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Information on EC 2.1.1.310 - 25S rRNA (cytosine2870-C5)-methyltransferase
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2.1.1.310 25S rRNA (cytosine2870-C5)-methyltransferaseIUBMB Comments
The enzyme, found in eukaryotes, is specific for cytosine2870 of the 25S ribosomal RNA. The numbering corresponds to the enzyme from the yeast Saccharomyces cerevisiae .
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The enzyme appears in viruses and cellular organisms
Reaction Schemes
+
=
+
+
cytosine2870 in 25S rRNA
=
+
5-methylcytosine2870 in 25S rRNA
Synonyms
protein p120, proliferation-associated nucleolar antigen, m5c-methyltransferase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
m5C-methyltransferase
NOP2
RNA:m5C-MTase
NOP2
-
-
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
S-adenosyl-L-methionine + cytosine2870 in 25S rRNA = S-adenosyl-L-homocysteine + 5-methylcytosine2870 in 25S rRNA
S-adenosyl-L-methionine + cytosine2870 in 25S rRNA = S-adenosyl-L-homocysteine + 5-methylcytosine2870 in 25S rRNA
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-
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S-adenosyl-L-methionine + cytosine2870 in 25S rRNA = S-adenosyl-L-homocysteine + 5-methylcytosine2870 in 25S rRNA
one of the catalytic cysteines in the m5C-MTase active site is required for initial attack to target cytosine, while the second serves for recycling function during the product release
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S-adenosyl-L-methionine + cytosine2870 in 25S rRNA = S-adenosyl-L-homocysteine + 5-methylcytosine2870 in 25S rRNA
one of the catalytic cysteines in the m5C-MTase active site is required for initial attack to target cytosine, while the second serves for recycling function during the product release
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SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:25S rRNA (cytosine2870-C5)-methyltransferase
The enzyme, found in eukaryotes, is specific for cytosine2870 of the 25S ribosomal RNA. The numbering corresponds to the enzyme from the yeast Saccharomyces cerevisiae [1].
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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
S-adenosyl-L-methionine + cytosine2870 in 25S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine2870 in 25S rRNA
S-adenosyl-L-methionine + cytosine2870 in 25S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine2870 in 25S rRNA
-
-
-
-
?
S-adenosyl-L-methionine + cytosine2870 in 25S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine2870 in 25S rRNA
-
-
-
-
?
S-adenosyl-L-methionine + cytosine2870 in 25S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine2870 in 25S rRNA
the enzyme is responsible for the methylation at cytosine2870 of the 25S ribosomal RNA
-
-
?
S-adenosyl-L-methionine + cytosine2870 in 25S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine2870 in 25S rRNA
the enzyme is specific for cytosine2870 of the 25S ribosomal RNA
-
-
?
S-adenosyl-L-methionine + cytosine2870 in 25S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine2870 in 25S rRNA
-
yeast proteins Nop2p and Rcm1p catalyze the formation of m5C in domains V and IV, respectively
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-
?
S-adenosyl-L-methionine + cytosine2870 in 25S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine2870 in 25S rRNA
the enzyme is responsible for the methylation at cytosine2870 of the 25S ribosomal RNA
-
-
?
S-adenosyl-L-methionine + cytosine2870 in 25S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine2870 in 25S rRNA
the enzyme is specific for cytosine2870 of the 25S ribosomal RNA
-
-
?
S-adenosyl-L-methionine + cytosine2870 in 25S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine2870 in 25S rRNA
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-
-
-
?
S-adenosyl-L-methionine + cytosine2870 in 25S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine2870 in 25S rRNA
-
yeast proteins Nop2p and Rcm1p catalyze the formation of m5C in domains V and IV, respectively
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-
?
additional information
?
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-
protein p120 displays an RNA:m5C-MTase activity, which restores m5C formation at position 2870 in domain V of 25S rRNA in a nop2DELTA yeast strain, functional complementation of Nop2-deficient yeasts by human protein p120
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-
?
additional information
?
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-
no evidence of m5C residues in yeast 18S rRNA
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-
?
additional information
?
-
-
no evidence of m5C residues in yeast 18S rRNA
-
-
?
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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-methionine + cytosine2870 in 25S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine2870 in 25S rRNA
S-adenosyl-L-methionine + cytosine2870 in 25S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine2870 in 25S rRNA
-
-
-
-
?
S-adenosyl-L-methionine + cytosine2870 in 25S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine2870 in 25S rRNA
the enzyme is responsible for the methylation at cytosine2870 of the 25S ribosomal RNA
-
-
?
S-adenosyl-L-methionine + cytosine2870 in 25S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine2870 in 25S rRNA
-
yeast proteins Nop2p and Rcm1p catalyze the formation of m5C in domains V and IV, respectively
-
-
?
S-adenosyl-L-methionine + cytosine2870 in 25S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine2870 in 25S rRNA
the enzyme is responsible for the methylation at cytosine2870 of the 25S ribosomal RNA
-
-
?
S-adenosyl-L-methionine + cytosine2870 in 25S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine2870 in 25S rRNA
-
yeast proteins Nop2p and Rcm1p catalyze the formation of m5C in domains V and IV, respectively
-
-
?
additional information
?
-
-
protein p120 displays an RNA:m5C-MTase activity, which restores m5C formation at position 2870 in domain V of 25S rRNA in a nop2DELTA yeast strain, functional complementation of Nop2-deficient yeasts by human protein p120
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-
?
additional information
?
-
-
no evidence of m5C residues in yeast 18S rRNA
-
-
?
additional information
?
-
-
no evidence of m5C residues in yeast 18S rRNA
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Acquired Immunodeficiency Syndrome
p120 Catenin is required for normal tubulogenesis but not epithelial integrity in developing mouse pancreas.
Adenocarcinoma
The prognostic significance of proliferation-associated nucleolar protein p120 expression in prostate adenocarcinoma: a comparison with cyclins A and B1, Ki-67, proliferating cell nuclear antigen, and p34cdc2.
Adenocarcinoma of Lung
Expression of nucleolar protein p120 predicts poor prognosis in patients with stage I lung adenocarcinoma.
Adenocarcinoma of Lung
Prognostic value of nucleolar protein p120 in patients with resected lung adenocarcinoma.
Atherosclerosis
p120 inhibits LPS/TNF?-induced endothelial Ang2 synthesis and release in an NF-?B independent fashion.
Breast Neoplasms
Proliferation-associated nucleolar antigen P120: a prognostic marker in node-negative breast cancer.
Carcinoma
p120 and AgNOR nucleolar protein expression: a comparison with nuclear proliferation markers in oral pathology.
Carcinoma, Squamous Cell
p120 and AgNOR nucleolar protein expression: a comparison with nuclear proliferation markers in oral pathology.
Colorectal Neoplasms
Significance of the expression of proliferation-associated nucleolar antigen p120 in human colorectal tumors.
Hemorrhagic Stroke
p120 inhibits LPS/TNF?-induced endothelial Ang2 synthesis and release in an NF-?B independent fashion.
Leukemia
Localization of the Abelson murine leukemia virus protein in a detergent-insoluble subcellular matrix: architecture of the protein.
Lung Neoplasms
Expression of nucleolar protein p120 in human lung cancer: difference in histological types as a marker for proliferation.
Neoplasms
A conserved motif in the yeast nucleolar protein Nop2p contains an essential cysteine residue.
Neoplasms
Analysis of a 17.4 kb DNA segment of yeast chromosome II encompassing the ribosomal protein L19 as well as proteins with homologies to components of the hnRNP and snRNP complexes and to the human proliferation-associated p120 antigen.
Neoplasms
Combinatorial effects of monoclonal anti-p120 antibody (MAbp120), liposomes and hyperthermia on MCF-7 and LOX tumor cell lines.
Neoplasms
Eukaryotic rRNA Modification by Yeast 5-Methylcytosine-Methyltransferases and Human Proliferation-Associated Antigen p120.
Neoplasms
Like p53, the proliferation-associated protein p120 accumulates in human cancer cells following exposure to anticancer drugs.
Neoplasms
Nucleolar and nuclear aberrations in human lox tumor cells following treatment with p120 antisense oligonucleotide ISIS-3466.
Neoplasms
Phosphorylation of the human cell proliferation-associated nucleolar protein p120.
Neoplasms
Prognostic value of nucleolar protein p120 in patients with resected lung adenocarcinoma.
Neoplasms
Relationship between quantitative expression of protein p120 and proliferative activity in cancer cells.
Neoplasms
Significance of the expression of proliferation-associated nucleolar antigen p120 in human colorectal tumors.
Neoplasms
The 58-kDa microspherule protein (MSP58), a nucleolar protein, interacts with nucleolar protein p120.
Neoplasms
Up-regulation, nuclear import, and tumor growth stimulation of the adhesion protein p120 in pancreatic cancer.
Pancreatic Neoplasms
Up-regulation, nuclear import, and tumor growth stimulation of the adhesion protein p120 in pancreatic cancer.
Sarcoma, Avian
Evidence that there exist four classes of RNA tumor viruses which encode proteins with associated tyrosine protein kinase activities.
Sepsis
p120 inhibits LPS/TNF?-induced endothelial Ang2 synthesis and release in an NF-?B independent fashion.
Vascular Malformations
p120 inhibits LPS/TNF?-induced endothelial Ang2 synthesis and release in an NF-?B independent fashion.
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
additional information
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whereas protein p120 is almost undetectable in normal tissues, it is overexpressed in virtually all types of cancer cells. The enzyme concentration varies during the cell cycle, reaching its maximum value in the G2 phase
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-
the N-terminal domain of the enzyme is important for its nucleolar localization
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the N-terminal domain of the enzyme is important for its nucleolar localization
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
metabolism
physiological function
additional information
evolution
-
the enzyme is a member of a protein family called Nop2/NSUN/NOL1. Nop2 belongs to the large family of pre-ribosomal proteins
evolution
-
the enzyme is a member of a protein family called Nop2/NSUN/NOL1. The human genome contains at least 9 genes encoding putative RNA:m5C-MTases which share sequence similarities with yeast Nop2/Trm4/Rcm1
evolution
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the enzyme is a member of a protein family called Nop2/NSUN/NOL1. Nop2 belongs to the large family of pre-ribosomal proteins
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malfunction
the loss of m5C2870 affects ribosome synthesis and processing
malfunction
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strains expressing Nop2DELTA(1-220) are viable, but exhibit a significant growth defect
malfunction
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strains expressing Nop2DELTA(1-220) are viable, but exhibit a significant growth defect
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malfunction
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the loss of m5C2870 affects ribosome synthesis and processing
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metabolism
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Nop2 and Rcm1 catalyze m5C formation in large subunit yeast rRNA, Nop2 forms 25S rRNA m5C2870, while Rcm1 forms 25S rRNA m5C2278
metabolism
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Nop2 and Rcm1 catalyze m5C formation in large subunit yeast rRNA, Nop2 forms 25S rRNA m5C2870, while Rcm1 forms 25S rRNA m5C2278
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physiological function
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nucleolar protein Nop2 is required for production of 25S rRNA and, consequently, during the biogenesis of 60S ribosomal subunits. Nop2 forms 25S rRNA m5C2870. the enzyme possesses two related functions in pre-rRNA processing: as an essential factor for cleavages and m5C:RNA:modification. The presence of Nop2, rather than the m5C modification in rRNA itself, is required for pre-rRNA processing
physiological function
-
p120 forms 28S rRNA m5C4447. It is required for the G1/S transition
physiological function
-
nucleolar protein Nop2 is required for production of 25S rRNA and, consequently, during the biogenesis of 60S ribosomal subunits. Nop2 forms 25S rRNA m5C2870. the enzyme possesses two related functions in pre-rRNA processing: as an essential factor for cleavages and m5C:RNA:modification. The presence of Nop2, rather than the m5C modification in rRNA itself, is required for pre-rRNA processing
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additional information
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importance of different sequence and structural domains of Nop2 and p120 for yeast growth and m5C-MTase activity, importance of Nop2 N-terminal domain for correct protein localization and its cellular function, overview
additional information
-
importance of different sequence and structural domains of Nop2 and p120 for yeast growth and m5C-MTase activity, importance of Nop2 N-terminal domain for correct protein localization and its cellular function, overview
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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). NOP2_YEAST
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
618
0
69812
Swiss-Prot
other Location (Reliability: 3)
A0A1Z5JEL5_FISSO
623
0
69974
TrEMBL
other Location (Reliability: 2)
A0A7R8CME0_LEPSM
151
0
17018
TrEMBL
other Location (Reliability: 1)
A0A8J5CMI0_9ASCO
611
0
68662
TrEMBL
other Location (Reliability: 3)
A0A1Z5K501_FISSO
621
0
69817
TrEMBL
other Location (Reliability: 2)
A0A6J8DEI2_MYTCO
1139
0
129423
TrEMBL
other Location (Reliability: 4)
A0A8J8WIV3_9EURO
743
0
81606
TrEMBL
other Location (Reliability: 3)
A0A6J8DHF1_MYTCO
258
0
29582
TrEMBL
other Location (Reliability: 1)
A0A812CSR8_SEPPH
664
0
75563
TrEMBL
other Location (Reliability: 2)
A0A8J5BBV5_9ASCO
605
0
68065
TrEMBL
other Location (Reliability: 3)
A0A7R8CMD1_LEPSM
370
0
41508
TrEMBL
other Location (Reliability: 2)
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
-
enzyme protein domain structure, overview
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C478A
additional information
C478A
the polysome profile from the mutant reveals defect in 60S biogenesis and significant reduction in polysome fractions compared with isogenic wild type
C478A
-
the polysome profile from the mutant reveals defect in 60S biogenesis and significant reduction in polysome fractions compared with isogenic wild type
-
additional information
-
generation of GFP-tagged chimeric protein formed by yeast Nop2 and p120 fragments. The HYB protein, which is composed of N-terminal Nop2 and C-terminal p120 domains, efficiently localizes within the nucleolus, demonstrating that all necessary cell sorting signals are indeed located in the Nop2 N-terminal domain
additional information
-
functional complementation of Nop2-deficient yeasts by human protein p120, the N-terminal domain of Nop2 is essential for efficient complementation by p120 in yeast. Generation of GFP-tagged chimeric protein formed by Nop2 and human p120 fragments. The HYB protein, which is composed of N-terminal Nop2 and C-terminal p120 domains, efficiently localizes within the nucleolus, demonstrating that all necessary cell sorting signals are indeed located in the Nop2 N-terminal domain. The yeast strain expressing N-terminal domain-truncated Nop2 is not viable, indicating that localization of Nop2 is important for its function. A double mutant of Nop2 protein with two mutated cysteines that are expected to be involved in catalysis, namely Cys424 and Cys478, shows no phenotype
additional information
-
functional complementation of Nop2-deficient yeasts by human protein p120, the N-terminal domain of Nop2 is essential for efficient complementation by p120 in yeast. Generation of GFP-tagged chimeric protein formed by Nop2 and human p120 fragments. The HYB protein, which is composed of N-terminal Nop2 and C-terminal p120 domains, efficiently localizes within the nucleolus, demonstrating that all necessary cell sorting signals are indeed located in the Nop2 N-terminal domain. The yeast strain expressing N-terminal domain-truncated Nop2 is not viable, indicating that localization of Nop2 is important for its function. A double mutant of Nop2 protein with two mutated cysteines that are expected to be involved in catalysis, namely Cys424 and Cys478, shows no phenotype
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged full-length Nop2 and Nop2(1-220) N-terminal domain from Escherichia coli strain BL21(DE3) CodonPlus by polyethyleneimine precipitation, anion exchange and nickel affinity chromatography, followed by dialysis
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
cloning from genomic DNA, expression in a Saccharomyces cerevisiae Nop2 enzyme mutant and partial complementation. Full-length human p120 when expressed in Saccharomyces cerevisiae strongly accumulates in the nucleolus
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cloning from genomic DNA, recombinant expression of His-tagged full-length Nop2 and Nop2(1-220) N-terminal domain in Escherichia coli strain BL21(DE3) CodonPlus
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
diagnostics
-
whereas protein p120 is almost undetectable in normal tissues, it is overexpressed in virtually all types of cancer cells and is therefore considered to be a predictive cancer marker
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Sharma, S.; Yang, J.; Watzinger, P.; Koetter, P.; Entian, K.D.
Yeast Nop2 and Rcm1 methylate C2870 and C2278 of the 25S rRNA, respectively
Nucleic Acids Res.
41
9062-9076
2013
Saccharomyces cerevisiae (P40991), Saccharomyces cerevisiae ATCC 204508 (P40991)
brenda
Bourgeois, G.; Ney, M.; Gaspar, I.; Aigueperse, C.; Schaefer, M.; Kellner, S.; Helm, M.; Motorin, Y.
Eukaryotic rRNA modification by yeast 5-methylcytosine-methyltransferases and human proliferation-associated antigen p120
PLoS ONE
10
e0133321
2015
Homo sapiens, Saccharomyces cerevisiae, Saccharomyces cerevisiae BY4742
brenda
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