DeoA. The AMP metabolized by this enzyme may be produced by ADP-dependent sugar kinases. Length = 500
Score = 68.3 bits (167), Expect = 3e-15
Identities = 33/66 (50%), Positives = 43/66 (65%), Gaps = 2/66 (3%)
Query: 13 AMLMAMFINGLTNEETIALTKSMVDSGETLSWGPEGIVVDKHSTGGV-GDKVSIPLVPAL 71
A L A ING+T +E ALT +M D+GE L W ++DKHS GGV G+K S+ +VP +
Sbjct: 123 AFLTASAINGMTMDEIEALTIAMADTGEMLEW-DREPIMDKHSIGGVPGNKTSLIVVPIV 181
Query: 72 AACGLK 77
AA GL
Sbjct: 182 AAAGLL 187
Members of this family are closely related to characterized examples of thymidine phosphorylase (EC 2.4.2.4) and pyrimidine nucleoside phosphorylase (RC 2.4.2.2). Most examples are found in the archaea, but other examples in Legionella pneumophila str. Paris and Rhodopseudomonas palustris CGA009. Length = 493
Score = 39.8 bits (94), Expect = 4e-06
Identities = 12/28 (42%), Positives = 15/28 (53%)
Query: 13 AMLMAMFINGLTNEETIALTKSMVDSGE 40
A LMA+ I G T EE K+M +S
Sbjct: 39 AFLMALRIKGETPEEIAGAAKAMRESAT 66
This family includes anthranilate phosphoribosyltransferase (TrpD), thymidine phosphorylase. All these proteins can transfer a phosphorylated ribose substrate. Length = 66
This family includes anthranilate phosphoribosyltransferase (TrpD), thymidine phosphorylase. All these proteins can transfer a phosphorylated ribose substrate. Length = 254
Score = 34.9 bits (81), Expect = 0.001
Identities = 22/68 (32%), Positives = 30/68 (44%), Gaps = 3/68 (4%)
Query: 13 AMLMAMFINGLTNEETIALTKSMVDSGETLSWGPEGIVVDKHSTGGVGDK---VSIPLVP 69
A+L A+ I G T EE K+M + + P +VD TGG G +S
Sbjct: 34 AILAALRIKGETPEEITGFAKAMREHAVKVPGRPVEDLVDIVGTGGDGANTINISTASAF 93
Query: 70 ALAACGLK 77
AA G+K
Sbjct: 94 VAAAAGVK 101
In many widely different species, including E. coli, Thermotoga maritima, and Archaeoglobus fulgidus, this enzymatic domain (anthranilate phosphoribosyltransferase) is found C-terminal to glutamine amidotransferase; the fusion protein is designated anthranilate synthase component II (EC 4.1.3.27) [Amino acid biosynthesis, Aromatic amino acid family]. Length = 330
In general, members of this protein family are designated pyrimidine-nucleoside phosphorylase, enzyme family EC 2.4.2.2, as in Bacillus subtilis, and more narrowly as the enzyme family EC 2.4.2.4, thymidine phosphorylase (alternate name: pyrimidine phosphorylase), as in Escherichia coli. The set of proteins encompassed by this model is designated subfamily rather than equivalog for this reason; the protein name from this model should be used when TIGR02643 does not score above trusted cutoff.
Probab=99.95 E-value=1e-28 Score=191.49 Aligned_cols=79 Identities=48% Similarity=0.708 Sum_probs=74.1
Q ss_pred CCCCCCChHHHHHHHHHHHhcCCCHHHHHHHHHHHHhhCCccCCC--CC-CCceeeeccCCCCCCcchHHHHHHhcCCCC
Q psy1333 1 MVTQSDTNNVPRAMLMAMFINGLTNEETIALTKSMVDSGETLSWG--PE-GIVVDKHSTGGVGDKVSIPLVPALAACGLK 77 (79)
Q Consensus 1 ~~~g~~~~~qiaafL~al~~kGet~~Ei~g~~~am~~~~~~~~~~--~~-~~~vD~~gTGGdg~niSt~~a~v~Aa~Gv~ 77 (79)
+++|+++|+|++|||||+++||||.+|+.+|+++|++++.+++|+ +. ++++|+|||||||+||||+++|++|+||++
T Consensus 28 i~~g~i~d~QiaAfLmAl~~kG~t~~Ei~~lt~aM~~sg~~i~~~~~~~~~~~vDkhgTGGdG~niSt~~apivAA~Gv~ 107 (437)
T TIGR02643 28 ITDGSVSEGQIAAFAMAVFFNGMNRDERVALTLAMRDSGDVLDWRSLDLNGPVVDKHSTGGVGDVVSLMLGPIVAACGGY 107 (437)
T ss_pred HHcCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhCCcccCcccccCCCeeEecCCCCCCcchhHHHHHHHHhCCCC
Confidence 478999999999999999999999999999999999999999987 21 468999999999999999999999999999
Q ss_pred CC
Q psy1333 78 PS 79 (79)
Q Consensus 78 Va 79 (79)
|+
T Consensus 108 Va 109 (437)
T TIGR02643 108 VP 109 (437)
T ss_pred ee
Confidence 86
Thymidine phosphorylase (alternate name: pyrimidine phosphorylase), EC 2.4.2.4, is the designation for the enzyme of E. coli and other Proteobacteria involved in (deoxy)nucleotide degradation. It often occurs in an operon with a deoxyribose-phosphate aldolase, phosphopentomutase and a purine nucleoside phosphorylase. In many other lineages, the corresponding enzyme is designated pyrimidine-nucleoside phosphorylase (EC 2.4.2.2); the naming convention imposed by this model represents standard literature practice.
Probab=99.93 E-value=2.7e-26 Score=171.41 Aligned_cols=79 Identities=28% Similarity=0.323 Sum_probs=72.8
Q ss_pred CCCCCCChHHHHHHHHHHHhcCCCHHHHHHHHHHHHhhCCccCCCCCCCceeeeccCCCCC---CcchHHHHHHhcCCCC
Q psy1333 1 MVTQSDTNNVPRAMLMAMFINGLTNEETIALTKSMVDSGETLSWGPEGIVVDKHSTGGVGD---KVSIPLVPALAACGLK 77 (79)
Q Consensus 1 ~~~g~~~~~qiaafL~al~~kGet~~Ei~g~~~am~~~~~~~~~~~~~~~vD~~gTGGdg~---niSt~~a~v~Aa~Gv~ 77 (79)
|++|+++|.|++|||+++|+||||++||++|+++|++++.++++++...++|+|||||||+ |+||+++|++|++|+|
T Consensus 22 il~g~~~~~q~~AfL~alr~kget~~Elag~~~a~~~~~~~~~~~~~~~~iD~~gtggdg~~t~nist~~a~vlA~~G~~ 101 (330)
T TIGR01245 22 IMSGEASPAQIAAILAALRIKGETPEEITGFAKAMREHAVKVPGRPVEDLVDIVGTGGDGANTINISTASAFVAAAAGVK 101 (330)
T ss_pred HHcCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhCCCCCCccCCCcccccCCCCCCCCccccHHHHHHHHHhCCCE
Confidence 5789999999999999999999999999999999999999988742245899999999998 7999999999999999
Q ss_pred CC
Q psy1333 78 PS 79 (79)
Q Consensus 78 Va 79 (79)
|+
T Consensus 102 V~ 103 (330)
T TIGR01245 102 VA 103 (330)
T ss_pred EE
Confidence 85
In many widely different species, including E. coli, Thermotoga maritima, and Archaeoglobus fulgidus, this enzymatic domain (anthranilate phosphoribosyltransferase) is found C-terminal to glutamine amidotransferase; the fusion protein is designated anthranilate synthase component II (EC 4.1.3.27)
This enzyme family is found, so far, strictly in the Archaea, and only in those with a type III Rubisco enzyme. Most of the members previously were annotated as thymidine phosphorylase, or DeoA. The AMP metabolized by this enzyme may be produced by ADP-dependent sugar kinases.
>PRK08136 glycosyl transferase family protein; Provisional
Members of this family are closely related to characterized examples of thymidine phosphorylase (EC 2.4.2.4) and pyrimidine nucleoside phosphorylase (RC 2.4.2.2). Most examples are found in the archaea, but other examples in Legionella pneumophila str. Paris and Rhodopseudomonas palustris CGA009.
Probab=99.89 E-value=9e-24 Score=158.32 Aligned_cols=76 Identities=14% Similarity=0.129 Sum_probs=69.7
Q ss_pred CCCCCCChHHHHHHHHHHHhcCCCHHHHHHHHHHHHhhCCccCCCCCCCceee-eccCCCCC-CcchHHHHHHhcCCCCC
Q psy1333 1 MVTQSDTNNVPRAMLMAMFINGLTNEETIALTKSMVDSGETLSWGPEGIVVDK-HSTGGVGD-KVSIPLVPALAACGLKP 78 (79)
Q Consensus 1 ~~~g~~~~~qiaafL~al~~kGet~~Ei~g~~~am~~~~~~~~~~~~~~~vD~-~gTGGdg~-niSt~~a~v~Aa~Gv~V 78 (79)
|++|+++|.|++|||++||+||||++||+||+++||+++.+++.+ ..+|+ ||||||+. +++|++||++|++|+||
T Consensus 33 il~g~~~~~q~aAfL~alr~kgeT~eEi~g~~~a~r~~~~~~~~~---~~iD~~~gtG~d~~~~~~~~~a~vlA~~G~~V 109 (323)
T PRK09071 33 ILDGEVEDDQLGAFLMLLRVKEETAEELAGFVEAIRERLQAPPLA---VDLDWPSYAGKRRHLPWYLLAAKLLAQNGYRV 109 (323)
T ss_pred HHcCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhcccCCCC---CceecCCcCCCCCCcccHHHHHHHHHHCCCeE
Confidence 578999999999999999999999999999999999999887633 34998 99999977 89999999999999998
Q ss_pred C
Q psy1333 79 S 79 (79)
Q Consensus 79 a 79 (79)
+
T Consensus 110 ~ 110 (323)
T PRK09071 110 L 110 (323)
T ss_pred E
Confidence 5
>PF02885 Glycos_trans_3N: Glycosyl transferase family, helical bundle domain Prosite entry for Thymidine and pyrimidine-nucleoside phosphorylases; InterPro: IPR017459 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases
These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. The glycosyl transferase family includes anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase (2.4.2.2 from EC) catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism. This N-terminal domain is found in various family 3 glycosyl transferases, including anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism.; PDB: 2DSJ_B 2ELC_B 2BPQ_A 1ZVW_B 3QR9_B 1V8G_B 2WK5_C 2J0F_C 2WK6_B 1UOU_A ....
>PF00591 Glycos_transf_3: Glycosyl transferase family, a/b domain Prosite entry for Thymidine and pyrimidine-nucleoside phosphorylases; InterPro: IPR000312 The glycosyl transferase family includes anthranilate phosphoribosyltransferase (TrpD, 2
4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase (2.4.2.2 from EC) catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism.; GO: 0016757 transferase activity, transferring glycosyl groups, 0008152 metabolic process; PDB: 1V8G_B 2ELC_B 2BPQ_A 1ZVW_B 3QR9_B 3H5Q_A 1KHD_A 1KGZ_B 1AZY_A 1OTP_A ....
>PF02885 Glycos_trans_3N: Glycosyl transferase family, helical bundle domain Prosite entry for Thymidine and pyrimidine-nucleoside phosphorylases; InterPro: IPR017459 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases
These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. The glycosyl transferase family includes anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase (2.4.2.2 from EC) catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism. This N-terminal domain is found in various family 3 glycosyl transferases, including anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism.; PDB: 2DSJ_B 2ELC_B 2BPQ_A 1ZVW_B 3QR9_B 1V8G_B 2WK5_C 2J0F_C 2WK6_B 1UOU_A ....
>pdb|2J0F|A Chain A, Structural Basis For Non-Competitive Product Inhibition In Human Thymidine Phosphorylase: Implication For Drug Design Length = 482
>pdb|1AZY|A Chain A, Structural And Theoretical Studies Suggest Domain Movement Produces An Active Conformation Of Thymidine Phosphorylase Length = 440
