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Information on EC 1.14.11.56 - L-proline cis-4-hydroxylase
for references in articles please use BRENDA:EC1.14.11.56
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EC Tree 1 Oxidoreductases
1.14 Acting on paired donors, with incorporation or reduction of molecular oxygen
1.14.11 With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
1.14.11.56 L-proline cis-4-hydroxylase
IUBMB Comments
Requires Fe2+ and ascorbate. The enzyme, isolated from Rhizobium species, only produces cis-4-hydroxy-L-proline (cf. EC 1.14.11.57, L-proline trans-4-hydroxylase).
The enzyme appears in viruses and cellular organisms
- 1.14.11.56
- cis-4-hydroxy-l-proline
-
sinorhizobium
- meliloti
- dioxygenase
- hydroxylases
-
regioselectivity
- loti
-
chop
-
non-heme
-
mesorhizobium
- synthesis
showSynonyms
smp4h, cis-p4h, l-proline cis-4-hydroxylase, more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
cis-P4H
mlr6283
R03107
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
L-proline + 2-oxoglutarate + O2 = cis-4-hydroxy-L-proline + succinate + CO2
-
-
-
-
L-proline + 2-oxoglutarate + O2 = cis-4-hydroxy-L-proline + succinate + CO2
proposed catalytic mechanism of cis-P4H with L-proline and L-pipecolate as substrates with 2-oxoglutarate and O2, overview
L-proline + 2-oxoglutarate + O2 = cis-4-hydroxy-L-proline + succinate + CO2
proposed catalytic mechanism of cis-P4H with L-proline and L-pipecolate as substrates with 2-oxoglutarate and O2, overview
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SYSTEMATIC NAME
IUBMB Comments
L-proline,2-oxoglutarate:oxygen oxidoreductase (cis-4-hydroxylating)
Requires Fe2+ and ascorbate. The enzyme, isolated from Rhizobium species, only produces cis-4-hydroxy-L-proline (cf. EC 1.14.11.57, L-proline trans-4-hydroxylase).
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
L-homophenylalanine + 2-oxoglutarate + O2
? + succinate + CO2
Substrates: mutant enzyme W40M shows 8.3fold increase in turnover number for L-homophenylalanine as compared to wild-type enzyme and mutant enzyme W40M/I103L shows 112fold increase in turnover number. Mutation reprograms the natural hydroxylase to predominantly act as a desaturase, giving almost exclusively 3,4-desaturated L-homophenylalanine, through capability of tyrosine to serve as a catalytic entity in the reaction mechanism
Products: -
Products: -
?
L-pipecolate + 2-oxoglutarate + O2
cis-5-hydroxypipecolate + cis-3-hydroxypipecolate + succinate + CO2
L-pipecolic acid + 2-oxoglutarate + O2
cis-5-hydroxy-L-pipecolic acid + cis-3-hydroxy-L-pipecolic acid + succinate + CO2
L-pipecolate + 2-oxoglutarate + O2
cis-5-hydroxypipecolate + cis-3-hydroxypipecolate + succinate + CO2
Substrates: -
Products: -
Products: -
?
L-pipecolate + 2-oxoglutarate + O2
cis-5-hydroxypipecolate + cis-3-hydroxypipecolate + succinate + CO2
Substrates: -
Products: -
Products: -
?
L-pipecolic acid + 2-oxoglutarate + O2
cis-5-hydroxy-L-pipecolic acid + cis-3-hydroxy-L-pipecolic acid + succinate + CO2
Substrates: -
Products: the ratio between cis-5/cis-3 isomers is about 1:7
Products: the ratio between cis-5/cis-3 isomers is about 1:7
?
L-pipecolic acid + 2-oxoglutarate + O2
cis-5-hydroxy-L-pipecolic acid + cis-3-hydroxy-L-pipecolic acid + succinate + CO2
Substrates: -
Products: the ratio between cis-5/cis-3 isomers is about 2:1
Products: the ratio between cis-5/cis-3 isomers is about 2:1
?
L-pipecolic acid + 2-oxoglutarate + O2
cis-5-hydroxy-L-pipecolic acid + cis-3-hydroxy-L-pipecolic acid + succinate + CO2
Substrates: -
Products: the ratio between cis-5/cis-3 isomers is about 2:1
Products: the ratio between cis-5/cis-3 isomers is about 2:1
?
L-pipecolic acid + 2-oxoglutarate + O2
cis-5-hydroxy-L-pipecolic acid + cis-3-hydroxy-L-pipecolic acid + succinate + CO2
Substrates: -
Products: the ratio between cis-5/cis-3 isomers is about 1:7
Products: the ratio between cis-5/cis-3 isomers is about 1:7
?
L-proline + 2-oxoglutarate + O2
cis-4-hydroxy-L-proline + succinate + CO2
Substrates: -
Products: -
Products: -
?
L-proline + 2-oxoglutarate + O2
cis-4-hydroxy-L-proline + succinate + CO2
Substrates: -
Products: -
Products: -
?
L-proline + 2-oxoglutarate + O2
cis-4-hydroxy-L-proline + succinate + CO2
Substrates: presence of 2-oxoglutarate is strictly required
Products: -
Products: -
?
L-proline + 2-oxoglutarate + O2
cis-4-hydroxy-L-proline + succinate + CO2
Substrates: -
Products: -
Products: -
?
L-proline + 2-oxoglutarate + O2
cis-4-hydroxy-L-proline + succinate + CO2
Substrates: presence of 2-oxoglutarate is strictly required
Products: -
Products: -
?
L-proline + 2-oxoglutarate + O2
cis-4-hydroxy-L-proline + succinate + CO2
Substrates: -
Products: -
Products: -
?
L-proline + 2-oxoglutarate + O2
cis-4-hydroxy-L-proline + succinate + CO2
Substrates: -
Products: -
Products: -
?
L-proline + 2-oxoglutarate + O2
cis-4-hydroxy-L-proline + succinate + CO2
Substrates: presence of 2-oxoglutarate is strictly required
Products: -
Products: -
?
L-proline + 2-oxoglutarate + O2
cis-4-hydroxy-L-proline + succinate + CO2
Substrates: acceptance of the native substrate L-proline is almost completely abolished in the mutant enzymes W40M und W40M/I103L
Products: -
Products: -
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
L-pipecolate + 2-oxoglutarate + O2
cis-5-hydroxypipecolate + cis-3-hydroxypipecolate + succinate + CO2
L-pipecolate + 2-oxoglutarate + O2
cis-5-hydroxypipecolate + cis-3-hydroxypipecolate + succinate + CO2
Substrates: -
Products: -
Products: -
?
L-pipecolate + 2-oxoglutarate + O2
cis-5-hydroxypipecolate + cis-3-hydroxypipecolate + succinate + CO2
Substrates: -
Products: -
Products: -
?
L-proline + 2-oxoglutarate + O2
cis-4-hydroxy-L-proline + succinate + CO2
Substrates: -
Products: -
Products: -
?
L-proline + 2-oxoglutarate + O2
cis-4-hydroxy-L-proline + succinate + CO2
Substrates: presence of 2-oxoglutarate is strictly required
Products: -
Products: -
?
L-proline + 2-oxoglutarate + O2
cis-4-hydroxy-L-proline + succinate + CO2
Substrates: presence of 2-oxoglutarate is strictly required
Products: -
Products: -
?
L-proline + 2-oxoglutarate + O2
cis-4-hydroxy-L-proline + succinate + CO2
Substrates: -
Products: -
Products: -
?
L-proline + 2-oxoglutarate + O2
cis-4-hydroxy-L-proline + succinate + CO2
Substrates: presence of 2-oxoglutarate is strictly required
Products: -
Products: -
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Co2+
exogenous Co2+ is coordinated by residues H106, H154, and D108. Co2+ is a mimic of the catalytic metal center because of its stability under aerobic conditions and its enzymatic inactivity under anaerobic conditions. The cis-face of the C4 carbon of L-Pro is properly oriented toward Co2+, which in nature exists as FeIV=O during the hydroxylation reaction, to generate the enantiopure cis-4-hydroxyproline
Fe2+
Iron
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.24
L-homophenylalanine
20°C, pH not specified in the publication, mutant enzyme W40M
0.3
L-homophenylalanine
20°C, pH not specified in the publication, mutant enzyme W40M/I103L
1.1
L-homophenylalanine
20°C, pH not specified in the publication, wild-type enzyme
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.00025
L-homophenylalanine
20°C, pH not specified in the publication, wild-type enzyme
0.0021
L-homophenylalanine
20°C, pH not specified in the publication, mutant enzyme W40M
0.028
L-homophenylalanine
20°C, pH not specified in the publication, mutant enzyme W40M/I103L
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0002
L-homophenylalanine
20°C, pH not specified in the publication, wild-type enzyme
0.0086
L-homophenylalanine
20°C, pH not specified in the publication, mutant enzyme W40M
0.07
L-homophenylalanine
20°C, pH not specified in the publication, mutant enzyme W40M/I103L
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
0.1
mutant V97F, product cis-3-hydroxy-L-pipecolic acid, pH 7.2, 30°C
0.29
wild-type, product cis-5-hydroxy-L-pipecolic acid, pH 7.2, 30°C
0.34
wild-type, product cis-3-hydroxy-L-pipecolic acid, pH 7.2, 30°C
0.79
mutant V97F, product cis-5-hydroxy-L-pipecolic acid, pH 7.2, 30°C
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.2
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25
30
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Highest Expressing Human Cell Lines
Cell Line LinksPlease wait a moment until the data is sorted. This message will disappear when the data is sorted.
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
physiological function
additional information
evolution
proline hydroxylases are representative members of the nonheme Fe2+/2-oxoglutarate-dependent dioxygenase family
evolution
proline hydroxylases are representative members of the nonheme Fe2+/2-oxoglutarate-dependent dioxygenase family
physiological function
the enzyme catalyze the hydroxylation of L-proline, generating cis-4-hydroxy-L-proline, as well as the hydroxylation of L-pipecolic acid (L-Pip), generating two regioisomers, cis-5-hydroxypipecolate and cis-3-hydroxypipecolate in a 6:4 ratio
physiological function
the enzyme catalyze the hydroxylation of L-proline, generating cis-4-hydroxy-L-proline, as well as the hydroxylation of L-pipecolic acid (L-Pip), generating two regioisomers, cis-5-hydroxypipecolate and cis-3-hydroxypipecolate in a 6:4 ratio
additional information
I95, I97, and E114 are active site residues, the active site was composed of a distorted jelly roll beta-sheet core, which is sandwiched by the N-terminal and C-terminal alpha-helical domains
additional information
-
I95, I97, and E114 are active site residues, the active site was composed of a distorted jelly roll beta-sheet core, which is sandwiched by the N-terminal and C-terminal alpha-helical domains
additional information
V95, V97, and G114 are active site residues, a structure homology model of the SmP4H triple mutant V97F/V95W/E114G is constructed based on the MlP4H crystal structure
additional information
-
V95, V97, and G114 are active site residues, a structure homology model of the SmP4H triple mutant V97F/V95W/E114G is constructed based on the MlP4H crystal structure
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). P4H_RHILO
Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
280
0
32217
Swiss-Prot
-
A0A6L5BUT8_9PSED
261
0
29149
TrEMBL
-
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
in complex with in complex with Co2+, 2-oxoglutarate as cofactors, and L-proline or L-pipecolic acid. The active site is composed of a distorted jelly roll beta-sheet core, which is sandwiched by the N-terminal and C-terminal alpha-helical domains. Co2+ is coordinated by residues H106, H154, and D108
purified recombinant enzyme MlP4H in complex with Co2+, 2-oxoglutarate and L-Pro or L-Pip, the MlP4H protein used for crystallization includes an extra (Met)-Ser-Ala-Trp-Ser-His-Pro-Gln-Phe-Gly-Lys-Gly-Ala strep-tag II peptide at its N-terminus, and the original start codon of the wild-type is replaced by the underlined alanine, followed by the second codon of the wild-type. Crystallization of L-Pro complex crystals by sitting-drop vapor diffusion method mixing 0.001 ml of 28 mg/ml protein solution containing 2 mM CoCl2, 10 mM 2-oxoglutarate, and 20 mM L-Pro with reservoir solution containing 0.1 M bis-Tris propane, pH 8.5, 0.2 M sodium malonate, and 25% v/v PEG 3350, or of L-Pip complex crystals by sitting drop vapour diffusion method mixing 0.001 ml of 28 mg/ml protein solution containing 2 mM CoCl2, 10 mM ?2-oxoglutarate, and 20 mM L-Pip with 0.001 ml of reservoir solution containing 0.1 M CAPS, pH 10.5, 0.1 M lithium sulfate, and 1.8 M ammonium sulfate, all at 15°C, X-ray diffraction structure determination and analysis at 1.3-2.8 A resolution, by single-wavelength dispersion method with the bound Co2+ at the active site used as the anomalous scatter or by molecular replacement using the first L-Pro-bound structure as a search model
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
V95A
no increase in hydroxylation activity nor any improvement in the cis-5/cis-3 product ratio
V95A/V97A
no increase in hydroxylation activity nor any improvement in the cis-5/cis-3 product ratio
V95W
mutation significantly reduces the amount of cis-3-hydroxy-L-pipecolic acid (<5%) production compared with that of cis-5-hydroxy-L-pipecolic acid
V97A
2.5fold increase in production of cis-5-hydroxy-L-pipecolic acid, ratio of cis-5/cis-3 products is similar to wild-type
V97C
4fold increase in production of cis-5-hydroxy-L-pipecolic acid, ration of §-cis/5cis products is similar to wild-type
V97F
the cis-5/cis-3 product ratio improves from 1.4 for the wild-type enzyme to 5.3, the total amount of product is similar to wild-type
V97F/V95W
significantly improved regioselectivity toward cis-5-hydroxy-L-pipecolic acid
V97F/V95W/E114G
significantly improved regioselectivity toward cis-5-hydroxy-L-pipecolic acid and high productivity
V97Y
the cis-5/cis-3 product ratio improves from 1.4 for the wild-type enzyme to 9.0, the total amount of product decreases
V95A
-
no increase in hydroxylation activity nor any improvement in the cis-5/cis-3 product ratio
-
V95A/V97A
-
no increase in hydroxylation activity nor any improvement in the cis-5/cis-3 product ratio
-
V97A
-
2.5fold increase in production of cis-5-hydroxy-L-pipecolic acid, ratio of cis-5/cis-3 products is similar to wild-type
-
V97C
-
4fold increase in production of cis-5-hydroxy-L-pipecolic acid, ration of §-cis/5cis products is similar to wild-type
-
V97F
-
the cis-5/cis-3 product ratio improves from 1.4 for the wild-type enzyme to 5.3, the total amount of product is similar to wild-type
-
D108G
remodeling of L-proline cis-4-hydroxylase into a halogenase. Halogenation of L-proline exclusively occurs at the C3-position, the retained hydroxylation activity leads to derivatization at the C4-position
V95A
site-directed mutagenesis, the mutant does not show any increase in hydroxylation activity nor any improvement in the cis-5/cis-3 ratio compared to the wild-type enzyme
V95A/V97A
site-directed mutagenesis, the mutant does not show any increase in hydroxylation activity nor any improvement in the cis-5/cis-3 ratio compared to the wild-type enzyme
V97A
site-directed mutagenesis, the mutant shows increased activity and production of cis-4-hydroxy-L-proline
V97F
site-directed mutagenesis, the mutant shows improved regioselectivity of hydroxylation, the cis-5/cis-3 ratio improves from 1.4 for the wild-type enzyme to 5.3 for the mutant, the increase in activity is similar compared to mutant V97A, the V97F mutant demonstrates higher selectivity of C5-hydroxylation
V97F/V95W
site-directed mutagenesis, the mutant shows improved regioselectivity and increased activity of hydroxylation
V97F/V95W/E114G
site-directed mutagenesis, protein engineering of L-proline cis-4-hydroxylase based on the X-ray crystal structure leading to refined regio- and stereoselective hydroxylation of L-pipecolic acid, the engineered mutant enzyme produces 96% cis-5-hydroxypipecolate and 4% cis-3-hydroxypipecolate while the wild-type produces 60% cis-5-hydroxypipecolate and 40% cis-3-hydroxypipecolate. A structure homology model of the SmP4H triple mutant V97F/V95W/E114G is constructed based on the MlP4H crystal structure. addition of the E114G mutation improves the activity approximately 2fold compared to double mutant V97F/V95W. The triple mutant shows the highest growth and productivity of cis-5-hydroxy-L-pipecolate in a regioselective manner
V97Y
site-directed mutagenesis, the mutant shows improved regioselectivity of hydroxylation, the cis-5/cis-3 ratio improves from 1.4 for the wild-type enzyme to 9.0 for the mutant, the increase in activity is decreased compared to mutant V97F
W40M
acceptance of the native substrate L-proline is almost completely abolished. 8.3fold increase in turnover number for L-homophenylalanine as compared to wild-type enzyme. Mutation reprograms the natural hydroxylase to predominantly act as a desaturase, giving almost exclusively 3,4-desaturated L-homophenylalanine, through capability of tyrosine to serve as a catalytic entity in the reaction mechanism
W40M/I103L
acceptance of the native substrate L-proline is almost completely abolished. 112fold increase in turnover number for L-homophenylalanine and and about 300fold improved kcat/Km compared to the wild-type enzyme
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant Strep-tagged wild-type enzyme from Escherichia coli strain W3110 extract by ultracentrifugation, affinity and anion exchange chrmatography, and gel filtration
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
recombinant expression of Strep-tagged wild-type enzyme in Escherichia coli strain W3110
recombinant expression of wild-type and mutant enzymes in Escherichia coli strain W3110
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
synthesis
-
coexpression of L-proline cis-4-hydroxylase and N-acetyltransferase Mpr1 from Saccharomyces cerevisiae converting cis-4-hydroxy-L-proline into N-acetyl cis-4-hydroxy-L-proline in Escherichia coli. M9 medium containing L-proline produces more N-acetyl cis-4-hydroxy-L-proline than LB medium containing L-proline. The addition of NaCl and L-ascorbate results in a 2fold increase in N-acetyl cis-4-hydroxy-L-proline production in the L-proline-containing M9 medium
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Hara, R.; Kino, K.
Characterization of novel 2-oxoglutarate dependent dioxygenases converting L-proline to cis-4-hydroxy-L-proline
Biochem. Biophys. Res. Commun.
379
882-886
2009
Mesorhizobium loti (Q989T9), Mesorhizobium loti, Mesorhizobium loti MAFF303099 (Q989T9), Sinorhizobium meliloti (Q92LF6), Sinorhizobium meliloti
brenda
Bach, T.M.; Hara, R.; Kino, K.; Ohtsu, I.; Yoshida, N.; Takagi, H.
Microbial production of N-acetyl cis-4-hydroxy-L-proline by coexpression of the Rhizobium L-proline cis-4-hydroxylase and the yeast N-acetyltransferase Mpr1
Appl. Microbiol. Biotechnol.
97
247-257
2013
Sinorhizobium meliloti
brenda
Koketsu, K.; Shomura, Y.; Moriwaki, K.; Hayashi, M.; Mitsuhashi, S.; Hara, R.; Kino, K.; Higuchi, Y.
Refined regio- and stereoselective hydroxylation of L-pipecolic acid by protein engineering of L-proline cis-4-hydroxylase based on the X-ray crystal structure
ACS Synth. Biol.
4
383-392
2015
Mesorhizobium loti (Q92LF6), Mesorhizobium loti (Q989T9), Mesorhizobium loti, Mesorhizobium loti 1021 (Q92LF6), Mesorhizobium loti MAFF303099 (Q989T9)
brenda
Koketsu, K.; Shomura, Y.; Moriwaki, K.; Hayashi, M.; Mitsuhashi, S.; Hara, R.; Kino, K.; Higuchi, Y.
Refined regio- and stereoselective hydroxylation of L-pipecolic acid by protein engineering of L-proline cis-4-hydroxylase based on the X-ray crystal structure
ACS Synth. Biol.
4
383-392
2015
Mesorhizobium loti (Q989T9), Mesorhizobium loti, Sinorhizobium meliloti (Q92LF6), Sinorhizobium meliloti
brenda
Meyer, F.; Frey, R.; Ligibel, M.; Sager, E.; Schroer, K.; Snajdrova, R.; Buller, R.
Modulating chemoselectivity in a Fe(II)/alpha-ketoglutarate-dependent dioxygenase for the oxidative modification of a nonproteinogenic amino acid
ACS Catal.
11
6261-6269
2021
Sinorhizobium meliloti (Q92LF6)
-
brenda
Papadopoulou, A.; Meierhofer, J.; Meyer, F.; Hayashi, T.; Schneider, S.; Sager, E.; Buller, R.
Re-programming and optimization of a L-proline cis-4-hydroxylase for the cis-3-halogenation of its native substrate
ChemCatChem
13
3914-3919
2021
Sinorhizobium meliloti (Q92LF6)
-
brenda
EXTERNAL LINKS (specific for EC-Number 1.14.11.56)
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