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Information on EC 2.1.1.127 - [ribulose-bisphosphate carboxylase]-lysine N-methyltransferase and Organism(s) Pisum sativum and UniProt Accession Q43088
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2.1.1.127 [ribulose-bisphosphate carboxylase]-lysine N-methyltransferaseIUBMB Comments
The enzyme catalyses three successive methylations of Lys-14 in the large subunits of hexadecameric higher plant ribulose-bisphosphate-carboxylase (EC 4.1.1.39). Only the three methylated form is observed . The enzyme from pea (Pisum sativum) also three-methylates a specific lysine in the chloroplastic isoforms of fructose-bisphosphate aldolase (EC 4.1.2.13) .
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Word Map
- 2.1.1.127
- histone
- methyltransferases
-
pkmts
- adomet
-
monomethylation
-
non-histone
-
adohcy
-
tri-methylation
-
lysine-14
-
trithorax
-
suv39h2
The taxonomic range for the selected organisms is: Pisum sativum
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
3
+
=
3
+
3
+
=
3
+
Synonyms
protein lysine methyltransferase, rubisco lsmt, rubisco large subunit methyltransferase, rbcmt, protein-lysine methyltransferase, rlsmt, rubisco ls methyltransferase, rubisco large-subunit dimethyltransferase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
Methyltransferase, ribulose diphosphate carboxylase large subunit(lysine)
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-
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rbcMT
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-
-
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Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit Nepsilon-methyltransferase
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Ribulose bisphosphate carboxylase large subunit methyltransferase
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Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit epsilonN-methyltransferase
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Ribulose-bisphosphate-carboxylase/oxygenase N-methyltransferase
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Rubisco large subunit epsilonN-methyltransferase
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Rubisco LSMT
Rubisco methyltransferase
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-
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[Ribulose-bisphosphate-carboxylase]-lysine N-methyltransferase
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-
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additional information
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Rubisco LSMT is a SET domain protein methyltransferase
Rubisco LSMT
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-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
3 S-adenosyl-L-methionine + [ribulose-1,5-bisphosphate carboxylase]-L-lysine = 3 S-adenosyl-L-homocysteine + [ribulose-1,5-bisphosphate carboxylase]-N6,N6,N6-trimethyl-L-lysine
S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine
3 S-adenosyl-L-methionine + [ribulose-1,5-bisphosphate carboxylase]-L-lysine = 3 S-adenosyl-L-homocysteine + [ribulose-1,5-bisphosphate carboxylase]-N6,N6,N6-trimethyl-L-lysine
catalytic reaction mechanism and specificity, molecular dynamics and hybrid quantum mechanics/molecular mechanics, overview
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3 S-adenosyl-L-methionine + [ribulose-1,5-bisphosphate carboxylase]-L-lysine = 3 S-adenosyl-L-homocysteine + [ribulose-1,5-bisphosphate carboxylase]-N6,N6,N6-trimethyl-L-lysine
substrate binding, leucine-rich motifscontribute to the contact surface with Rubisco, overview
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S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine
catalytic mechanism
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S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine
substrate and inhibitor binding site
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S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine
amino acid sequence comparison
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S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine
enzyme is encoded on genes containing the SET-domain sequence, substrate specificity is connected to SET sequence
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S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine
SET structure
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
methyl group transfer
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-
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SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:[3-phospho-D-glycerate-carboxy-lyase (dimerizing)]-lysine N6-methyltransferase
The enzyme catalyses three successive methylations of Lys-14 in the large subunits of hexadecameric higher plant ribulose-bisphosphate-carboxylase (EC 4.1.1.39). Only the three methylated form is observed [3]. The enzyme from pea (Pisum sativum) also three-methylates a specific lysine in the chloroplastic isoforms of fructose-bisphosphate aldolase (EC 4.1.2.13) [5].
CAS REGISTRY NUMBER
COMMENTARY
139171-98-5
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
3 S-adenosyl-L-methionine + [chloroplastic fructose 1,6-bisphosphate aldolase]-L-lysine
3 S-adenosyl-L-homocysteine + [chloroplastic fructose 1,6-bisphosphate aldolase]-N6,N6,N6-trimethyl-L-lysine
reaction of EC 2.1.1.259
-
-
?
3 S-adenosyl-L-methionine + [ribulose-1,5-bisphosphate-carboxylase]-lysine
S-adenosyl-L-homocysteine + [ribulose-1,5-bisphosphate-carboxylase]-N6,N6,N6-trimethyl-L-lysine
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-
-
?
S-adenosyl-L-methionine + L-Lys
S-adenosyl-L-homocysteine + methyl-L-Lys
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-
-
?
S-adenosyl-L-methionine + methyl-L-Lys
S-adenosyl-L-homocysteine + dimethyl-L-Lys + trimethyl-L-Lys
about 2fold higher activity than with Lys
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-
?
S-adenosyl-L-methionine + [ribulose-1,5-bisphosphate-carboxylase]-lysine
S-adenosyl-L-homocysteine + [ribulose-1,5-bisphosphate-carboxylase]-N6-methyl-L-lysine
-
-
-
?
S-adenosyl-L-homocysteine + [gamma-tocopherol methyltransferase]-L-lysine
S-adenosyl-L-homocysteine [gamma-tocopherol methyltransferase]-N6-methyl-L-lysine
-
-
-
-
?
S-adenosyl-L-methionine + histone L-lysine
S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine
S-adenosyl-L-methionine + [chloroplastic fructose 1,6-bisphosphate aldolase isoform 2]-L-lysine
S-adenosyl-L-homocysteine + [chloroplastic fructose 1,6-bisphosphate aldolase isoform 2]-N6-methyl-L-lysine
-
-
-
-
?
S-adenosyl-L-methionine + [chloroplastic fructose 1,6-bisphosphate aldolase isoform 3]-L-lysine
S-adenosyl-L-homocysteine + [chloroplastic fructose 1,6-bisphosphate aldolase isoform 3]-N6-methyl-L-lysine
-
-
-
-
?
S-adenosyl-L-methionine + [fructose-1,6-bisphosphate aldolase]-lysine
S-adenosyl-L-homocysteine + [fructose-1,6-bisphosphate aldolase]-N6-methyl-L-lysine
-
-
-
-
?
S-adenosyl-L-methionine + [gamma-tocopherol methyltransferase]-lysine
S-adenosyl-L-homocysteine + [gamma-tocopherol methyltransferase]-N6-methyl-L-lysine
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methylation is required for gamma-tocopherol methyltransferase activity
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-
?
S-adenosyl-L-methionine + [large subunit of Rubisco]-L-lysine
S-adenosyl-L-homocysteine + [large subunit of Rubisco]-N6-methyl-L-lysine
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methylation occurs at Lys-394
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-
?
S-adenosyl-L-methionine + [ribulose-1,5-bisphosphate carboxylase]-lysine
S-adenosyl-L-homocysteine + [ribulose-1,5-bisphosphate carboxylase]-N6-methyl-L-lysine
S-adenosyl-L-methionine + [ribulose-1,5-bisphosphate-carboxylase]-L-lysine
S-adenosyl-L-homocysteine + [ribulose-1,5-bisphosphate-carboxylase]-N6-methyl-L-lysine
S-adenosyl-L-methionine + histone L-lysine
S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine
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-
-
?
S-adenosyl-L-methionine + histone L-lysine
S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine
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-
-
?
S-adenosyl-L-methionine + [ribulose-1,5-bisphosphate carboxylase]-lysine
S-adenosyl-L-homocysteine + [ribulose-1,5-bisphosphate carboxylase]-N6-methyl-L-lysine
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LSMT transfers one or two methyl groups to a single lysine
-
-
?
S-adenosyl-L-methionine + [ribulose-1,5-bisphosphate carboxylase]-lysine
S-adenosyl-L-homocysteine + [ribulose-1,5-bisphosphate carboxylase]-N6-methyl-L-lysine
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LSMT transfers two methyl groups to a single lysine
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-
?
S-adenosyl-L-methionine + [ribulose-1,5-bisphosphate carboxylase]-lysine
S-adenosyl-L-homocysteine + [ribulose-1,5-bisphosphate carboxylase]-N6-methyl-L-lysine
-
Rubisco LSMT utilizes a processive reaction mechanism to catalyse exclusively trimethylation of Lys14 without disassociation from Rubisco
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-
?
S-adenosyl-L-methionine + [ribulose-1,5-bisphosphate carboxylase]-lysine
S-adenosyl-L-homocysteine + [ribulose-1,5-bisphosphate carboxylase]-N6-methyl-L-lysine
-
methylation of lysine 14 of the large subunit
-
-
?
S-adenosyl-L-methionine + [ribulose-1,5-bisphosphate carboxylase]-lysine
S-adenosyl-L-homocysteine + [ribulose-1,5-bisphosphate carboxylase]-N6-methyl-L-lysine
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Rubisco from spinach or tobacco leaves. LSMT transfers one or two methyl groups to a single lysine
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-
?
S-adenosyl-L-methionine + [ribulose-1,5-bisphosphate-carboxylase]-L-lysine
S-adenosyl-L-homocysteine + [ribulose-1,5-bisphosphate-carboxylase]-N6-methyl-L-lysine
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-
-
-
?
S-adenosyl-L-methionine + [ribulose-1,5-bisphosphate-carboxylase]-L-lysine
S-adenosyl-L-homocysteine + [ribulose-1,5-bisphosphate-carboxylase]-N6-methyl-L-lysine
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catalyzes methylation of the epsilon-amino group of Lys-14 in the large subunit of ribulose-bisphosphate-carboxylase from Spinacia oleracea
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?
additional information
?
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histone methylation has significant effects on heterochromatin formation and transcriptional regulation
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?
additional information
?
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LSMT has both mono-and di-methylation activities. Determination of free energy reaction profiles and transition state geometries using the crystal structure and on-the-fly ab initio QM/MM MD simulations in two simulation systems: LSMTAdoMet-Lys and LSMT-AdoMet-MeLys, which are enzyme-substrate complexes for mono- and di-methylation reactions in LSMT, method, overview. Methylation state specificity, overview
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?
additional information
?
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several chloroplast-localized proteins are potential protein substrates for Rubisco LSMT
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-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-homocysteine + [gamma-tocopherol methyltransferase]-L-lysine
S-adenosyl-L-homocysteine [gamma-tocopherol methyltransferase]-N6-methyl-L-lysine
-
-
-
-
?
S-adenosyl-L-methionine + histone L-lysine
S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine
S-adenosyl-L-methionine + [chloroplastic fructose 1,6-bisphosphate aldolase isoform 2]-L-lysine
S-adenosyl-L-homocysteine + [chloroplastic fructose 1,6-bisphosphate aldolase isoform 2]-N6-methyl-L-lysine
-
-
-
-
?
S-adenosyl-L-methionine + [chloroplastic fructose 1,6-bisphosphate aldolase isoform 3]-L-lysine
S-adenosyl-L-homocysteine + [chloroplastic fructose 1,6-bisphosphate aldolase isoform 3]-N6-methyl-L-lysine
-
-
-
-
?
S-adenosyl-L-methionine + [fructose-1,6-bisphosphate aldolase]-lysine
S-adenosyl-L-homocysteine + [fructose-1,6-bisphosphate aldolase]-N6-methyl-L-lysine
-
-
-
-
?
S-adenosyl-L-methionine + [large subunit of Rubisco]-L-lysine
S-adenosyl-L-homocysteine + [large subunit of Rubisco]-N6-methyl-L-lysine
-
methylation occurs at Lys-394
-
-
?
S-adenosyl-L-methionine + [ribulose-1,5-bisphosphate carboxylase]-lysine
S-adenosyl-L-homocysteine + [ribulose-1,5-bisphosphate carboxylase]-N6-methyl-L-lysine
additional information
?
-
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histone methylation has significant effects on heterochromatin formation and transcriptional regulation
-
-
?
S-adenosyl-L-methionine + histone L-lysine
S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine
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-
-
?
S-adenosyl-L-methionine + histone L-lysine
S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine
-
-
-
?
S-adenosyl-L-methionine + [ribulose-1,5-bisphosphate carboxylase]-lysine
S-adenosyl-L-homocysteine + [ribulose-1,5-bisphosphate carboxylase]-N6-methyl-L-lysine
-
LSMT transfers one or two methyl groups to a single lysine
-
-
?
S-adenosyl-L-methionine + [ribulose-1,5-bisphosphate carboxylase]-lysine
S-adenosyl-L-homocysteine + [ribulose-1,5-bisphosphate carboxylase]-N6-methyl-L-lysine
-
LSMT transfers two methyl groups to a single lysine
-
-
?
S-adenosyl-L-methionine + [ribulose-1,5-bisphosphate carboxylase]-lysine
S-adenosyl-L-homocysteine + [ribulose-1,5-bisphosphate carboxylase]-N6-methyl-L-lysine
-
Rubisco LSMT utilizes a processive reaction mechanism to catalyse exclusively trimethylation of Lys14 without disassociation from Rubisco
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0129
[chloroplastic fructose 1,6-bisphosphate aldolase isoform 2]-L-lysine
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at pH 7.8 and 30°C
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0.014
[chloroplastic fructose 1,6-bisphosphate aldolase isoform 3]-L-lysine
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at pH 7.8 and 30°C
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1.32
[chloroplastic fructose 1,6-bisphosphate aldolase isoform 2]-L-lysine
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at pH 7.8 and 30°C
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0.57
[chloroplastic fructose 1,6-bisphosphate aldolase isoform 3]-L-lysine
-
at pH 7.8 and 30°C
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1.05
[chloroplastic fructose 1,6-bisphosphate aldolase isoform 3]-L-lysine
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at pH 7.8 and 30°C
-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
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). RBCMT_PEA
489
0
55110
Swiss-Prot
Chloroplast (Reliability: 2)
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
the full-length enzyme is processed by removing the N-terminal 36 amino acids when expressed in E. coli cells
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging drop vapour diffusion method, the crystal structure of the large subunit of the enzyme in ternary complex with either Lys or epsilon-N-methyllysine and the product S-adenosylhomocysteine are determined to resolution of 2.65 and 2.55 A, respectively
complexed with S-adenosyl-L-homocysteine, hanging drop method, 25°C, reservoir solution contains HEPES 100 mM, pH 6.8, sodium acetate 1.2-1.35 M, structure analysis
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Y305F
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the SET7/9 Y305F mutant not only has a high efficiency for mono-methylation but also becomes a dimethylase. The Y305F mutation leads to a less tight active site
additional information
additional information
construction of chimera between Pisum sativum and Arabidopsis thaliana enzymes to localize regions of the enzymes responsible for the observed difference in substrate specificity. Contrary to the Pisum sativum enzyme, Arabidopsis thaliana LSMT is not able to trimethylate Rubisco
additional information
-
mapping of the polypeptide specificity determinants for Rubisco LSMT by site-directed mutagenesis of the sequence and residues flanking the Lys14 methylation site
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
nickel-Sepharose column chromatography, Sephadex G-25 gel filtration, and Q-Sepharose column chromatography
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
enzyme expression in enzyme-deficient Nicotiana tabacum plants, recombinant substrate identification
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Wang, P.; Royer, M.; Houtz, R.L.
Affinity purification of ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit epsilonN-methyltransferase
Protein Expr. Purif.
6
528-536
1995
Pisum sativum
Zheng, Q.; Simel, E.J.; Klein, P.E.; Royer, M.T.; Houtz, R.L.
Expression, purification, and characterization of recombinant ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit Nepsilon-methyltransferase
Protein Expr. Purif.
14
104-112
1998
Pisum sativum
Trievel, R.C.; Beach, B.M.; Dirk, L.M.A.; Houtz, R.L.; Hurley, J.H.
Structure and catalytic mechanism of a SET domain protein methyltransferase
Cell
111
91-103
2002
Pisum sativum
Yeates, T.O.
Structures of SET domain proteins: protein lysine methyltransferases make their mark
Cell
111
5-7
2002
Pisum sativum
Trievel, R.C.; Flynn, E.M.; Houtz, R.L.; Hurley, J.H.
Mechanism of multiple lysine methylation by the SET domain enzyme Rubisco LSMT
Nat. Struct. Biol.
10
545-552
2003
Pisum sativum (Q43088), Pisum sativum
Hu, P.; Wang, S.; Zhang, Y.
How do SET-domain protein lysine methyltransferases achieve the methylation state specificity? Revisited by ab initio QM/MM molecular dynamics simulations
J. Am. Chem. Soc.
130
3806-3813
2008
Pisum sativum
Houtz, R.; Magnani, R.; Nayak, N.; Dirk, L.
Co- and post-translational modifications in Rubisco: unanswered questions
J. Exp. Bot.
59
1635-1645
2008
Arabidopsis thaliana, Nicotiana tabacum, Pisum sativum, Spinacia oleracea
Zhang, X.; Bruice, T.C.
Enzymatic mechanism and product specificity of SET-domain protein lysine methyltransferases
Proc. Natl. Acad. Sci. USA
105
5728-5732
2008
Pisum sativum
Raunser, S.; Magnani, R.; Huang, Z.; Houtz, R.L.; Trievel, R.C.; Penczek, P.A.; Walz, T.
Rubisco in complex with Rubisco large subunit methyltransferase
Proc. Natl. Acad. Sci. USA
106
3160-3165
2009
Pisum sativum
Mininno, M.; Brugiere, S.; Pautre, V.; Gilgen, A.; Ma, S.; Ferro, M.; Tardif, M.; Alban, C.; Ravanel, S.
Characterization of chloroplastic fructose 1,6-bisphosphate aldolases as lysine-methylated proteins in plants
J. Biol. Chem.
287
21034-21044
2012
Arabidopsis thaliana, Pisum sativum
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