An uncharacterized subgroup of the PBGD family; the type 2 periplasmic binding protein fold; ...
13-283
0e+00
An uncharacterized subgroup of the PBGD family; the type 2 periplasmic binding protein fold; Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophyll, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). This subfamily includes the three domains of HMBS. The enzyme is believed to bind substrate through a hinge-bending motion of domains 1 and 2. The C-terminal domain 3 contains an invariant cysteine that forms the covalent attachment site for the DPM (dipyrromethane) cofactor. HMBS is found in all organisms except viruses. The domains 1 and 2 have the same overall topology as found in the type 2 periplasmic-binding proteins (PBP2), many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor.
Pssm-ID: 270366 [Multi-domain] Cd Length: 278 Bit Score: 513.50 E-value: 0e+00
hydroxymethylbilane synthase; Alternate name hydroxymethylbilane synthase Biosynthesis of ...
12-305
1.36e-125
hydroxymethylbilane synthase; Alternate name hydroxymethylbilane synthase Biosynthesis of cofactors, prosthetic groups, and carriers: Heme and porphyrin [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]
Pssm-ID: 272963 [Multi-domain] Cd Length: 292 Bit Score: 360.82 E-value: 1.36e-125
An uncharacterized subgroup of the PBGD family; the type 2 periplasmic binding protein fold; ...
13-283
0e+00
An uncharacterized subgroup of the PBGD family; the type 2 periplasmic binding protein fold; Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophyll, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). This subfamily includes the three domains of HMBS. The enzyme is believed to bind substrate through a hinge-bending motion of domains 1 and 2. The C-terminal domain 3 contains an invariant cysteine that forms the covalent attachment site for the DPM (dipyrromethane) cofactor. HMBS is found in all organisms except viruses. The domains 1 and 2 have the same overall topology as found in the type 2 periplasmic-binding proteins (PBP2), many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor.
Pssm-ID: 270366 [Multi-domain] Cd Length: 278 Bit Score: 513.50 E-value: 0e+00
Hydroxymethylbilane synthase possesses the type 2 periplasmic binding protein fold; ...
12-283
1.21e-128
Hydroxymethylbilane synthase possesses the type 2 periplasmic binding protein fold; Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophyll, vitamin B12 and related macrocycles. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). This family includes the three domains of HMBS. The enzyme is believed to bind substrate through a hinge-bending motion of domains 1 and 2. The C-terminal domain 3 contains an invariant cysteine that forms the covalent attachment site for the DPM (dipyrromethane) cofactor. HMBS is found in all organisms except viruses. The domains 1 and 2 have the same overall topology as found in the type 2 periplasmic-binding proteins (PBP2), many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor.
Pssm-ID: 270213 [Multi-domain] Cd Length: 274 Bit Score: 367.77 E-value: 1.21e-128
hydroxymethylbilane synthase; Alternate name hydroxymethylbilane synthase Biosynthesis of ...
12-305
1.36e-125
hydroxymethylbilane synthase; Alternate name hydroxymethylbilane synthase Biosynthesis of cofactors, prosthetic groups, and carriers: Heme and porphyrin [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]
Pssm-ID: 272963 [Multi-domain] Cd Length: 292 Bit Score: 360.82 E-value: 1.36e-125
cd00494; Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), ...
13-283
5.22e-122
cd00494; Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophyll, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). This subfamily includes the three domains of Escherichia coli HMBS and its closely related proteins. The enzyme is believed to bind substrate through a hinge-bending motion of domains 1 and 2. The C-terminal domain 3 contains an invariant cysteine that forms the covalent attachment site for the DPM (dipyrromethane) cofactor. HMBS is found in all organisms except viruses. The domains 1 and 2 have the same overall topology as found in the type 2 periplasmic-binding proteins (PBP2), many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor.
Pssm-ID: 270364 [Multi-domain] Cd Length: 274 Bit Score: 350.77 E-value: 5.22e-122
An uncharacterized subgroup of the PBGD family; the type 2 periplasmic binding protein fold; ...
12-280
6.37e-107
An uncharacterized subgroup of the PBGD family; the type 2 periplasmic binding protein fold; Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophyll, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). This subfamily includes the three domains of HMBS. The enzyme is believed to bind substrate through a hinge-bending motion of domains 1 and 2. The C-terminal domain 3 contains an invariant cysteine that forms the covalent attachment site for the DPM (dipyrromethane) cofactor. HMBS is found in all organisms except viruses. The domains 1 and 2 have the same overall topology as found in the type 2 periplasmic-binding proteins (PBP2), many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor.
Pssm-ID: 270365 [Multi-domain] Cd Length: 282 Bit Score: 313.07 E-value: 6.37e-107
Human porphobilinogen deaminase possess type 2 periplasmic binding protein fold; ...
12-284
7.54e-106
Human porphobilinogen deaminase possess type 2 periplasmic binding protein fold; Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophyll, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). This subfamily includes the three domains of human PBGD and its closely related proteins. Mutations in human PBGD cause AIP (acute intermittent porphyria), an inherited autosomal dominant disorder. The enzyme is believed to bind substrate through a hinge-bending motion of domains 1 and 2. The C-terminal domain 3 contains an invariant cysteine that forms the covalent attachment site for the DPM (dipyrromethane) cofactor. HMBS is found in all organisms except viruses. The domains 1 and 2 have the same overall topology as found in the type 2 periplasmic-binding proteins (PBP2), many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor.
Pssm-ID: 270363 [Multi-domain] Cd Length: 282 Bit Score: 310.32 E-value: 7.54e-106
Archaeal HemC of hydroxymethylbilane synthase family; the type 2 periplasmic binding protein ...
13-284
5.90e-86
Archaeal HemC of hydroxymethylbilane synthase family; the type 2 periplasmic binding protein fold; Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophyll, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). This subfamily includes the three domains of HMBS. The enzyme is believed to bind substrate through a hinge-bending motion of domains 1 and 2. The C-terminal domain 3 contains an invariant cysteine that forms the covalent attachment site for the DPM (dipyrromethane) cofactor. HMBS is found in all organisms except viruses. The domains 1 and 2 have the same overall topology as found in the type 2 periplasmic-binding proteins (PBP2), many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor.
Pssm-ID: 270362 [Multi-domain] Cd Length: 273 Bit Score: 259.16 E-value: 5.90e-86
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
of the residues that compose this conserved feature have been mapped to the query sequence.
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Functional characterization of the conserved domain architecture found on the query.
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The table lists conserved domains identified on the query sequence. Click on the plus sign (+) on the left to display full descriptions, alignments, and scores.
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(labeled illustration) Standard Display shows only the best scoring domain model from each source, in each hit category listed below for each region on the query sequence.
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