2-succinyl-6-hydroxy-2,4-cyclohexadiene-1- carboxylate synthase [Synechocystis sp. PCC 6803]
Protein Classification
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase( domain architecture ID 11439380)
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase catalyzes the thiamin diphosphate (TPP)-dependent decarboxylative carboligation of alpha-ketoglutarate and isochorismate in the menaquinone biosynthetic pathway
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||||||
| MenD | COG1165 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase [Coenzyme transport ... |
6-587 | 0e+00 | |||||||||
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase [Coenzyme transport and metabolism]; 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase is part of the Pathway/BioSystem: Menaquinone biosynthesis : Pssm-ID: 440779 [Multi-domain] Cd Length: 567 Bit Score: 676.12 E-value: 0e+00
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| Name | Accession | Description | Interval | E-value | |||||||||
| MenD | COG1165 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase [Coenzyme transport ... |
6-587 | 0e+00 | |||||||||
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase [Coenzyme transport and metabolism]; 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase is part of the Pathway/BioSystem: Menaquinone biosynthesis Pssm-ID: 440779 [Multi-domain] Cd Length: 567 Bit Score: 676.12 E-value: 0e+00
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| menD | TIGR00173 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase; MenD was thought ... |
12-464 | 0e+00 | |||||||||
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase; MenD was thought until recently to act as SHCHC synthase, but has recently been shown to act instead as SEPHCHC synthase. Conversion of SEPHCHC into SHCHC and pyruvate may occur spontaneously but is catalyzed efficiently, at least in some organisms, by MenH (see TIGR03695). 2-oxoglutarate decarboxylase/SHCHC synthase (menD) is a thiamine pyrophosphate enzyme involved in menaquinone biosynthesis. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone] Pssm-ID: 272941 [Multi-domain] Cd Length: 432 Bit Score: 547.59 E-value: 0e+00
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| TPP_PYR_MenD | cd07037 | Pyrimidine (PYR) binding domain of ... |
13-175 | 1.85e-83 | |||||||||
Pyrimidine (PYR) binding domain of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate synthase (MenD) and related proteins; Thiamine pyrophosphate (TPP family), pyrimidine (PYR) binding domain of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate (SEPHCHC) synthase (MenD) subfamily. The PYR domain is found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this sub-family. Most TPP-dependent enzymes have the PYR and PP domains on the same subunit although these domains can be alternatively arranged in the primary structure. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites. Escherichia coli MenD (EcMenD) is a homotetramer (dimer-of-homodimers), having two active sites per homodimer lying between PYR and PP domains of different subunits. EcMenD catalyzes a Stetter-like conjugate addition of alpha-ketoglutarate to isochorismate, leading to the formation of SEPHCHC and carbon dioxide, this addition is the first committed step in the biosynthesis of vitamin K2 (menaquinone). Pssm-ID: 132920 [Multi-domain] Cd Length: 162 Bit Score: 257.81 E-value: 1.85e-83
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| PLN02980 | PLN02980 | 2-oxoglutarate decarboxylase/ hydro-lyase/ magnesium ion binding / thiamin pyrophosphate ... |
3-543 | 5.08e-67 | |||||||||
2-oxoglutarate decarboxylase/ hydro-lyase/ magnesium ion binding / thiamin pyrophosphate binding Pssm-ID: 215530 [Multi-domain] Cd Length: 1655 Bit Score: 237.45 E-value: 5.08e-67
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| TPP_enzyme_N | pfam02776 | Thiamine pyrophosphate enzyme, N-terminal TPP binding domain; |
11-183 | 8.44e-30 | |||||||||
Thiamine pyrophosphate enzyme, N-terminal TPP binding domain; Pssm-ID: 460690 [Multi-domain] Cd Length: 169 Bit Score: 115.41 E-value: 8.44e-30
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| Name | Accession | Description | Interval | E-value | |||||||||
| MenD | COG1165 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase [Coenzyme transport ... |
6-587 | 0e+00 | |||||||||
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase [Coenzyme transport and metabolism]; 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase is part of the Pathway/BioSystem: Menaquinone biosynthesis Pssm-ID: 440779 [Multi-domain] Cd Length: 567 Bit Score: 676.12 E-value: 0e+00
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| menD | TIGR00173 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase; MenD was thought ... |
12-464 | 0e+00 | |||||||||
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase; MenD was thought until recently to act as SHCHC synthase, but has recently been shown to act instead as SEPHCHC synthase. Conversion of SEPHCHC into SHCHC and pyruvate may occur spontaneously but is catalyzed efficiently, at least in some organisms, by MenH (see TIGR03695). 2-oxoglutarate decarboxylase/SHCHC synthase (menD) is a thiamine pyrophosphate enzyme involved in menaquinone biosynthesis. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone] Pssm-ID: 272941 [Multi-domain] Cd Length: 432 Bit Score: 547.59 E-value: 0e+00
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| TPP_PYR_MenD | cd07037 | Pyrimidine (PYR) binding domain of ... |
13-175 | 1.85e-83 | |||||||||
Pyrimidine (PYR) binding domain of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate synthase (MenD) and related proteins; Thiamine pyrophosphate (TPP family), pyrimidine (PYR) binding domain of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate (SEPHCHC) synthase (MenD) subfamily. The PYR domain is found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this sub-family. Most TPP-dependent enzymes have the PYR and PP domains on the same subunit although these domains can be alternatively arranged in the primary structure. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites. Escherichia coli MenD (EcMenD) is a homotetramer (dimer-of-homodimers), having two active sites per homodimer lying between PYR and PP domains of different subunits. EcMenD catalyzes a Stetter-like conjugate addition of alpha-ketoglutarate to isochorismate, leading to the formation of SEPHCHC and carbon dioxide, this addition is the first committed step in the biosynthesis of vitamin K2 (menaquinone). Pssm-ID: 132920 [Multi-domain] Cd Length: 162 Bit Score: 257.81 E-value: 1.85e-83
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| TPP_SHCHC_synthase | cd02009 | Thiamine pyrophosphate (TPP) family, SHCHC synthase subfamily, TPP-binding module; composed of ... |
402-572 | 1.94e-79 | |||||||||
Thiamine pyrophosphate (TPP) family, SHCHC synthase subfamily, TPP-binding module; composed of proteins similar to Escherichia coli 2-succinyl-6-hydroxyl-2,4-cyclohexadiene-1-carboxylic acid (SHCHC) synthase (also called MenD). SHCHC synthase plays a key role in the menaquinone biosynthetic pathway, converting isochorismate and 2-oxoglutarate to SHCHC, pyruvate and carbon dioxide. The enzyme requires TPP and a divalent metal cation for activity. Pssm-ID: 238967 [Multi-domain] Cd Length: 175 Bit Score: 247.89 E-value: 1.94e-79
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| PLN02980 | PLN02980 | 2-oxoglutarate decarboxylase/ hydro-lyase/ magnesium ion binding / thiamin pyrophosphate ... |
3-543 | 5.08e-67 | |||||||||
2-oxoglutarate decarboxylase/ hydro-lyase/ magnesium ion binding / thiamin pyrophosphate binding Pssm-ID: 215530 [Multi-domain] Cd Length: 1655 Bit Score: 237.45 E-value: 5.08e-67
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| TPP_enzyme_N | pfam02776 | Thiamine pyrophosphate enzyme, N-terminal TPP binding domain; |
11-183 | 8.44e-30 | |||||||||
Thiamine pyrophosphate enzyme, N-terminal TPP binding domain; Pssm-ID: 460690 [Multi-domain] Cd Length: 169 Bit Score: 115.41 E-value: 8.44e-30
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| IlvB | COG0028 | Acetolactate synthase large subunit or other thiamine pyrophosphate-requiring enzyme [Amino ... |
11-542 | 1.66e-20 | |||||||||
Acetolactate synthase large subunit or other thiamine pyrophosphate-requiring enzyme [Amino acid transport and metabolism, Coenzyme transport and metabolism]; Acetolactate synthase large subunit or other thiamine pyrophosphate-requiring enzyme is part of the Pathway/BioSystem: Isoleucine, leucine, valine biosynthesis Pssm-ID: 439799 [Multi-domain] Cd Length: 548 Bit Score: 95.23 E-value: 1.66e-20
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| TPP_PYR_POX_like | cd07035 | Pyrimidine (PYR) binding domain of POX and related proteins; Thiamine pyrophosphate (TPP ... |
14-174 | 1.10e-19 | |||||||||
Pyrimidine (PYR) binding domain of POX and related proteins; Thiamine pyrophosphate (TPP family), pyrimidine (PYR) binding domain of pyruvate oxidase (POX) and related protiens subfamily. The PYR domain is found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. A polar interaction between the conserved glutamate of the PYR domain and the N1' of the TPP aminopyrimidine ring is shared by most TPP-dependent enzymes, and participates in the activation of TPP. For glyoxylate carboligase, which belongs to this subfamily, but lacks this conserved glutamate, the rate of the initial TPP activation step is reduced but the ensuing steps of the enzymic reaction proceed efficiently. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this sub-family. Most TPP-dependent enzymes have the PYR and PP domains on the same subunit although these domains can be alternatively arranged in the primary structure. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites, for many the active sites lie between PP and PYR domains on different subunits. POX decarboxylates pyruvate, producing hydrogen peroxide and the energy-storage metabolite acetylphosphate. This subfamily includes pyruvate decarboxylase (PDC) and indolepyruvate decarboxylase (IPDC). PDC catalyzes the conversion of pyruvate to acetaldehyde and CO2 in alcoholic fermentation. IPDC plays a role in the indole-3-pyruvic acid (IPA) pathway in plants and various plant-associated bacteria, it catalyzes the decarboxylation of IPA to IAA. This subfamily also includes the large catalytic subunit of acetohydroxyacid synthase (AHAS). AHAS catalyzes the condensation of two molecules of pyruvate to give the acetohydroxyacid, 2-acetolactate, a precursor of the branched chain amino acids, valine and leucine. AHAS also catalyzes the condensation of pyruvate and 2-ketobutyrate to form 2-aceto-2-hydroxybutyrate in isoleucine biosynthesis. Methanococcus jannaschii sulfopyruvate decarboxylase (MjComDE) and phosphonopyruvate decarboxylase (PpyrDc) also belong to this subfamily. PpyrDc is a homotrimeric enzyme having the PP and PYR domains tandemly arranged on the same subunit. It functions in the biosynthesis of C-P compounds such as bialaphos tripeptide in Streptomyces hygroscopicus. MjComDE is a dodecamer having the PYR and PP domains on different subunits, it has six alpha (PYR/ComD) subunits and six beta (PP/ComE) subunits. MjComDE catalyzes the decarboxylation of sulfopyruvic acid to sulfoacetaldehyde in the coenzyme M pathway. Pssm-ID: 132918 [Multi-domain] Cd Length: 155 Bit Score: 86.05 E-value: 1.10e-19
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| TPP_enzyme_PYR | cd06586 | Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Thiamine ... |
14-175 | 1.57e-15 | |||||||||
Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Thiamine pyrophosphate (TPP) family, pyrimidine (PYR) binding domain; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. A polar interaction between the conserved glutamate of the PYR domain and the N1' of the TPP aminopyrimidine ring is shared by most TPP-dependent enzymes, and participates in the activation of TPP. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this group. Most TPP-dependent enzymes have the PYR and PP domains on the same subunit although these domains can be alternatively arranged in the primary structure. In the case of 2-oxoisovalerate dehydrogenase (2OXO), sulfopyruvate decarboxylase (ComDE), and the E1 component of human pyruvate dehydrogenase complex (E1- PDHc) the PYR and PP domains appear on different subunits. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites. For many of these enzymes the active sites lie between PP and PYR domains on different subunits. However, for the homodimeric enzymes 1-deoxy-D-xylulose 5-phosphate synthase (DXS) and Desulfovibrio africanus pyruvate:ferredoxin oxidoreductase (PFOR), each active site lies at the interface of the PYR and PP domains from the same subunit. Pssm-ID: 132915 [Multi-domain] Cd Length: 154 Bit Score: 74.30 E-value: 1.57e-15
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| TPP_enzymes | cd00568 | Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic ... |
405-554 | 3.19e-12 | |||||||||
Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and the branched chain alpha-keto acid dehydrogenase complexes. Pssm-ID: 238318 [Multi-domain] Cd Length: 168 Bit Score: 64.97 E-value: 3.19e-12
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| TPP_PYR_POX | cd07039 | Pyrimidine (PYR) binding domain of POX; Thiamine pyrophosphate (TPP family), pyrimidine (PYR) ... |
11-127 | 1.03e-09 | |||||||||
Pyrimidine (PYR) binding domain of POX; Thiamine pyrophosphate (TPP family), pyrimidine (PYR) binding domain of pyruvate oxidase (POX) subfamily. The PYR domain is found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this sub-family. Most TPP-dependent enzymes have the PYR and PP domains on the same subunit although these domains can be alternatively arranged in the primary structure. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites. Lactobacillus plantarum POX is a homotetramer (dimer-of-homodimers), having two active sites per homodimer lying between PYR and PP domains of different subunits. POX decarboxylates pyruvate, producing hydrogen peroxide and the energy-storage metabolite acetylphosphate. Pssm-ID: 132922 [Multi-domain] Cd Length: 164 Bit Score: 57.56 E-value: 1.03e-09
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| TPP_enzyme_M_2 | pfam16582 | Middle domain of thiamine pyrophosphate; TPP_enzyme_M_2 is the middle domain of thiamine ... |
239-420 | 1.63e-08 | |||||||||
Middle domain of thiamine pyrophosphate; TPP_enzyme_M_2 is the middle domain of thiamine pyrophosphate in sequences not captured by pfam00205. This enzyme is necessary for the first step of the biosynthesis of menaquinone, or vitamin K2, an important cofactor in electron transport in bacteria. Pssm-ID: 435442 Cd Length: 207 Bit Score: 55.01 E-value: 1.63e-08
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| PRK08155 | PRK08155 | acetolactate synthase large subunit; |
12-128 | 1.91e-08 | |||||||||
acetolactate synthase large subunit; Pssm-ID: 181257 [Multi-domain] Cd Length: 564 Bit Score: 57.02 E-value: 1.91e-08
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| TPP_enzyme_C | pfam02775 | Thiamine pyrophosphate enzyme, C-terminal TPP binding domain; |
427-554 | 5.55e-08 | |||||||||
Thiamine pyrophosphate enzyme, C-terminal TPP binding domain; Pssm-ID: 460689 [Multi-domain] Cd Length: 151 Bit Score: 52.20 E-value: 5.55e-08
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| PLN02470 | PLN02470 | acetolactate synthase |
12-112 | 6.71e-08 | |||||||||
acetolactate synthase Pssm-ID: 215261 [Multi-domain] Cd Length: 585 Bit Score: 55.51 E-value: 6.71e-08
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| PRK07282 | PRK07282 | acetolactate synthase large subunit; |
12-106 | 2.18e-07 | |||||||||
acetolactate synthase large subunit; Pssm-ID: 180919 [Multi-domain] Cd Length: 566 Bit Score: 53.67 E-value: 2.18e-07
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| PRK06457 | PRK06457 | pyruvate dehydrogenase; Provisional |
12-176 | 8.13e-07 | |||||||||
pyruvate dehydrogenase; Provisional Pssm-ID: 180570 [Multi-domain] Cd Length: 549 Bit Score: 51.75 E-value: 8.13e-07
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| PRK08199 | PRK08199 | thiamine pyrophosphate protein; Validated |
5-136 | 1.65e-06 | |||||||||
thiamine pyrophosphate protein; Validated Pssm-ID: 181285 [Multi-domain] Cd Length: 557 Bit Score: 51.03 E-value: 1.65e-06
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| PRK08979 | PRK08979 | acetolactate synthase 3 large subunit; |
12-112 | 2.36e-06 | |||||||||
acetolactate synthase 3 large subunit; Pssm-ID: 181602 [Multi-domain] Cd Length: 572 Bit Score: 50.59 E-value: 2.36e-06
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| PRK06725 | PRK06725 | acetolactate synthase large subunit; |
12-106 | 5.41e-06 | |||||||||
acetolactate synthase large subunit; Pssm-ID: 180672 [Multi-domain] Cd Length: 570 Bit Score: 49.20 E-value: 5.41e-06
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| PRK11269 | PRK11269 | glyoxylate carboligase; Provisional |
11-122 | 1.07e-05 | |||||||||
glyoxylate carboligase; Provisional Pssm-ID: 183066 [Multi-domain] Cd Length: 591 Bit Score: 48.44 E-value: 1.07e-05
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| PRK06882 | PRK06882 | acetolactate synthase 3 large subunit; |
12-122 | 1.21e-05 | |||||||||
acetolactate synthase 3 large subunit; Pssm-ID: 168717 [Multi-domain] Cd Length: 574 Bit Score: 48.37 E-value: 1.21e-05
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| PRK07979 | PRK07979 | acetolactate synthase 3 large subunit; |
12-112 | 1.59e-05 | |||||||||
acetolactate synthase 3 large subunit; Pssm-ID: 181185 [Multi-domain] Cd Length: 574 Bit Score: 47.92 E-value: 1.59e-05
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| PRK06048 | PRK06048 | acetolactate synthase large subunit; |
11-109 | 5.59e-04 | |||||||||
acetolactate synthase large subunit; Pssm-ID: 180368 [Multi-domain] Cd Length: 561 Bit Score: 42.84 E-value: 5.59e-04
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| PRK07064 | PRK07064 | thiamine pyrophosphate-binding protein; |
37-106 | 1.21e-03 | |||||||||
thiamine pyrophosphate-binding protein; Pssm-ID: 180820 [Multi-domain] Cd Length: 544 Bit Score: 41.90 E-value: 1.21e-03
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| PRK06276 | PRK06276 | acetolactate synthase large subunit; |
12-122 | 4.71e-03 | |||||||||
acetolactate synthase large subunit; Pssm-ID: 235766 [Multi-domain] Cd Length: 586 Bit Score: 39.74 E-value: 4.71e-03
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| PRK12474 | PRK12474 | hypothetical protein; Provisional |
12-107 | 4.98e-03 | |||||||||
hypothetical protein; Provisional Pssm-ID: 139002 [Multi-domain] Cd Length: 518 Bit Score: 39.86 E-value: 4.98e-03
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| PRK07710 | PRK07710 | acetolactate synthase large subunit; |
12-106 | 9.02e-03 | |||||||||
acetolactate synthase large subunit; Pssm-ID: 236076 [Multi-domain] Cd Length: 571 Bit Score: 38.97 E-value: 9.02e-03
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| Blast search parameters | ||||
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