RecName: Full=Formate-dependent phosphoribosylglycinamide formyltransferase; AltName: Full=5'-phosphoribosylglycinamide transformylase 2; AltName: Full=Formate-dependent GAR transformylase; AltName: Full=GAR transformylase 2; Short=GART 2; AltName: Full=Non-folate glycinamide ribonucleotide transformylase; AltName: Full=Phosphoribosylglycinamide formyltransferase 2
Protein Classification
phosphoribosylglycinamide formyltransferase 2( domain architecture ID 11483776)
phosphoribosylglycinamide formyltransferase 2 catalyzes the transfer of formate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR)
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||
| purT | PRK09288 | formate-dependent phosphoribosylglycinamide formyltransferase; |
1-388 | 0e+00 | ||||||
formate-dependent phosphoribosylglycinamide formyltransferase; : Pssm-ID: 236454 [Multi-domain] Cd Length: 395 Bit Score: 717.69 E-value: 0e+00
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| Name | Accession | Description | Interval | E-value | ||||||
| purT | PRK09288 | formate-dependent phosphoribosylglycinamide formyltransferase; |
1-388 | 0e+00 | ||||||
formate-dependent phosphoribosylglycinamide formyltransferase; Pssm-ID: 236454 [Multi-domain] Cd Length: 395 Bit Score: 717.69 E-value: 0e+00
|
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| PurT | COG0027 | Formate-dependent phosphoribosylglycinamide formyltransferase (GAR transformylase) [Nucleotide ... |
5-385 | 0e+00 | ||||||
Formate-dependent phosphoribosylglycinamide formyltransferase (GAR transformylase) [Nucleotide transport and metabolism]; Formate-dependent phosphoribosylglycinamide formyltransferase (GAR transformylase) is part of the Pathway/BioSystem: Purine biosynthesis Pssm-ID: 439798 [Multi-domain] Cd Length: 393 Bit Score: 668.75 E-value: 0e+00
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| purT | TIGR01142 | phosphoribosylglycinamide formyltransferase 2; This enzyme is an alternative to PurN ... |
7-385 | 0e+00 | ||||||
phosphoribosylglycinamide formyltransferase 2; This enzyme is an alternative to PurN (TIGR00639) [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis] Pssm-ID: 130212 Cd Length: 380 Bit Score: 552.42 E-value: 0e+00
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| ATP-grasp | pfam02222 | ATP-grasp domain; This family does not contain all known ATP-grasp domain members. This family ... |
117-288 | 1.53e-69 | ||||||
ATP-grasp domain; This family does not contain all known ATP-grasp domain members. This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity. Pssm-ID: 396689 [Multi-domain] Cd Length: 169 Bit Score: 216.35 E-value: 1.53e-69
|
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| Zn_ADH7 | cd08261 | Alcohol dehydrogenases of the MDR family; This group contains members identified as related to ... |
7-85 | 4.61e-04 | ||||||
Alcohol dehydrogenases of the MDR family; This group contains members identified as related to zinc-dependent alcohol dehydrogenase and other members of the MDR family. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P)-binding Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group includes various activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Pssm-ID: 176222 [Multi-domain] Cd Length: 337 Bit Score: 41.79 E-value: 4.61e-04
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| Name | Accession | Description | Interval | E-value | ||||||
| purT | PRK09288 | formate-dependent phosphoribosylglycinamide formyltransferase; |
1-388 | 0e+00 | ||||||
formate-dependent phosphoribosylglycinamide formyltransferase; Pssm-ID: 236454 [Multi-domain] Cd Length: 395 Bit Score: 717.69 E-value: 0e+00
|
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| PurT | COG0027 | Formate-dependent phosphoribosylglycinamide formyltransferase (GAR transformylase) [Nucleotide ... |
5-385 | 0e+00 | ||||||
Formate-dependent phosphoribosylglycinamide formyltransferase (GAR transformylase) [Nucleotide transport and metabolism]; Formate-dependent phosphoribosylglycinamide formyltransferase (GAR transformylase) is part of the Pathway/BioSystem: Purine biosynthesis Pssm-ID: 439798 [Multi-domain] Cd Length: 393 Bit Score: 668.75 E-value: 0e+00
|
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| purT | TIGR01142 | phosphoribosylglycinamide formyltransferase 2; This enzyme is an alternative to PurN ... |
7-385 | 0e+00 | ||||||
phosphoribosylglycinamide formyltransferase 2; This enzyme is an alternative to PurN (TIGR00639) [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis] Pssm-ID: 130212 Cd Length: 380 Bit Score: 552.42 E-value: 0e+00
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| PurK | COG0026 | Phosphoribosylaminoimidazole carboxylase (NCAIR synthetase) [Nucleotide transport and ... |
16-379 | 1.17e-70 | ||||||
Phosphoribosylaminoimidazole carboxylase (NCAIR synthetase) [Nucleotide transport and metabolism]; Phosphoribosylaminoimidazole carboxylase (NCAIR synthetase) is part of the Pathway/BioSystem: Purine biosynthesis Pssm-ID: 439797 [Multi-domain] Cd Length: 353 Bit Score: 225.34 E-value: 1.17e-70
|
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| ATP-grasp | pfam02222 | ATP-grasp domain; This family does not contain all known ATP-grasp domain members. This family ... |
117-288 | 1.53e-69 | ||||||
ATP-grasp domain; This family does not contain all known ATP-grasp domain members. This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity. Pssm-ID: 396689 [Multi-domain] Cd Length: 169 Bit Score: 216.35 E-value: 1.53e-69
|
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| purK | TIGR01161 | phosphoribosylaminoimidazole carboxylase, PurK protein; Phosphoribosylaminoimidazole ... |
7-360 | 4.97e-67 | ||||||
phosphoribosylaminoimidazole carboxylase, PurK protein; Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. This model represents PurK, N5-carboxyaminoimidazole ribonucleotide synthetase, which hydrolyzes ATP and converts AIR to N5-CAIR. PurE converts N5-CAIR to CAIR. In the presence of high concentrations of bicarbonate, PurE is reported able to convert AIR to CAIR directly and without ATP. [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis] Pssm-ID: 273473 [Multi-domain] Cd Length: 352 Bit Score: 216.05 E-value: 4.97e-67
|
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| PRK06019 | PRK06019 | phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed |
7-384 | 8.30e-66 | ||||||
phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed Pssm-ID: 235674 [Multi-domain] Cd Length: 372 Bit Score: 213.48 E-value: 8.30e-66
|
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| PLN02948 | PLN02948 | phosphoribosylaminoimidazole carboxylase |
8-378 | 5.12e-51 | ||||||
phosphoribosylaminoimidazole carboxylase Pssm-ID: 178534 [Multi-domain] Cd Length: 577 Bit Score: 179.87 E-value: 5.12e-51
|
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| AccC | COG0439 | Biotin carboxylase [Lipid transport and metabolism]; Biotin carboxylase is part of the Pathway ... |
59-279 | 1.96e-23 | ||||||
Biotin carboxylase [Lipid transport and metabolism]; Biotin carboxylase is part of the Pathway/BioSystem: Fatty acid biosynthesis Pssm-ID: 440208 [Multi-domain] Cd Length: 263 Bit Score: 98.41 E-value: 1.96e-23
|
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| DdlA | COG1181 | D-alanine-D-alanine ligase or related ATP-grasp enzyme [Cell wall/membrane/envelope biogenesis, ... |
56-271 | 1.04e-16 | ||||||
D-alanine-D-alanine ligase or related ATP-grasp enzyme [Cell wall/membrane/envelope biogenesis, General function prediction only]; D-alanine-D-alanine ligase or related ATP-grasp enzyme is part of the Pathway/BioSystem: Mureine biosynthesis Pssm-ID: 440794 [Multi-domain] Cd Length: 303 Bit Score: 79.77 E-value: 1.04e-16
|
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| COG3919 | COG3919 | Predicted ATP-dependent carboligase, ATP-grasp superfamily [General function prediction only]; |
1-211 | 5.20e-16 | ||||||
Predicted ATP-dependent carboligase, ATP-grasp superfamily [General function prediction only]; Pssm-ID: 443124 [Multi-domain] Cd Length: 382 Bit Score: 78.82 E-value: 5.20e-16
|
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| PRK12767 | PRK12767 | carbamoyl phosphate synthase-like protein; Provisional |
27-277 | 3.81e-15 | ||||||
carbamoyl phosphate synthase-like protein; Provisional Pssm-ID: 237195 [Multi-domain] Cd Length: 326 Bit Score: 75.69 E-value: 3.81e-15
|
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| Dala_Dala_lig_C | pfam07478 | D-ala D-ala ligase C-terminus; This family represents the C-terminal, catalytic domain of the ... |
136-278 | 2.27e-14 | ||||||
D-ala D-ala ligase C-terminus; This family represents the C-terminal, catalytic domain of the D-alanine--D-alanine ligase enzyme EC:6.3.2.4. D-Alanine is one of the central molecules of the cross-linking step of peptidoglycan assembly. There are three enzymes involved in the D-alanine branch of peptidoglycan biosynthesis: the pyridoxal phosphate-dependent D-alanine racemase (Alr), the ATP-dependent D-alanine:D-alanine ligase (Ddl), and the ATP-dependent D-alanine:D-alanine-adding enzyme (MurF). Pssm-ID: 429483 [Multi-domain] Cd Length: 204 Bit Score: 71.19 E-value: 2.27e-14
|
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| LysX | COG0189 | Glutathione synthase, LysX or RimK-type ligase, ATP-grasp superfamily [Amino acid transport ... |
18-278 | 2.32e-13 | ||||||
Glutathione synthase, LysX or RimK-type ligase, ATP-grasp superfamily [Amino acid transport and metabolism, Coenzyme transport and metabolism, Translation, ribosomal structure and biogenesis, Secondary metabolites biosynthesis, transport and catabolism]; Glutathione synthase, LysX or RimK-type ligase, ATP-grasp superfamily is part of the Pathway/BioSystem: Lysine biosynthesis Pssm-ID: 439959 [Multi-domain] Cd Length: 289 Bit Score: 69.97 E-value: 2.32e-13
|
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| PurD | COG0151 | Phosphoribosylamine-glycine ligase [Nucleotide transport and metabolism]; ... |
8-192 | 2.09e-12 | ||||||
Phosphoribosylamine-glycine ligase [Nucleotide transport and metabolism]; Phosphoribosylamine-glycine ligase is part of the Pathway/BioSystem: Purine biosynthesis Pssm-ID: 439921 [Multi-domain] Cd Length: 422 Bit Score: 68.12 E-value: 2.09e-12
|
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| purD | TIGR00877 | phosphoribosylamine--glycine ligase; Alternate name: glycinamide ribonucleotide synthetase ... |
8-219 | 4.24e-12 | ||||||
phosphoribosylamine--glycine ligase; Alternate name: glycinamide ribonucleotide synthetase (GARS). This enzyme appears as a monofunctional protein in prokaryotes but as part of a larger, multidomain protein in eukaryotes. [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis] Pssm-ID: 273315 [Multi-domain] Cd Length: 422 Bit Score: 66.95 E-value: 4.24e-12
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| carB | PRK12815 | carbamoyl phosphate synthase large subunit; Reviewed |
62-311 | 6.22e-12 | ||||||
carbamoyl phosphate synthase large subunit; Reviewed Pssm-ID: 237215 [Multi-domain] Cd Length: 1068 Bit Score: 67.30 E-value: 6.22e-12
|
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| CarB | COG0458 | Carbamoylphosphate synthase large subunit [Amino acid transport and metabolism, Nucleotide ... |
60-277 | 6.41e-12 | ||||||
Carbamoylphosphate synthase large subunit [Amino acid transport and metabolism, Nucleotide transport and metabolism]; Carbamoylphosphate synthase large subunit is part of the Pathway/BioSystem: Arginine biosynthesis Pssm-ID: 440226 [Multi-domain] Cd Length: 536 Bit Score: 66.83 E-value: 6.41e-12
|
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| CPSaseII_lrg | TIGR01369 | carbamoyl-phosphate synthase, large subunit; Carbamoyl-phosphate synthase (CPSase) catalyzes ... |
61-277 | 1.05e-10 | ||||||
carbamoyl-phosphate synthase, large subunit; Carbamoyl-phosphate synthase (CPSase) catalyzes the first committed step in pyrimidine, arginine, and urea biosynthesis. In general, it is a glutamine-dependent enzyme, EC 6.3.5.5, termed CPSase II in eukaryotes. An exception is the mammalian mitochondrial urea-cycle form, CPSase I, in which the glutamine amidotransferase domain active site Cys on the small subunit has been lost, and the enzyme is ammonia-dependent. In both CPSase I and the closely related, glutamine-dependent CPSase III (allosterically activated by acetyl-glutamate) demonstrated in some other vertebrates, the small and large chain regions are fused in a single polypeptide chain. This model represents the large chain of glutamine-hydrolysing carbamoyl-phosphate synthases, or the corresponding regions of larger, multifunctional proteins, as found in all domains of life, and CPSase I forms are considered exceptions within the family. In several thermophilic species (Methanobacterium thermoautotrophicum, Methanococcus jannaschii, Aquifex aeolicus), the large subunit appears split, at different points, into two separate genes. [Purines, pyrimidines, nucleosides, and nucleotides, Pyrimidine ribonucleotide biosynthesis] Pssm-ID: 273581 [Multi-domain] Cd Length: 1050 Bit Score: 63.48 E-value: 1.05e-10
|
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| ddl | PRK01966 | D-alanine--D-alanine ligase; |
100-271 | 1.07e-10 | ||||||
D-alanine--D-alanine ligase; Pssm-ID: 234993 [Multi-domain] Cd Length: 333 Bit Score: 62.45 E-value: 1.07e-10
|
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| PRK02186 | PRK02186 | argininosuccinate lyase; Provisional |
95-392 | 1.17e-09 | ||||||
argininosuccinate lyase; Provisional Pssm-ID: 235010 [Multi-domain] Cd Length: 887 Bit Score: 60.25 E-value: 1.17e-09
|
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| ddl | PRK01372 | D-alanine--D-alanine ligase; Reviewed |
1-256 | 1.32e-09 | ||||||
D-alanine--D-alanine ligase; Reviewed Pssm-ID: 234948 [Multi-domain] Cd Length: 304 Bit Score: 58.58 E-value: 1.32e-09
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| CPSaseII_lrg | TIGR01369 | carbamoyl-phosphate synthase, large subunit; Carbamoyl-phosphate synthase (CPSase) catalyzes ... |
5-207 | 1.03e-08 | ||||||
carbamoyl-phosphate synthase, large subunit; Carbamoyl-phosphate synthase (CPSase) catalyzes the first committed step in pyrimidine, arginine, and urea biosynthesis. In general, it is a glutamine-dependent enzyme, EC 6.3.5.5, termed CPSase II in eukaryotes. An exception is the mammalian mitochondrial urea-cycle form, CPSase I, in which the glutamine amidotransferase domain active site Cys on the small subunit has been lost, and the enzyme is ammonia-dependent. In both CPSase I and the closely related, glutamine-dependent CPSase III (allosterically activated by acetyl-glutamate) demonstrated in some other vertebrates, the small and large chain regions are fused in a single polypeptide chain. This model represents the large chain of glutamine-hydrolysing carbamoyl-phosphate synthases, or the corresponding regions of larger, multifunctional proteins, as found in all domains of life, and CPSase I forms are considered exceptions within the family. In several thermophilic species (Methanobacterium thermoautotrophicum, Methanococcus jannaschii, Aquifex aeolicus), the large subunit appears split, at different points, into two separate genes. [Purines, pyrimidines, nucleosides, and nucleotides, Pyrimidine ribonucleotide biosynthesis] Pssm-ID: 273581 [Multi-domain] Cd Length: 1050 Bit Score: 57.32 E-value: 1.03e-08
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| carB | PRK12815 | carbamoyl phosphate synthase large subunit; Reviewed |
6-277 | 7.99e-08 | ||||||
carbamoyl phosphate synthase large subunit; Reviewed Pssm-ID: 237215 [Multi-domain] Cd Length: 1068 Bit Score: 54.59 E-value: 7.99e-08
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| CPSase_L_D2 | pfam02786 | Carbamoyl-phosphate synthase L chain, ATP binding domain; Carbamoyl-phosphate synthase ... |
107-277 | 1.22e-07 | ||||||
Carbamoyl-phosphate synthase L chain, ATP binding domain; Carbamoyl-phosphate synthase catalyzes the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesize carbamoyl phosphate. See pfam00988. The small chain has a GATase domain in the carboxyl terminus. See pfam00117. The ATP binding domain (this one) has an ATP-grasp fold. Pssm-ID: 397079 [Multi-domain] Cd Length: 209 Bit Score: 51.92 E-value: 1.22e-07
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| PLN02257 | PLN02257 | phosphoribosylamine--glycine ligase |
71-392 | 6.42e-07 | ||||||
phosphoribosylamine--glycine ligase Pssm-ID: 177899 [Multi-domain] Cd Length: 434 Bit Score: 50.89 E-value: 6.42e-07
|
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| GARS_A | pfam01071 | Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Phosphoribosylglycinamide ... |
117-202 | 6.99e-07 | ||||||
Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Phosphoribosylglycinamide synthetase catalyzes the second step in the de novo biosynthesis of purine. The reaction catalyzed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide. This domain is related to the ATP-grasp domain of biotin carboxylase/carbamoyl phosphate synthetase (see pfam02786). Pssm-ID: 395851 [Multi-domain] Cd Length: 194 Bit Score: 49.20 E-value: 6.99e-07
|
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| PRK14016 | PRK14016 | cyanophycin synthetase; Provisional |
128-192 | 1.13e-06 | ||||||
cyanophycin synthetase; Provisional Pssm-ID: 237586 [Multi-domain] Cd Length: 727 Bit Score: 50.54 E-value: 1.13e-06
|
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| PylC | COG2232 | Pyrrolysine biosynthesis ligase PylC and related enzymes, ATP-grasp superfamily [Amino acid ... |
230-392 | 1.90e-06 | ||||||
Pyrrolysine biosynthesis ligase PylC and related enzymes, ATP-grasp superfamily [Amino acid transport and metabolism]; Pssm-ID: 441833 [Multi-domain] Cd Length: 370 Bit Score: 49.53 E-value: 1.90e-06
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| carB | PRK05294 | carbamoyl-phosphate synthase large subunit; |
54-207 | 2.28e-06 | ||||||
carbamoyl-phosphate synthase large subunit; Pssm-ID: 235393 [Multi-domain] Cd Length: 1066 Bit Score: 49.71 E-value: 2.28e-06
|
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| PRK07206 | PRK07206 | hypothetical protein; Provisional |
17-192 | 4.53e-06 | ||||||
hypothetical protein; Provisional Pssm-ID: 180883 [Multi-domain] Cd Length: 416 Bit Score: 48.49 E-value: 4.53e-06
|
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| RfbD | COG1091 | dTDP-4-dehydrorhamnose reductase [Cell wall/membrane/envelope biogenesis]; |
8-95 | 1.08e-05 | ||||||
dTDP-4-dehydrorhamnose reductase [Cell wall/membrane/envelope biogenesis]; Pssm-ID: 440708 [Multi-domain] Cd Length: 279 Bit Score: 46.66 E-value: 1.08e-05
|
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| carB | PRK05294 | carbamoyl-phosphate synthase large subunit; |
62-277 | 5.36e-05 | ||||||
carbamoyl-phosphate synthase large subunit; Pssm-ID: 235393 [Multi-domain] Cd Length: 1066 Bit Score: 45.47 E-value: 5.36e-05
|
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| PRK08654 | PRK08654 | acetyl-CoA carboxylase biotin carboxylase subunit; |
129-192 | 1.14e-04 | ||||||
acetyl-CoA carboxylase biotin carboxylase subunit; Pssm-ID: 236325 [Multi-domain] Cd Length: 499 Bit Score: 44.20 E-value: 1.14e-04
|
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| PRK08462 | PRK08462 | acetyl-CoA carboxylase biotin carboxylase subunit; |
35-178 | 3.87e-04 | ||||||
acetyl-CoA carboxylase biotin carboxylase subunit; Pssm-ID: 236269 [Multi-domain] Cd Length: 445 Bit Score: 42.42 E-value: 3.87e-04
|
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| PycA | COG1038 | Pyruvate carboxylase [Energy production and conversion]; Pyruvate carboxylase is part of the ... |
129-192 | 4.28e-04 | ||||||
Pyruvate carboxylase [Energy production and conversion]; Pyruvate carboxylase is part of the Pathway/BioSystem: Urea cycle Pssm-ID: 440660 [Multi-domain] Cd Length: 1144 Bit Score: 42.37 E-value: 4.28e-04
|
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| Zn_ADH7 | cd08261 | Alcohol dehydrogenases of the MDR family; This group contains members identified as related to ... |
7-85 | 4.61e-04 | ||||||
Alcohol dehydrogenases of the MDR family; This group contains members identified as related to zinc-dependent alcohol dehydrogenase and other members of the MDR family. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P)-binding Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group includes various activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Pssm-ID: 176222 [Multi-domain] Cd Length: 337 Bit Score: 41.79 E-value: 4.61e-04
|
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| LDH_like | cd01619 | D-Lactate and related Dehydrogenases, NAD-binding and catalytic domains; D-Lactate ... |
6-119 | 6.84e-04 | ||||||
D-Lactate and related Dehydrogenases, NAD-binding and catalytic domains; D-Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate, and is a member of the 2-hydroxyacid dehydrogenase family. LDH is homologous to D-2-Hydroxyisocaproic acid dehydrogenase (D-HicDH) and shares the 2 domain structure of formate dehydrogenase. D-HicDH is a NAD-dependent member of the hydroxycarboxylate dehydrogenase family, and shares the Rossmann fold typical of many NAD binding proteins. D-HicDH from Lactobacillus casei forms a monomer and catalyzes the reaction R-CO-COO(-) + NADH + H+ to R-COH-COO(-) + NAD+. Similar to the structurally distinct L-HicDH, D-HicDH exhibits low side-chain R specificity, accepting a wide range of 2-oxocarboxylic acid side chains. (R)-2-hydroxyglutarate dehydrogenase (HGDH) catalyzes the NAD-dependent reduction of 2-oxoglutarate to (R)-2-hydroxyglutarate. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Pssm-ID: 240620 [Multi-domain] Cd Length: 323 Bit Score: 41.13 E-value: 6.84e-04
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| dTDP_HR_like_SDR_e | cd05254 | dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; ... |
8-87 | 1.09e-03 | ||||||
dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; dTDP-6-deoxy-L-lyxo-4-hexulose reductase, an extended SDR, synthesizes dTDP-L-rhamnose from alpha-D-glucose-1-phosphate, providing the precursor of L-rhamnose, an essential cell wall component of many pathogenic bacteria. This subgroup has the characteristic active site tetrad and NADP-binding motif. This subgroup also contains human MAT2B, the regulatory subunit of methionine adenosyltransferase (MAT); MAT catalyzes S-adenosylmethionine synthesis. The human gene encoding MAT2B encodes two major splicing variants which are induced in human cell liver cancer and regulate HuR, an mRNA-binding protein which stabilizes the mRNA of several cyclins, to affect cell proliferation. Both MAT2B variants include this extended SDR domain. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Pssm-ID: 187564 [Multi-domain] Cd Length: 280 Bit Score: 40.30 E-value: 1.09e-03
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| Epimerase | pfam01370 | NAD dependent epimerase/dehydratase family; This family of proteins utilize NAD as a cofactor. ... |
12-73 | 1.13e-03 | ||||||
NAD dependent epimerase/dehydratase family; This family of proteins utilize NAD as a cofactor. The proteins in this family use nucleotide-sugar substrates for a variety of chemical reactions. Pssm-ID: 396097 [Multi-domain] Cd Length: 238 Bit Score: 40.36 E-value: 1.13e-03
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| PRK08591 | PRK08591 | acetyl-CoA carboxylase biotin carboxylase subunit; Validated |
129-192 | 1.25e-03 | ||||||
acetyl-CoA carboxylase biotin carboxylase subunit; Validated Pssm-ID: 236307 [Multi-domain] Cd Length: 451 Bit Score: 40.56 E-value: 1.25e-03
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| 17beta-HSD-like_SDR_c | cd05374 | 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; 17beta-hydroxysteroid ... |
12-73 | 1.69e-03 | ||||||
17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; 17beta-hydroxysteroid dehydrogenases are a group of isozymes that catalyze activation and inactivation of estrogen and androgens. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. Pssm-ID: 187632 [Multi-domain] Cd Length: 248 Bit Score: 39.52 E-value: 1.69e-03
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| 2-Hacid_dh_C | pfam02826 | D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain; This domain is inserted ... |
6-42 | 1.78e-03 | ||||||
D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain; This domain is inserted into the catalytic domain, the large dehydrogenase and D-lactate dehydrogenase families in SCOP. N-terminal portion of which is represented by family pfam00389. Pssm-ID: 427007 [Multi-domain] Cd Length: 178 Bit Score: 39.02 E-value: 1.78e-03
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| FDH_GDH_like | cd12154 | Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related ... |
5-62 | 2.00e-03 | ||||||
Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; The formate/glycerate dehydrogenase like family contains a diverse group of enzymes such as formate dehydrogenase (FDH), glycerate dehydrogenase (GDH), D-lactate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine hydrolase, that share a common 2-domain structure. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar domains of the alpha/beta Rossmann fold NAD+ binding form. The NAD(P) binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD(P) is bound, primarily to the C-terminal portion of the 2nd (internal) domain. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of a hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases. Pssm-ID: 240631 [Multi-domain] Cd Length: 310 Bit Score: 39.91 E-value: 2.00e-03
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| PGDH_2 | cd05303 | Phosphoglycerate dehydrogenase (PGDH) NAD-binding and catalytic domains; Phosphoglycerate ... |
6-99 | 2.62e-03 | ||||||
Phosphoglycerate dehydrogenase (PGDH) NAD-binding and catalytic domains; Phosphoglycerate dehydrogenase (PGDH) catalyzes the initial step in the biosynthesis of L-serine from D-3-phosphoglycerate. PGDH comes in 3 distinct structural forms, with this first group being related to 2-hydroxy acid dehydrogenases, sharing structural similarity to formate and glycerate dehydrogenases. PGDH in E. coli and Mycobacterium tuberculosis form tetramers, with subunits containing a Rossmann-fold NAD binding domain. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine Hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. Pssm-ID: 240628 [Multi-domain] Cd Length: 301 Bit Score: 39.44 E-value: 2.62e-03
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| 2-Hacid_dh_11 | cd12175 | Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains; ... |
6-42 | 3.88e-03 | ||||||
Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains; 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240652 [Multi-domain] Cd Length: 311 Bit Score: 38.71 E-value: 3.88e-03
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| PRK06111 | PRK06111 | acetyl-CoA carboxylase biotin carboxylase subunit; Validated |
129-201 | 4.48e-03 | ||||||
acetyl-CoA carboxylase biotin carboxylase subunit; Validated Pssm-ID: 180406 [Multi-domain] Cd Length: 450 Bit Score: 38.86 E-value: 4.48e-03
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| PRK12999 | PRK12999 | pyruvate carboxylase; Reviewed |
73-192 | 7.57e-03 | ||||||
pyruvate carboxylase; Reviewed Pssm-ID: 237263 [Multi-domain] Cd Length: 1146 Bit Score: 38.58 E-value: 7.57e-03
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| PGDH_like_3 | cd12174 | Putative D-3-Phosphoglycerate Dehydrogenases, NAD-binding and catalytic domains; ... |
6-124 | 8.80e-03 | ||||||
Putative D-3-Phosphoglycerate Dehydrogenases, NAD-binding and catalytic domains; Phosphoglycerate dehydrogenases (PGDHs) catalyze the initial step in the biosynthesis of L-serine from D-3-phosphoglycerate. PGDHs come in 3 distinct structural forms, with this first group being related to 2-hydroxy acid dehydrogenases, sharing structural similarity to formate and glycerate dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily, which also include groups such as L-alanine dehydrogenase and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. Many, not all, members of this family are dimeric. Pssm-ID: 240651 [Multi-domain] Cd Length: 305 Bit Score: 37.93 E-value: 8.80e-03
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| ATP-grasp_4 | pfam13535 | ATP-grasp domain; This family includes a diverse set of enzymes that possess ATP-dependent ... |
141-212 | 9.20e-03 | ||||||
ATP-grasp domain; This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity. Pssm-ID: 316093 [Multi-domain] Cd Length: 160 Bit Score: 36.49 E-value: 9.20e-03
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