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Literature summary extracted from

  • Chek, M.F.; Hiroe, A.; Hakoshima, T.; Sudesh, K.; Taguchi, S.
    PHA synthase (PhaC) interpreting the functions of bioplastic-producing enzyme from a structural perspective (2019), Appl. Microbiol. Biotechnol., 103, 1131-1141 .
    View publication on PubMed

Application

EC Number Application Comment Organism
2.3.1.304 synthesis biodegradable bio-based polyhydroxyalkanoate (PHA) is gaining much attention as a promising biomaterial that can replace some conventional petroleum-based plastics especially the single use plastics Aeromonas caviae
2.3.1.304 synthesis biodegradable bio-based polyhydroxyalkanoate (PHA) is gaining much attention as a promising biomaterial that can replace some conventional petroleum-based plastics especially the single use plastics Chromobacterium sp. USM2
2.3.1.304 synthesis biodegradable bio-based polyhydroxyalkanoate (PHA) is gaining much attention as a promising biomaterial that can replace some conventional petroleum-based plastics especially the single use plastics. The most studied class I PhaC from Cupriavidus necator (PhaCCn) is often used as a study model to increase its ability to incorporate medium-chain length (MCL) monomers into PHA Cupriavidus necator
2.3.1.304 synthesis biodegradable bio-based polyhydroxyalkanoate (PHA) is gaining much attention as a promising biomaterial that could replace some conventional petroleum-based plastics especially the single use plastics. Class II PhaC1 from Pseudomonas sp. 61-3 (PhaC1Ps) is useful in terms of its broad substrate specificity, and engineering of PhaC1Ps successfully increases its short-chain-length (SCL) incorporation into PHA Pseudomonas sp. 61-3

Cloned(Commentary)

EC Number Cloned (Comment) Organism
2.3.1.304 gene phaC Aeromonas caviae
2.3.1.304 gene phaC Chromobacterium sp. USM2
2.3.1.304 gene phaC (H16_A1437) Cupriavidus necator
2.3.1.304 gene phaC1 Pseudomonas sp. 61-3

Protein Variants

EC Number Protein Variants Comment Organism
2.3.1.304 A479S the mutant shows an increased activity towards short-chain length (SCL) PHA, but a decreased activity towards medium-chain length (MCL) PHA Chromobacterium sp. USM2
2.3.1.304 F362I/F518I the double mutation of Phe362Ile and Phe518Ile of PhaCAc causes a 6% increment in the specific synthase activity and an 11% increment of PHA accumulation compared to wild-type synthase Aeromonas caviae
2.3.1.304 F518I in broad-range class I PhaCAc, mutation of Phe518Ile increases the relative activity to 480% in the in vitro synthase activity assay, and 120% in the in vivo PHA accumulation Aeromonas caviae
2.3.1.304 additional information mutation of Phe333 may directly impact the geometry of the catalytic Asp447 in the dimer. Since Phe333 and His448 are highly conserved in class I and II PhaC, it is highly possible that this architecture is shared among synthases from different classes Aeromonas caviae
2.3.1.304 additional information mutation of Phe333 may directly impact the geometry of the catalytic Asp447 in the dimer. Since Phe333 and His448 are highly conserved in class I and II PhaC, it is highly possible that this architecture is shared among synthases from different classes Cupriavidus necator
2.3.1.304 additional information mutation of Phe333 may directly impact the geometry of the catalytic Asp447 in the dimer. Since Phe333 and His448 are highly conserved in class I and II PhaC, it is highly possible that this architecture is shared among synthases from different classes. Beneficial mutations displayed on PhaCCs-CAT, structure, overview Chromobacterium sp. USM2
2.3.1.304 additional information the double mutations of Ser325X and Gln481X show further increments in the production of P(3HB), up by 340 to 400fold higher than the wild-type. Mutation of Phe333 may directly impact the geometry of the catalytic Asp447 in the dimer. Since Phe333 and His448 are highly conserved in class I and II PhaC, it is highly possible that this architecture is shared among synthases from different classes Pseudomonas sp. 61-3
2.3.1.304 Q481K in class II PhaC1Ps, the mutations Gln481Met/Lys/Arg allow the incorporation of non-native substrates, such as smaller 3-hydroxybutyrate fractions into the copolymer Pseudomonas sp. 61-3
2.3.1.304 Q481M in class II PhaC1Ps, the mutations Gln481Met/Lys/Arg allow the incorporation of non-native substrates, such as smaller 3-hydroxybutyrate fractions into the copolymer Pseudomonas sp. 61-3
2.3.1.304 Q481R in class II PhaC1Ps, the mutations Gln481Met/Lys/Arg allow the incorporation of non-native substrates, such as smaller 3-hydroxybutyrate fractions into the copolymer Pseudomonas sp. 61-3
2.3.1.304 S325C the mutation causes a significant increase in the incorporation of short-chain-length (SCL) in the PHA synthesized Pseudomonas sp. 61-3
2.3.1.304 S325T the mutation causes a significant increase in the incorporation of short-chain-length (SCL) in the PHA synthesized Pseudomonas sp. 61-3
2.3.1.304 S325T/Q481K the mutat shows significantly increased incorporation of short-chain-length (SCL) substrates in the polymer synthesized by class II PhaCs Pseudomonas sp. 61-3
2.3.1.304 S477G the mutant of PhaC1Ps shows enhancement in the in vitro activity with both short-chain-length (SCL) and medium-chain-length (MCL) substrates Pseudomonas sp. 61-3

Localization

EC Number Localization Comment Organism GeneOntology No. Textmining
2.3.1.304 intracellular
-
 Aeromonas caviae 5622
-

Organism

EC Number Organism UniProt Comment Textmining
2.3.1.304 Aeromonas caviae
-
-
-
2.3.1.304 Chromobacterium sp. USM2 E1APK1
-
-
2.3.1.304 Cupriavidus necator P23608 i.e. Ralstonia eutropha
-
2.3.1.304 Cupriavidus necator 17699 P23608 i.e. Ralstonia eutropha
-
2.3.1.304 Cupriavidus necator DSM 428 P23608 i.e. Ralstonia eutropha
-
2.3.1.304 Cupriavidus necator Stanier 337 P23608 i.e. Ralstonia eutropha
-
2.3.1.304 Pseudomonas sp. 61-3 Q9Z3Y1
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.3.1.304 additional information structure-function relationship of PhaCs, and substrate specificity, overview Aeromonas caviae ?
-
-
2.3.1.304 additional information structure-function relationship of PhaCs, and substrate specificity, overview Cupriavidus necator ?
-
-
2.3.1.304 additional information structure-function relationship of PhaCs, and substrate specificity, overview Chromobacterium sp. USM2 ?
-
-
2.3.1.304 additional information structure-function relationship of PhaCs, and substrate specificity, overview Pseudomonas sp. 61-3 ?
-
-
2.3.1.304 additional information structure-function relationship of PhaCs, and substrate specificity, overview Cupriavidus necator Stanier 337 ?
-
-
2.3.1.304 additional information structure-function relationship of PhaCs, and substrate specificity, overview Cupriavidus necator 17699 ?
-
-
2.3.1.304 additional information structure-function relationship of PhaCs, and substrate specificity, overview Cupriavidus necator DSM 428 ?
-
-

Subunits

EC Number Subunits Comment Organism
2.3.1.304 dimer
-
 Aeromonas caviae
2.3.1.304 dimer
-
 Cupriavidus necator
2.3.1.304 dimer
-
 Chromobacterium sp. USM2
2.3.1.304 dimer
-
 Pseudomonas sp. 61-3
2.3.1.304 More Phe362 and Phe518 of PhaC from Aeromonas caviae (PhaCAc) are assisting the dimer formation and maintaining the integrity of the core beta-sheet, respectively. Structure analysis and comparison. Monomer-dimer equilibration of PhaC Aeromonas caviae
2.3.1.304 More structure analysis and comparison. Domain organization of class I PhaCCn from Cupriavidus necator. Monomer-dimer equilibration of PhaC Cupriavidus necator
2.3.1.304 More structure analysis and comparison. Domain organization of class I PhaCCs from Chromobacterium sp. USM2. Monomer-dimer equilibration of PhaC Chromobacterium sp. USM2
2.3.1.304 More structure analysis and comparison. Monomer-dimer equilibration of PhaC Pseudomonas sp. 61-3

Synonyms

EC Number Synonyms Comment Organism
2.3.1.304 broad-range class I PhaCAc
-
 Aeromonas caviae
2.3.1.304 Class I PhaC
-
 Aeromonas caviae
2.3.1.304 Class I PhaC
-
 Cupriavidus necator
2.3.1.304 Class I PhaC
-
 Chromobacterium sp. USM2
2.3.1.304 class II PhaC1
-
 Pseudomonas sp. 61-3
2.3.1.304 H16_A1437 locus name Cupriavidus necator
2.3.1.304 intracellular polyhydroxyalkanoate synthase UniProt Aeromonas caviae
2.3.1.304 intracellular polyhydroxyalkanoate synthase UniProt Chromobacterium sp. USM2
2.3.1.304 PHA synthase
-
 Aeromonas caviae
2.3.1.304 PHA synthase
-
 Cupriavidus necator
2.3.1.304 PHA synthase
-
 Chromobacterium sp. USM2
2.3.1.304 PHA synthase
-
 Pseudomonas sp. 61-3
2.3.1.304 PHA synthase 1
-
 Pseudomonas sp. 61-3
2.3.1.304 PhaC
-
 Aeromonas caviae
2.3.1.304 PhaC
-
 Cupriavidus necator
2.3.1.304 PhaC
-
 Chromobacterium sp. USM2
2.3.1.304 PhaC
-
 Pseudomonas sp. 61-3
2.3.1.304 PhaC1
-
 Pseudomonas sp. 61-3
2.3.1.304 PhaC1Ps
-
 Pseudomonas sp. 61-3
2.3.1.304 PhaCAc
-
 Aeromonas caviae
2.3.1.304 PhaCCn-CAT
-
 Cupriavidus necator
2.3.1.304 PhaCCs-CAT
-
 Chromobacterium sp. USM2
2.3.1.304 PhbC
-
 Cupriavidus necator

General Information

EC Number General Information Comment Organism
2.3.1.304 evolution there is a total of four classes of PhaCs, where class I, III, and IV prefer to synthesize PHA-SCL containing 3-5 carbons in the monomer unit, while class II PhaC prefers to synthesize PHA-MCL which contains 6-14 carbons in the monomer unit Pseudomonas sp. 61-3
2.3.1.304 evolution there is a total of four classes of PhaCs, where class I, III, and IV prefer to synthesize PHASCL containing 3-5 carbons in the monomer unit, while class II PhaC prefers to synthesize PHAMCL which contains 6-14 carbons in the monomer unit Aeromonas caviae
2.3.1.304 evolution there is a total of four classes of PhaCs, where class I, III, and IV prefer to synthesize PHASCL containing 3-5 carbons in the monomer unit, while class II PhaC prefers to synthesize PHAMCL which contains 6-14 carbons in the monomer unit Cupriavidus necator
2.3.1.304 evolution there is a total of four classes of PhaCs, where class I, III, and IV prefer to synthesize PHASCL containing 3-5 carbons in the monomer unit, while class II PhaC prefers to synthesize PHAMCL which contains 6-14 carbons in the monomer unit Chromobacterium sp. USM2
2.3.1.304 malfunction mutation of residues S320, F333, S475, A479, Y492, and L506 affects the positioning of the catalytic triad residues, while mutation of F387 affects the enzyme's dimerization Chromobacterium sp. USM2
2.3.1.304 malfunction mutation of residues S325, F338, S477, Q481, Y494, and Q508 affects the positioning of the catalytic triad residues, while mutation of F392 affects the enzyme's dimerization Pseudomonas sp. 61-3
2.3.1.304 malfunction mutation of residues T348, F361, S506, A510, H523, and L537 affects the positioning of the catalytic triad residues, while mutation of class I/II-conserved Phe420 of PhaCCn to serine greatly reduced the lag phase and affects the enzyme's dimerization Cupriavidus necator
2.3.1.304 malfunction mutation of residues T349, F362, S501, A505, F518, and L532 affects the positioning of the catalytic triad residues, while mutation of F416 affects the enzyme's dimerization Aeromonas caviae
2.3.1.304 additional information in the class II PhaC1 from Pseudomonas sp. 61-3 (PhaC1Ps), Ser325 stabilizes the catalytic cysteine through hydrogen bonding. Another residue, Gln508 of PhaC1Ps is located in a conserved hydrophobic pocket which is next to the catalytic Asp and His. Ala510 of PhaCCn and its corresponding residues in other PhaCs are important in regulating the enzymes' substrate specificities Pseudomonas sp. 61-3
2.3.1.304 additional information residue Ala510 of PhaCCn is near catalytic His508 and may be involved in the open-close regulation, which presumably play an important role in substrate specificity and activity. Class I/II-conserved Phe420 of PhaCCn is one of the residues involved in dimerization. Structure comparisons and structure-function relationship of PhaCs, overview. A flexible CAP subdomain is observed covering the alpha/beta core subdomain from the top. The conformation of the CAP subdomain is the key indicator of the enzyme's active status. A short stretch of highly dynamic amino acids named LID region in the partially opened PhaCCn-CAT undergoes structural changes to allow substrate entry. The catalytic triad residues come together in the core, forming a catalytic pocket, indicating the involvement of the catalytic triad in the catalysis. Ala510 of PhaCCn and its corresponding residues in other PhaCs are important in regulating the enzymes' substrate specificities Cupriavidus necator
2.3.1.304 additional information structure comparisons and structure-function relationship of PhaCs, overview. A flexible CAP subdomain is observed covering the Balpha/beta core subdomain from the top. The conformation of the CAP subdomain is the key indicator of the enzyme's active status. Closed form PhaCCs-CAT blocks the substrates from entering the catalytic pocket by covering the active site within the CAP subdomain, in particular, a short stretch of highly dynamic amino acids named LID region. Ala510 of PhaCCn and its corresponding residues in other PhaCs are important in regulating the enzymes' substrate specificities Chromobacterium sp. USM2
2.3.1.304 additional information structure comparisons and structure-function relationship of PhaCs, overview. Phe362 and Phe518 of PhaC from Aeromonas caviae (PhaCAc) are assisting the dimer formation and maintaining the integrity of the core beta-sheet, respectively. Ala510 of PhaCCn and its corresponding residues in other PhaCs are important in regulating the enzymes' substrate specificities Aeromonas caviae
2.3.1.304 physiological function PHA synthase (PhaC) is the key enzyme in the polymerization of polyhydroxyalkanoates (PHAs) Aeromonas caviae
2.3.1.304 physiological function PHA synthase (PhaC) is the key enzyme in the polymerization of polyhydroxyalkanoates (PHAs) Cupriavidus necator
2.3.1.304 physiological function PHA synthase (PhaC) is the key enzyme in the polymerization of polyhydroxyalkanoates (PHAs) Chromobacterium sp. USM2
2.3.1.304 physiological function PHA synthase (PhaC) is the key enzyme in the polymerization of polyhydroxyalkanoates (PHAs). Structure comparisons and structure-function relationship of PhaCs, overview Pseudomonas sp. 61-3