BRENDA - Enzyme Database show
show all sequences of 2.5.1.44

Comprehensive structural characterization of the bacterial homospermidine synthase - an essential enzyme of the polyamine metabolism

Krossa, S.; Faust, A.; Ober, D.; Scheidig, A.J.; Sci. Rep. 6, 19501 (2016)

Data extracted from this reference:

Crystallization (Commentary)
Crystallization
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
Engineering
Amino acid exchange
Commentary
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
Commentary
Organism
Structure
K+
dependent on, best at 50 mM
Blastochloris viridis
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
putrescine
Blastochloris viridis
-
sym-homospermidine + NH3 + H+
-
-
?
putrescine + spermidine
Blastochloris viridis
-
sym-homospermidine + propane-1,3-diamine
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Blastochloris viridis
O32323
-
-
Reaction
Reaction
Commentary
Organism
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
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2 spermidine
-
739672
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
739672
Blastochloris viridis
?
-
-
-
-
putrescine
-
739672
Blastochloris viridis
sym-homospermidine + NH3 + H+
-
-
-
?
putrescine + spermidine
-
739672
Blastochloris viridis
sym-homospermidine + propane-1,3-diamine
-
-
-
?
spermidine + cadaverine
-
739672
Blastochloris viridis
(4-aminobutyl)(5-aminopentyl)amine + sym-homospermidine + propane-1,3-diamine + putrescine
-
-
-
?
spermidine + putrescine
-
739672
Blastochloris viridis
sym-homospermidine + propane-1,3-diamine + putrescine
-
-
-
?
Subunits
Subunits
Commentary
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
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
9
-
-
Blastochloris viridis
Cofactor
Cofactor
Commentary
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
Cofactor (protein specific)
Cofactor
Commentary
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
Crystallization (Commentary) (protein specific)
Crystallization
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
Engineering (protein specific)
Amino acid exchange
Commentary
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 (protein specific)
Metals/Ions
Commentary
Organism
Structure
K+
dependent on, best at 50 mM
Blastochloris viridis
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
putrescine
Blastochloris viridis
-
sym-homospermidine + NH3 + H+
-
-
?
putrescine + spermidine
Blastochloris viridis
-
sym-homospermidine + propane-1,3-diamine
-
-
?
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2 spermidine
-
739672
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
739672
Blastochloris viridis
?
-
-
-
-
putrescine
-
739672
Blastochloris viridis
sym-homospermidine + NH3 + H+
-
-
-
?
putrescine + spermidine
-
739672
Blastochloris viridis
sym-homospermidine + propane-1,3-diamine
-
-
-
?
spermidine + cadaverine
-
739672
Blastochloris viridis
(4-aminobutyl)(5-aminopentyl)amine + sym-homospermidine + propane-1,3-diamine + putrescine
-
-
-
?
spermidine + putrescine
-
739672
Blastochloris viridis
sym-homospermidine + propane-1,3-diamine + putrescine
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
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
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
9
-
-
Blastochloris viridis
General Information
General Information
Commentary
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
General Information (protein specific)
General Information
Commentary
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
Other publictions for EC 2.5.1.44
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
739378
Lopez-Gomez
-
Homospermidine synthase contri ...
Rhizobium tropici, Rhizobium tropici Rt CIAT899
Plant Soil
404
413-425
2016
-
-
1
-
1
-
-
-
-
-
-
6
-
2
-
-
-
-
-
-
-
-
6
-
-
-
-
-
-
-
-
-
-
-
-
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-
1
-
-
1
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-
-
-
-
-
-
-
6
-
-
-
-
-
-
-
-
6
-
-
-
-
-
-
-
-
-
-
2
2
-
-
-
739672
Krossa
Comprehensive structural chara ...
Blastochloris viridis
Sci. Rep.
6
19501
2016
-
-
-
1
2
-
-
-
-
1
-
2
-
5
-
-
-
2
-
-
-
-
6
1
-
-
-
-
1
-
-
2
-
-
-
-
-
-
2
1
2
-
-
-
-
-
-
1
-
2
-
-
-
-
-
-
-
-
6
1
-
-
-
-
1
-
-
-
-
3
3
-
-
-
739108
Li
Different polyamine pathways f ...
Paramecium tetraurelia, Paramecium tetraurelia d4-2
Mol. Microbiol.
97
791-807
2015
-
-
-
-
-
-
-
-
-
-
-
-
-
11
-
-
-
-
-
-
-
-
-
-
-
-
-
-
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-
-
-
-
-
-
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-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
3
3
-
-
-
704662
Shaw
Evolution and multifarious hor ...
Acinetobacter tartarogenes, Blastochloris viridis, Bradyrhizobium japonicum, Opitutus terrae, Paramecium tetraurelia, Ralstonia phage phiRSL1, Rhizobium leguminosarum
J. Biol. Chem.
285
14711-14723
2010
-
-
7
-
-
-
-
3
-
-
-
-
-
15
-
-
-
-
-
-
-
-
7
-
6
-
-
3
6
-
-
7
-
-
-
-
-
7
7
-
-
-
-
-
-
3
-
-
-
-
-
-
-
-
-
-
-
-
7
-
6
-
-
3
6
-
-
-
-
1
1
-
3
3
288701
Tholl
Purification, molecular clonin ...
Blastochloris viridis
Eur. J. Biochem.
240
373-379
1996
-
-
1
-
-
-
-
1
-
-
3
1
-
6
-
-
1
-
-
1
1
-
1
1
-
-
-
-
-
-
-
1
-
-
-
-
-
1
1
-
-
-
-
-
-
1
-
-
3
1
-
-
-
1
-
1
1
-
1
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
288702
Ober
-
Homospermidine synthase of Rho ...
Blastochloris viridis
J. Gen. Appl. Microbiol.
42
411-420
1996
-
-
-
-
-
-
-
4
-
1
-
1
-
1
-
-
-
-
-
1
-
-
9
-
1
-
1
-
1
-
-
2
-
-
-
-
-
-
2
-
-
-
-
-
-
4
-
1
-
1
-
-
-
-
-
1
-
-
9
-
1
-
1
-
1
-
-
-
-
-
-
-
-
-
288699
Böttcher
-
Biosynthesis of pyrrolizidine ...
Blastochloris viridis
Can. J. Chem.
72
80-85
1994
-
-
-
-
-
-
-
3
-
-
-
1
-
1
-
-
1
-
-
1
1
1
9
-
-
-
1
-
-
-
-
1
-
-
-
-
-
-
1
-
-
-
-
-
-
3
-
-
-
1
-
-
-
1
-
1
1
1
9
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
288700
Yamamoto
Purification and characterizat ...
Acinetobacter tartarogenes
J. Biochem.
114
45-49
1993
-
-
-
-
-
-
3
1
-
1
2
1
-
6
-
-
1
-
-
-
1
1
1
1
-
-
1
-
-
-
-
1
-
-
-
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-
-
1
-
-
-
-
3
-
1
-
1
2
1
-
-
-
1
-
-
1
1
1
1
-
-
1
-
-
-
-
-
-
-
-
-
-
-
288698
Srivenugopal
Enzymic synthesis of sym-homos ...
Lathyrus sativus, Santalum album
Biochem. J.
190
461-464
1980
-
-
-
-
-
-
4
1
-
-
1
2
-
2
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1
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-
2
2
-
2
-
1
-
1
-
1
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2
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-
-
2
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4
-
1
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1
2
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1
-
2
2
-
2
-
1
-
1
-
1
-
-
-
-
-
-
-
-
-
288697
Tait
The formation of homospermidin ...
Blastochloris viridis, Blastochloris viridis N.C.I.B. 10028
Biochem. Soc. Trans.
7
199-200
1979
-
-
-
-
-
-
4
2
-
3
1
2
-
2
-
-
1
-
-
1
-
-
2
-
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-
-
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1
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1
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4
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2
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3
1
2
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1
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1
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2
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