Literature summary for 2.3.1.304 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 .

Search for more literature for 2.3.1.304

Application

Application	Comment	Organism
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
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
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
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)

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

Protein Variants

Protein Variants	Comment	Organism
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
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
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
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
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
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
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
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
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
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
S325C	the mutation causes a significant increase in the incorporation of short-chain-length (SCL) in the PHA synthesized	Pseudomonas sp. 61-3
S325T	the mutation causes a significant increase in the incorporation of short-chain-length (SCL) in the PHA synthesized	Pseudomonas sp. 61-3
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
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

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

Organism

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

Substrates and Products (Substrate)

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

Subunits

Subunits	Comment	Organism
dimer	-	Aeromonas caviae
dimer	-	Cupriavidus necator
dimer	-	Chromobacterium sp. USM2
dimer	-	Pseudomonas sp. 61-3
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
More	structure analysis and comparison. Domain organization of class I PhaCCn from Cupriavidus necator. Monomer-dimer equilibration of PhaC	Cupriavidus necator
More	structure analysis and comparison. Domain organization of class I PhaCCs from Chromobacterium sp. USM2. Monomer-dimer equilibration of PhaC	Chromobacterium sp. USM2
More	structure analysis and comparison. Monomer-dimer equilibration of PhaC	Pseudomonas sp. 61-3

Synonyms

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

General Information

General Information	Comment	Organism
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
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
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
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
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
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
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
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
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
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
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
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
physiological function	PHA synthase (PhaC) is the key enzyme in the polymerization of polyhydroxyalkanoates (PHAs)	Aeromonas caviae
physiological function	PHA synthase (PhaC) is the key enzyme in the polymerization of polyhydroxyalkanoates (PHAs)	Cupriavidus necator
physiological function	PHA synthase (PhaC) is the key enzyme in the polymerization of polyhydroxyalkanoates (PHAs)	Chromobacterium sp. USM2
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