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Literature summary for 2.5.1.44 extracted from
- Comprehensive structural characterization of the bacterial homospermidine synthase - an essential enzyme of the polyamine metabolism (2016), Sci. Rep., 6, 19501.
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| the BvHSS structure is solved from crystals belonging to space group P212121 with bound NAD+, PDB ID 4PLP. Crystals from BvHSS and BvHSS variants with bound NAD+ in complex with various polyamines all belong to space group P22121 with cell parameters in approximately the same order of magnitude. Structure analysis | Blastochloris viridis |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| E237Q | site-directed mutagenesis, altered active site structure and impaired subsrate binding compared to wild-type, overview | Blastochloris viridis |
| H296S | site-directed mutagenesis, altered active site structure and impaired subsrate binding compared to wild-type, overview | Blastochloris viridis |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| K+ | dependent on, best at 50 mM | Blastochloris viridis |  |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| putrescine | Blastochloris viridis | - |
sym-homospermidine + NH3 + H+ | - |
? | |
| putrescine + spermidine | Blastochloris viridis | - |
sym-homospermidine + propane-1,3-diamine | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Blastochloris viridis | O32323 | - |
- |
Reaction
| Reaction | Comment | Organism | Reaction ID |
|---|---|---|---|
| 2 putrescine = sym-homospermidine + NH3 + H+ | the reaction mechanism emphasizes cation-Pi interaction through a conserved Trp residue as a key stabilizer of high energetic transition states. The enzyme has two distinct substrate binding sites, one of which is highly specific for putrescine. Enzyme HSS features a side pocket in the direct vicinity of the active site formed by conserved amino acids and a potential substrate discrimination, guiding, and sensing mechanism | Blastochloris viridis | |
| putrescine + spermidine = sym-homospermidine + propane-1,3-diamine | the reaction mechanism emphasizes cation-Pi interaction through a conserved Trp residue as a key stabilizer of high energetic transition states. The enzyme has two distinct substrate binding sites, one of which is highly specific for putrescine. Enzyme HSS features a side pocket in the direct vicinity of the active site formed by conserved amino acids and a potential substrate discrimination, guiding, and sensing mechanism | Blastochloris viridis |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| 2 spermidine | - |
Blastochloris viridis | sym-homospermidine + propane-1,3-diamine + putrescine | - |
? | |
| additional information | the enzyme has two distinct substrate binding sites, one of which is highly specific for putrescine. Enzyme HSS features a side pocket in the direct vicinity of the active site formed by conserved amino acids and a potential substrate discrimination, guiding, and sensing mechanism. The enzyme is capable of catalyzing side reactions to produce a variety of N-aminobutyl-linked triamines utilizing putrescine together with respective linear diamines with C3 to C7 carbon chains, overview. Bacterial HSS does not produce sym-norspermidine from two 1,4-diaminopropanes | Blastochloris viridis | ? | - |
? | |
| putrescine | - |
Blastochloris viridis | sym-homospermidine + NH3 + H+ | - |
? | |
| putrescine + spermidine | - |
Blastochloris viridis | sym-homospermidine + propane-1,3-diamine | - |
? | |
| spermidine + cadaverine | - |
Blastochloris viridis | (4-aminobutyl)(5-aminopentyl)amine + sym-homospermidine + propane-1,3-diamine + putrescine | - |
? | |
| spermidine + putrescine | - |
Blastochloris viridis | sym-homospermidine + propane-1,3-diamine + putrescine | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| dimer | the active site is not formed by the interface of two subunits but resides within one subunit of the bacterial enzyme, structure analysis | Blastochloris viridis |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| BvHSS | - |
Blastochloris viridis |
| HSS | - |
Blastochloris viridis |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 9 | - |
- |
Blastochloris viridis |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| NAD+ | unique usage of NAD(H) as a prosthetic group. the cofactor is coordinated through hydrogen bonding via residues Ser21, Ile22, Ser230 (phosphate), Asp45, Val66 (adenosine), Ser92,Thr114, Ala161, Asn162, and Pro163 (nicotineamide riboside). The phosphate-binding motif (18GFGSIG23) is located in the loop connecting beta-strand 2 and alpha-helix A of the Rossmann fold. The adenosine part of NAD+ is bound via loop regions located between beta-strand 4, 5, 6 and alpha-helix C, D, E. Nicotineamide-riboside-binding residues are found in loop regions between beta-strand 7 and 8 and alpha-helix F and O | Blastochloris viridis | |
| NADH | unique usage of NAD(H) as a prosthetic group. the cofactor is coordinated through hydrogen bonding via residues Ser21, Ile22, Ser230 (phosphate), Asp45, Val66 (adenosine), Ser92,Thr114, Ala161, Asn162, and Pro163 (nicotineamide riboside). The phosphate-binding motif (18GFGSIG23) is located in the loop connecting beta-strand 2 and alpha-helix A of the Rossmann fold. The adenosine part of NAD+ is bound via loop regions located between beta-strand 4, 5, 6 and alpha-helix C, D, E. Nicotineamide-riboside-binding residues are found in loop regions between beta-strand 7 and 8 and alpha-helix F and O | Blastochloris viridis | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | bacterial homospermidine synthase is highly conserved and is proposed to be evolutionarily related to carboxy(nor)spermidine dehydrogenase, EC 1.5.1.43. Despite of the low amino acid sequence identity between plant HSS and bacterial HSS of about 12% (Senecio vulgaris vs. Blastochloris viridis HSS), a conserved fold within the three dimensional structure of bacterial HSS might be responsible for the similarity of the reaction mechanism | Blastochloris viridis |
| metabolism | essential enzyme of the bacterial polyamine metabolism | Blastochloris viridis |
| additional information | the structure of the bacterial enzyme does not possess a lysine residue in the active center and does not form an enzyme-substrate Schiff base intermediate as observed for deoxyhypusine synthase. The active site is not formed by the interface of two subunits but resides within one subunit of the bacterial enzyme. The enzyme has two distinct substrate binding sites, one of which is highly specific for putrescine. Enzyme HSS features a side pocket in the direct vicinity of the active site formed by conserved amino acids and a potential substrate discrimination, guiding, and sensing mechanism. Three-dimensional structure analysis, PDB ID 4PLP, and substrate binding analysis | Blastochloris viridis |
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