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Information on EC 2.1.1.244 - protein N-terminal methyltransferase and Organism(s) Homo sapiens and UniProt Accession Q9BV86
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2.1.1.244 protein N-terminal methyltransferaseIUBMB Comments
This enzyme methylates the N-terminus of target proteins containing the N-terminal motif [Ala/Pro/Ser]-Pro-Lys after the initiator L-methionine is cleaved. When the terminal amino acid is L-proline, the enzyme catalyses two successive methylations of its alpha-amino group. When the first amino acid is either L-alanine or L-serine, the enzyme catalyses three successive methylations.
The Pro-Lys in positions 2-3 cannot be exchanged for other amino acids [1,2].
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Word Map
- 2.1.1.244
- methyltransferases
-
rna-dependent
- mtase
-
trimethylation
- dengue
- flavivirus
-
bisubstrate
-
methyltransferase-like
- drug development
- pharmacology
The taxonomic range for the selected organisms is: Homo sapiens
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria
Reaction Schemes
hide(Overall reactions are displayed. Show all >>)
3
+
=
3
+
3
+
N-terminal-(A,S)PK-[protein]
=
3
+
N-terminal-N,N,N-trimethyl-N-(A,S)PK-[protein]
2
+
=
2
+
2
+
N-terminal-PPK-[protein]
=
2
+
N-terminal-N,N-dimethyl-N-PPK-[protein]
Synonyms
nrmt1, ntmt1, mettl13, n-terminal methyltransferase, protein n-terminal methyltransferase 1, n-terminal rcc1 methyltransferase, mettl11a, ylr285w, ybr261c/tae1, n6amt2, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
NTMT1
FEAT
i.e. faint expression in normal tissues, aberrant overexpression in tumors
METTL11A
NMT1
-
-
-
-
METTL11A
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:N-terminal-(A,P,S)PK-[protein] methyltransferase
This enzyme methylates the N-terminus of target proteins containing the N-terminal motif [Ala/Pro/Ser]-Pro-Lys after the initiator L-methionine is cleaved. When the terminal amino acid is L-proline, the enzyme catalyses two successive methylations of its alpha-amino group. When the first amino acid is either L-alanine or L-serine, the enzyme catalyses three successive methylations.
The Pro-Lys in positions 2-3 cannot be exchanged for other amino acids [1,2].
CAS REGISTRY NUMBER
COMMENTARY
9068-28-4
-
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
2 S-adenosyl-L-methionine + CPKRIA
2 S-adenosyl-L-homocysteine + ?
mono- and dimethylation by NTMT1
-
-
?
2 S-adenosyl-L-methionine + FPKRIA
2 S-adenosyl-L-homocysteine + ?
dimethylation and low level trimethylation by NTMT1
-
-
?
2 S-adenosyl-L-methionine + HPKRIA
2 S-adenosyl-L-homocysteine + ?
dimethylation by NTMT1
-
-
?
2 S-adenosyl-L-methionine + IPKRIA
2 S-adenosyl-L-homocysteine + ?
mono- and dimethylation by NTMT1
-
-
?
2 S-adenosyl-L-methionine + KPKRIA
2 S-adenosyl-L-homocysteine + ?
dimethylation and low level trimethylation by NTMT1
-
-
?
2 S-adenosyl-L-methionine + LPKRIA
2 S-adenosyl-L-homocysteine + ?
dimethylation and low level trimethylation by NTMT1
-
-
?
2 S-adenosyl-L-methionine + MPKRIA
2 S-adenosyl-L-homocysteine + ?
dimethylation and low level trimethylation by NTMT1
-
-
?
2 S-adenosyl-L-methionine + N-terminal-histone 2B
2 S-adenosyl-L-homocysteine + ?
dimethylation of fruit fly histone 2B by NTMT1 over an N-terminal sequence of 1PPKTSGKAA9
-
-
?
2 S-adenosyl-L-methionine + NPKRIA
2 S-adenosyl-L-homocysteine + ?
dimethylation by NTMT1
-
-
?
2 S-adenosyl-L-methionine + PPKRIA
2 S-adenosyl-L-homocysteine + ?
dimethylation by NTMT1
-
-
?
2 S-adenosyl-L-methionine + QPKRIA
2 S-adenosyl-L-homocysteine + ?
dimethylation by NTMT1
-
-
?
2 S-adenosyl-L-methionine + RPKRIA
2 S-adenosyl-L-homocysteine + ?
dimethylation and low level trimethylation by NTMT1
-
-
?
2 S-adenosyl-L-methionine + TPKRIA
2 S-adenosyl-L-homocysteine + ?
mono- and dimethylation by NTMT1
-
-
?
2 S-adenosyl-L-methionine + VPKRIA
2 S-adenosyl-L-homocysteine + ?
mono- and dimethylation by NTMT1
-
-
?
2 S-adenosyl-L-methionine + WPKRIA
2 S-adenosyl-L-homocysteine + ?
mono- and dimethylation by NTMT1
-
-
?
2 S-adenosyl-L-methionine + YPKRIA
2 S-adenosyl-L-homocysteine + ?
dimethylation by NTMT1
-
-
?
3 (E)-hex-2-en-5-ynyl-S-adenosyl-L-methionine + N-terminal-OLA1
?
-
-
-
?
3 S-adenosyl-L-methionine + APKRIA
3 S-adenosyl-L-homocysteine + ?
trimethylation by NTMT1
-
-
?
3 S-adenosyl-L-methionine + GPKRIA
3 S-adenosyl-L-homocysteine + ?
trimethylation by NTMT1
-
-
?
3 S-adenosyl-L-methionine + N-terminal-CENP-A
3 S-adenosyl-L-homocysteine + ?
human CENP-A histone, molecular details for CENP-A recognition by NRMT1. State-specific trimethylation of CENP-A by NRMT1
-
-
?
3 S-adenosyl-L-methionine + N-terminal-PPKRIA-[RCC1]
3 S-adenosyl-L-homocysteine + N-terminal-trimethyl-PPKRIA-[RCC1]
-
-
-
?
3 S-adenosyl-L-methionine + SPKRIA
3 S-adenosyl-L-homocysteine + ?
trimethylation by NTMT1
-
-
?
N-terminal L-alanyl-L-prolyl-L-lysyl-[protein] + 3 S-adenosyl-L-methionine
N-terminal N,N,N-trimethyl-L-alanyl-L-prolyl-L-lysyl-[protein] + 3 S-adenosyl-L-homocysteine
-
-
-
?
S-adenosyl-L-methionine + APKQQLSKY
?
synthetic peptide, modified yeast protein Rps25a/Rps25b-derived peptide
-
-
?
S-adenosyl-L-methionine + DPKRIA
S-adenosyl-L-homocysteine + ?
monomethylation by NTMT1
-
-
?
S-adenosyl-L-methionine + EPKRIA
S-adenosyl-L-homocysteine + ?
monomethylation by NTMT1
-
-
?
S-adenosyl-L-methionine + N-terminal-(A,P,S)PK-[protein]
S-adenosyl-L-homocysteine + N-terminal-N-methyl-N-(A,P,S)PK-[protein]
-
-
-
?
S-adenosyl-L-methionine + N-terminal-CENP-A
S-adenosyl-L-homocysteine + ?
human CENP-A histone
-
-
?
S-adenosyl-L-methionine + N-terminal-histone 2B
S-adenosyl-L-homocysteine + ?
fruit fly histone 2B
-
-
?
S-adenosyl-L-methionine + PPKQQLSKY
?
synthetic peptide, yeast protein Rps25a/Rps25b-derived peptide
-
-
?
S-adenosyl-L-methionine + SPKQQLSKY
?
synthetic peptide, modified yeast protein Rps25a/Rps25b-derived peptide
-
-
?
S-adenosyl-L-methionine + SPKRIAKRRSPPADA
?
substrate peptide consisting of the first 15 amino acids of RCC1. NRMT2 V224L is able to significantly decrease the NRMT1 Km with the RCC1 peptide
-
-
?
S-adenosyl-L-methionine + SSKRAKAKTTKKRP
?
substrate peptide consisting of the first 14 amino acids of MYL9
-
-
?
3 S-adenosyl-L-methionine + eukaryotic elongation factor 1A
3 S-adenosyl-L-homocysteine + ?
3 S-adenosyl-L-methionine + N-terminal-dimethyl-SPKRIAKRRS-[RCC1]
3 S-adenosyl-L-homocysteine + N-terminal-trimethyl-SPKRIAKRRS-[RCC1]
-
-
-
-
?
3 S-adenosyl-L-methionine + N-terminal-LPKRIA-[RCC1]
3 S-adenosyl-L-homocysteine + N-terminal-trimethyl-LPKRIA-[RCC1]
-
-
-
-
?
3 S-adenosyl-L-methionine + N-terminal-methyl-SPKRIAKRRS-[RCC1]
3 S-adenosyl-L-homocysteine + N-terminal-trimethyl-SPKRIAKRRS-[RCC1]
-
-
-
-
?
3 S-adenosyl-L-methionine + N-terminal-peptide-[BAP1 protein]
3 S-adenosyl-L-homocysteine + N-terminal-trimethyl-peptide-[BAP1 protein]
-
i.e. BRCA1 associated protein 1, a DNA repair protein
-
-
?
3 S-adenosyl-L-methionine + N-terminal-peptide-[DDB2 protein]
3 S-adenosyl-L-homocysteine + N-terminal-trimethyl-peptide-[DDB2 protein]
-
DDB2 is a DNA repair protein
-
-
?
3 S-adenosyl-L-methionine + N-terminal-peptide-[PARP3 protein]
3 S-adenosyl-L-homocysteine + N-terminal-trimethyl-peptide-[PARP3 protein]
-
i.e. poly-ADP-ribosylase 3, a DNA repair protein
-
-
?
3 S-adenosyl-L-methionine + N-terminal-PPKRIA-[RCC1]
3 S-adenosyl-L-homocysteine + N-terminal-trimethyl-PPKRIA-[RCC1]
-
best substrate
-
-
?
3 S-adenosyl-L-methionine + N-terminal-RPKRIA-[RCC1]
3 S-adenosyl-L-homocysteine + N-terminal-trimethyl-RPKRIA-[RCC1]
-
-
-
-
?
3 S-adenosyl-L-methionine + N-terminal-SPKRIA-[RCC1]
3 S-adenosyl-L-homocysteine + N-terminal-trimethyl-SPKRIA-[RCC1]
3 S-adenosyl-L-methionine + N-terminal-SPKRIAKRR-[RCC1]
3 S-adenosyl-L-homocysteine + N-terminal-trimethyl-SPKRIAKRR-[RCC1]
-
-
-
-
?
3 S-adenosyl-L-methionine + N-terminal-SPKRIAKRRS-[RCC1]
3 S-adenosyl-L-homocysteine + N-terminal-trimethyl-SPKRIAKRRS-[RCC1]
-
-
-
-
?
3 S-adenosyl-L-methionine + N-terminal-SPKRIAKRRSPP-[RCC1]
3 S-adenosyl-L-homocysteine + N-terminal-trimethyl-SPKRIAKRRSPP-[RCC1]
-
-
-
-
?
3 S-adenosyl-L-methionine + N-terminal-WPKRIA-[RCC1]
3 S-adenosyl-L-homocysteine + N-terminal-trimethyl-WPKRIA-[RCC1]
-
-
-
-
?
3 S-adenosyl-L-methionine + N-terminal-YPKRIA-[RCC1]
3 S-adenosyl-L-homocysteine + N-terminal-trimethyl-YPKRIA-[RCC1]
-
-
-
-
?
S-adenosyl-L-methionine + human histone H3
S-adenosyl-L-homocysteine + ?
-
lower activity with histone H3 compared to histone H4
-
-
?
S-adenosyl-L-methionine + human histone H4
S-adenosyl-L-homocysteine + ?
-
-
-
-
?
S-adenosyl-L-methionine + N-terminal peptide sequence of a protein
S-adenosyl-L-homocysteine + methylated N-terminal peptide sequence of a protein
-
all known substrates of NTMT1 contain the N-terminal consensus sequence XPK (X = S/P/A/G), although NTMT1 can also methylate peptides with X being F, Y, C, M, K, R, N, Q, or H in vitro, substrate specificity of NTMT1, overview. Structural basis for the specific N-terminal methylation of a consensus motif, XPK, by NTMT1, overview. Hexapeptides composed of the first six residues of RCC1, i.e. regulator of chromosome condensation 1, are recognized by the enzyme. The first residue within the consensus sequence of the NTMT1 substrates is anchored through a hydrogen bond with the conserved Asn168 of NTMT1 in a spacious binding pocket, which exposes the substrate's reactive alpha-amino group to S-adenosyl-L-methionine in the complex structures, and this very N-terminal residue can tolerate most residue substitutions except the negatively charged residues D and E. Asp180 and His140 can act as bases to facilitate deprotonation of the target alpha-N-terminal amino group. Catalytic reaction proceeds probably involving a SN1 mechanism, overview
S-adenosyl-L-homocysteine is bound to NTMT1 in an extended conformation. The carboxylate moiety of SAH forms a salt bridge interaction with the highly conserved Arg74, and the ribosyl group stacks with the indole ring of Trp20. In addition, the adenine moiety of SAH is flanked by the hydrophobic side chains of Ile92 and Val137 and interacts with the main chain amide group of Leu119 and the side chain of Gln120 through hydrogen bonding
-
?
S-adenosyl-L-methionine + Ran guanine nucleotide-exchange factor RCC1
S-adenosyl-L-homocysteine + ?
S-adenosyl-L-methionine + retinoblastoma protein
S-adenosyl-L-homocysteine + ?
-
-
-
-
?
S-adenosyl-L-methionine + SET/TAF-I/PHAPII
S-adenosyl-L-homocysteine + ?
-
only the SETalpha splicing variant is a substrate for NRMT, since it begins with the NRMT consensus in contrast to the beta splicing variant
-
-
?
3 S-adenosyl-L-methionine + N-terminal-OLA1
3 S-adenosyl-L-homocysteine + ?
i.e. Obg-like ATPase 1 (OLA1) protein, target validation using normal and NTMT1 knockout HEK-293FT cells demonstrates that OLA1, a protein involved in many critical cellular functions, is methylated in vivo by NTMT1
-
-
?
3 S-adenosyl-L-methionine + N-terminal-OLA1
3 S-adenosyl-L-homocysteine + ?
i.e. Obg-like ATPase 1 (OLA1) protein
-
-
?
3 S-adenosyl-L-methionine + N-terminal-[RCC1]
3 S-adenosyl-L-homocysteine + ?
-
-
-
?
3 S-adenosyl-L-methionine + N-terminal-[RCC1]
3 S-adenosyl-L-homocysteine + ?
-
-
-
?
3 S-adenosyl-L-methionine + N-terminal-[RCC1]
3 S-adenosyl-L-homocysteine + ?
-
-
-
?
3 S-adenosyl-L-methionine + N-terminal-[RCC1]
3 S-adenosyl-L-homocysteine + ?
RCC1p and methionine-removed RCC1
-
-
?
3 S-adenosyl-L-methionine + eukaryotic elongation factor 1A
3 S-adenosyl-L-homocysteine + ?
enzyme N6AMT2 trimethylates eEF1A at the N-terminal site and at the adjacent lysine 79, protein substrate from Homo sapiens or Saccharomyces cerevisiae
-
-
?
3 S-adenosyl-L-methionine + eukaryotic elongation factor 1A
3 S-adenosyl-L-homocysteine + ?
enzyme N6AMT2 trimethylates eEF1A at the N-terminal site and at the adjacent lysine 79, protein substrate from Homo sapiens or Saccharomyces cerevisiae. Yeast eEF1A is trimethylated at its N-terminus and dimethylated at lysine 3. Human eEF1A is trimethylated at its N-terminus
-
-
?
3 S-adenosyl-L-methionine + N-terminal-SPKRIA-[RCC1]
3 S-adenosyl-L-homocysteine + N-terminal-trimethyl-SPKRIA-[RCC1]
-
-
-
-
?
3 S-adenosyl-L-methionine + N-terminal-SPKRIA-[RCC1]
3 S-adenosyl-L-homocysteine + N-terminal-trimethyl-SPKRIA-[RCC1]
-
high activity
-
-
?
3 S-adenosyl-L-methionine + N-terminal-SPKRIA-[RCC1]
3 S-adenosyl-L-homocysteine + N-terminal-trimethyl-SPKRIA-[RCC1]
-
i.e. regulator of chromosome condensation 1
-
-
?
3 S-adenosyl-L-methionine + N-terminal-[eEF1A]
3 S-adenosyl-L-homocysteine + ?
-
-
-
?
3 S-adenosyl-L-methionine + N-terminal-[eEF1A]
3 S-adenosyl-L-homocysteine + ?
specifically, the C-terminal domain is able to methylate peptides derived from the first 15 amino acids of eEF1A, whereas the N-terminal domain is sufficient for methylation of Lys55. High specificity of METTL13 for eEF1A
-
-
?
S-adenosyl-L-methionine + Ran guanine nucleotide-exchange factor RCC1
S-adenosyl-L-homocysteine + ?
-
NRMT is the predominant alpha-N-methyltransferase for RCC1
-
-
?
S-adenosyl-L-methionine + Ran guanine nucleotide-exchange factor RCC1
S-adenosyl-L-homocysteine + ?
-
substrate docking and mutational analysis of RCC1 defining the NRMT recognition sequence, the first 3 residues Ser-Pro-Lys interact with NRMT, overview
-
-
?
additional information
?
-
the methyltransferases specifically recognizes the N-terminal X-Pro-Lys sequence motif. Localization of methylation sites by top down mass spectrometry using collisionally activated dissociation or electron capture dissociation. The enzyme can also recognize species with N-terminal alanine and serine residues in addition to those with proline residues, but the proline residue in position 1 is a preferred substrate
-
-
?
additional information
?
-
-
the methyltransferases specifically recognizes the N-terminal X-Pro-Lys sequence motif. Localization of methylation sites by top down mass spectrometry using collisionally activated dissociation or electron capture dissociation. The enzyme can also recognize species with N-terminal alanine and serine residues in addition to those with proline residues, but the proline residue in position 1 is a preferred substrate
-
-
?
additional information
?
-
protein N-terminal methyltransferase 1 (NTMT1/NRMT1) catalyzes the transfer of a methyl group from S-adenosyl-L-methionine (SAM) to protein alpha-N-terminal amines. It recognizes a specific motif X-P-K/R (X represents any amino acid other than D/E)
-
-
-
additional information
?
-
substrate of NTMT1 are regulator of chromosome condensation 1 (RCC1), tumor suppressor retinoblastoma1 (RB1), oncoprotein SET (also known as I2PP2A, TAF1a), damaged DNA-binding protein2 (DDB2), poly(ADP-ribose) polymerase3 (PARP3), and centromere proteins A and B
-
-
-
additional information
?
-
substrate of NTMT1 are regulator of chromosome condensation 1 (RCC1), tumor suppressor retinoblastoma1 (RB1), oncoprotein SET (also known as I2PP2A, TAF1a), damaged DNA-binding protein2 (DDB2), poly(ADP-ribose) polymerase3 (PARP3), and centromere proteins A and B
-
-
-
additional information
?
-
histone peptide profiling reveals that human NRMT1is highly selective to human CENP-A and fruit fly H2B, which share a common Xaa-Pro-Lys/Arg motif
-
-
-
additional information
?
-
-
histone peptide profiling reveals that human NRMT1is highly selective to human CENP-A and fruit fly H2B, which share a common Xaa-Pro-Lys/Arg motif
-
-
-
additional information
?
-
motif sequence and signal peptide analyses, and activity-based substrate profiling of NTMT1 utilizing (E)-hex-2-en-5-ynyl-S-adenosyl-L-methionine (Hey-SAM) reveals 72 potential targets, overview
-
-
-
additional information
?
-
NRMT1 exhibits distributive trimethylase activity in vitro. Isozymes NRMT1 and NRMT2 can interact both in vitro and in vivo, modeling of NRMT1 and NRMT2 interactions. The Ser-Pro-Lys consensus sequence of the RCC1 peptide is a preferred substrate for NRMT1
-
-
-
additional information
?
-
the substrate recognition motif is X-P-K/R. NTMT1 is able to methylate hexamer peptides. NTMT1 is known to be a trimethylase that catalyzes mono-, di-, and trimethylation. During the process of multiple methylations, the substrate can be released and rebind to NTMT1, which proceeds through a distributive mechanism for multiple methylations
-
-
-
additional information
?
-
the substrate recognition motif is X-P-K/R. NTMT1 is able to methylate hexamer peptides. NTMT1 is known to be a trimethylase that catalyzes mono-, di-, and trimethylation. During the process of multiple methylations, the substrate can be released and rebind to NTMT1, which proceeds through a distributive mechanism for multiple methylations
-
-
-
additional information
?
-
-
enzyme substrates have a unique N-terminal motif, Met-(Ala/Pro/Ser)-Pro-Lys. The initiating Met is cleaved, and the exposed alpha-amino group is mono-, di-, or trimethylated
-
-
?
additional information
?
-
-
the enzyme shows a ternary complex mechanism of catalysis, involving formation of a SAM-enzyme-acceptor complex and direct transfer of the methyl group from SAM to the acceptor protein
-
-
?
additional information
?
-
-
the protein N-terminal methyltransferase 1 (NTMT1) methylates the alpha-N-terminal amines of proteins
-
-
?
additional information
?
-
-
enzyme NTMT1 catalyzes the transfer of the methyl group from the S-adenosyl-L-methionine to the protein alpha-amine, resulting in formation of S-adenosyl-L-homocysteine and alpha-N-methylated proteins. Inhibition pattern and methylation progress analyses are performed to determine the kinetic mechanism and processivity of NTMT1, the enzyme NTMT1 utilizes a random sequential bi bi mechanism and proceeds in a distributive manner. Residues of RCC1, i.e. regulator of chromosome condensation 1, are recognized by the enzyme. Methylation status of products is analyzed by MALDI-mass spectrometry
-
-
?
additional information
?
-
human MTase-like protein 13 (METTL13) is a dual MTase for both N-terminal Gly1 and Lys55 of human eEF1A. To date, eEF1A is the only validated biological substrate for METTL13
-
-
-
additional information
?
-
human MTase-like protein 13 (METTL13) is a dual MTase for both N-terminal Gly1 and Lys55 of human eEF1A. To date, eEF1A is the only validated biological substrate for METTL13
-
-
-
additional information
?
-
the methyltransferase N6AMT2 is responsible for Lys79 methylation of human eEF1A, but has been previously documented as a putative N(6)-adenine-specific DNA methyltransferase. It is renamed eEF1A-KMT1
-
-
-
additional information
?
-
-
the methyltransferase N6AMT2 is responsible for Lys79 methylation of human eEF1A, but has been previously documented as a putative N(6)-adenine-specific DNA methyltransferase. It is renamed eEF1A-KMT1
-
-
-
additional information
?
-
analysis of methylation sites, method, detailed overview
-
-
-
additional information
?
-
-
analysis of methylation sites, method, detailed overview
-
-
-
additional information
?
-
the substrate recognition sequence is GKEKTH
-
-
-
additional information
?
-
the substrate recognition sequence is GKEKTH
-
-
-
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
3 S-adenosyl-L-methionine + GPKRIA
3 S-adenosyl-L-homocysteine + ?
trimethylation by NTMT1
-
-
?
3 S-adenosyl-L-methionine + N-terminal-OLA1
3 S-adenosyl-L-homocysteine + ?
i.e. Obg-like ATPase 1 (OLA1) protein, target validation using normal and NTMT1 knockout HEK-293FT cells demonstrates that OLA1, a protein involved in many critical cellular functions, is methylated in vivo by NTMT1
-
-
?
3 S-adenosyl-L-methionine + N-terminal-PPKRIA-[RCC1]
3 S-adenosyl-L-homocysteine + N-terminal-trimethyl-PPKRIA-[RCC1]
-
-
-
?
N-terminal L-alanyl-L-prolyl-L-lysyl-[protein] + 3 S-adenosyl-L-methionine
N-terminal N,N,N-trimethyl-L-alanyl-L-prolyl-L-lysyl-[protein] + 3 S-adenosyl-L-homocysteine
-
-
-
?
S-adenosyl-L-methionine + N-terminal-(A,P,S)PK-[protein]
S-adenosyl-L-homocysteine + N-terminal-N-methyl-N-(A,P,S)PK-[protein]
-
-
-
?
S-adenosyl-L-methionine + N-terminal-CENP-A
S-adenosyl-L-homocysteine + ?
human CENP-A histone
-
-
?
S-adenosyl-L-methionine + N-terminal-histone 2B
S-adenosyl-L-homocysteine + ?
fruit fly histone 2B
-
-
?
3 S-adenosyl-L-methionine + eukaryotic elongation factor 1A
3 S-adenosyl-L-homocysteine + ?
enzyme N6AMT2 trimethylates eEF1A at the N-terminal site and at the adjacent lysine 79, protein substrate from Homo sapiens or Saccharomyces cerevisiae
-
-
?
3 S-adenosyl-L-methionine + N-terminal-[eEF1A]
3 S-adenosyl-L-homocysteine + ?
-
-
-
?
S-adenosyl-L-methionine + Ran guanine nucleotide-exchange factor RCC1
S-adenosyl-L-homocysteine + ?
-
NRMT is the predominant alpha-N-methyltransferase for RCC1
-
-
?
S-adenosyl-L-methionine + retinoblastoma protein
S-adenosyl-L-homocysteine + ?
-
-
-
-
?
3 S-adenosyl-L-methionine + N-terminal-[RCC1]
3 S-adenosyl-L-homocysteine + ?
-
-
-
?
3 S-adenosyl-L-methionine + N-terminal-[RCC1]
3 S-adenosyl-L-homocysteine + ?
-
-
-
?
additional information
?
-
protein N-terminal methyltransferase 1 (NTMT1/NRMT1) catalyzes the transfer of a methyl group from S-adenosyl-L-methionine (SAM) to protein alpha-N-terminal amines. It recognizes a specific motif X-P-K/R (X represents any amino acid other than D/E)
-
-
-
additional information
?
-
substrate of NTMT1 are regulator of chromosome condensation 1 (RCC1), tumor suppressor retinoblastoma1 (RB1), oncoprotein SET (also known as I2PP2A, TAF1a), damaged DNA-binding protein2 (DDB2), poly(ADP-ribose) polymerase3 (PARP3), and centromere proteins A and B
-
-
-
additional information
?
-
substrate of NTMT1 are regulator of chromosome condensation 1 (RCC1), tumor suppressor retinoblastoma1 (RB1), oncoprotein SET (also known as I2PP2A, TAF1a), damaged DNA-binding protein2 (DDB2), poly(ADP-ribose) polymerase3 (PARP3), and centromere proteins A and B
-
-
-
additional information
?
-
-
the protein N-terminal methyltransferase 1 (NTMT1) methylates the alpha-N-terminal amines of proteins
-
-
?
additional information
?
-
human MTase-like protein 13 (METTL13) is a dual MTase for both N-terminal Gly1 and Lys55 of human eEF1A. To date, eEF1A is the only validated biological substrate for METTL13
-
-
-
additional information
?
-
human MTase-like protein 13 (METTL13) is a dual MTase for both N-terminal Gly1 and Lys55 of human eEF1A. To date, eEF1A is the only validated biological substrate for METTL13
-
-
-
additional information
?
-
the methyltransferase N6AMT2 is responsible for Lys79 methylation of human eEF1A, but has been previously documented as a putative N(6)-adenine-specific DNA methyltransferase. It is renamed eEF1A-KMT1
-
-
-
additional information
?
-
-
the methyltransferase N6AMT2 is responsible for Lys79 methylation of human eEF1A, but has been previously documented as a putative N(6)-adenine-specific DNA methyltransferase. It is renamed eEF1A-KMT1
-
-
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
5'-([3-[(2S)-2-acetylpyrrolidin-1-yl]propyl][(3S)-3-amino-3-carboxypropyl]amino)-5'-deoxyadenosine
-
NAM-C3-PKRIA-NH2
discovery of the potent NTMT1 bisubstrate inhibitor NAM-C3-PKRIA-NH2 that exhibits greater than 100fold selectivity against a panel of methyltransferases. Crystal structure analysis of NTMT1 in complex with the inhibitor reveals that NAM-C3-PKRIA-NH2 occupies substrate and cofactor binding sites of NTMT1
N-terminal-acetyl-SPKRIAKRRS-[RCC1]
-
noncompetitive versus S-adenosyl-L-methionine and protein substrate
-
N-terminal-trimethyl-SPKRIA-[RCC1]
-
product inhibition, competitive inhibitor versus protein substrate, noncompetitive versus S-adenosyl-L-methionine
-
NAM-TZ-SPKRIA
-
the inhibitor is enzyme-specific with a competitive inhibition pattern for both substrates, selective versus protein lysine methyltransferase G9a and arginine methyltransferase 1. The inhibitor substantially suppresses the methylation progression. The sulfur is replaced with a less reactive nitrogen to yield N-adenosyl-L-methionine as a stable analogue of S-adenosyl-L-methionine. Hexapeptide SPKRIA is derived from the N-terminus of regulator of chromosome condensation 1, RCC1. Binding structure modeling using the crystal structure of NTMT1 with S-adenosyl-L-homocysteine, PDB ID 2EX4. The two parts are connected via the triazole linker. NAM-TZ-SPKRIA acts as a competitive inhibitor when the concentration of S-adenosyl-L-methionine is varied from 0.003-0.010 mM and RCC1-10 substrate peptide is at a fixed concentration at 0.003 mM
sinefungin
-
noncompetitive versus S-adenosyl-L-methionine and protein substrate
NAM-C3-GPRRRS
GPKRRS peptide derived from CENP-A is linked through a propylene group
S-adenosyl-L-homocysteine
-
product inhibition, competitive inhibitor versus S-adenosyl-L-methionine, noncompetitive versus protein substrate
additional information
development of potent and specific inhibitors, bisubstrate analogues that simultaneously target both binding sites are proven to be an effective strategy to obtain potent and selective inhibitors for many enzymes with two binding sites. Because NTMT1 forms a ternary complex during catalysis, a bisubstrate strategy has been applied to design and synthesize bisubstrate inhibitors by covalently linking a SAM analogue with a peptide substrate to mimic the transition state. NTMT1 bisubstrate inhibitors contain three components: an N-adenosyl-L-methionine (NAM) that replaces the sulfonium ion of SAM with a nitrogen atom, a hexapeptide derived from the N-terminal sequence of NTMT1 substrate, and a linker. The potency of such bisubstrate inhibitors corroborate the Bi Bi mechanism of NTMT1 methylation
-
additional information
development of potent and specific inhibitors, bisubstrate analogues that simultaneously target both binding sites are proven to be an effective strategy to obtain potent and selective inhibitors for many enzymes with two binding sites. Because NTMT1 forms a ternary complex during catalysis, a bisubstrate strategy has been applied to design and synthesize bisubstrate inhibitors by covalently linking a SAM analogue with a peptide substrate to mimic the transition state. NTMT1 bisubstrate inhibitors contain three components: an N-adenosyl-L-methionine (NAM) that replaces the sulfonium ion of SAM with a nitrogen atom, a hexapeptide derived from the N-terminal sequence of NTMT1 substrate, and a linker. The potency of such bisubstrate inhibitors corroborate the Bi Bi mechanism of NTMT1 methylation
-
additional information
-
feasibility of using a triazole group to link an S-adenosyl-L-methionine analogue with a peptide substrate to construct bisubstrate analogues as NTMT1 potent and selective inhibitors, a general strategy for the development of selective protein methyltransferase inhibitors
-
additional information
-
the inhibition patterns indicate a rapid equilibrium random kinetic mechanism
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
isozyme NRMT2 expression activates isozyme NRMT1 activity, not through priming, but by increasing its stability and substrate affinity. NRMT1 has increased N-terminal trimethylation activity when co-expressed with NRMT2. Catalytic activity of NRMT2 is not necessary for increased trimethylation by NRMT1
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0014
(E)-hex-2-en-5-ynyl-S-adenosyl-L-methionine
with RCC1, pH and temperature not specified in the publication
0.00038
S-adenosyl-L-methionine
with RCC1, pH and temperature not specified in the publication
0.0043
N-terminal-dimethyl-SPKRIAKRRS-[RCC1]
-
recombinant detagged enzyme, pH 7.5, 37°C
0.0014
N-terminal-methyl-SPKRIAKRRS-[RCC1]
-
recombinant detagged enzyme, pH 7.5, 37°C
0.00089
N-terminal-SPKRIAKRRS-[RCC1]
-
recombinant detagged enzyme, pH 7.5, 37°C
0.00196
N-terminal-[RCC1]
with S-adenosyl-L-methionine, pH and temperature not specified in the publication
-
0.00209
N-terminal-[RCC1]
with (E)-hex-2-en-5-ynyl-S-adenosyl-L-methionine, pH and temperature not specified in the publication
-
0.0009
SPKRIAKRRSPPADA
recombinant NRMT1, in presence of NRMT2, pH and temperature not specified in the publication
0.0011
SPKRIAKRRSPPADA
recombinant NRMT1, pH and temperature not specified in the publication
0.0044
SSKRAKAKTTKKRP
recombinant NRMT1, in presence of NRMT2 catalytically inactive V224L mutant, pH and temperature not specified in the publication
0.0066
SSKRAKAKTTKKRP
recombinant NRMT1, in presence of NRMT2, pH and temperature not specified in the publication
0.0156
SSKRAKAKTTKKRP
recombinant NRMT1, pH and temperature not specified in the publication
0.0031
N-terminal-SPKRIAKRRSPP-[RCC1]
-
recombinant detagged enzyme, pH 7.5, 37°C
0.0049
N-terminal-SPKRIAKRRSPP-[RCC1]
-
recombinant His6-tagged enzyme, pH 7.5, 37°C
additional information
additional information
-
Michaelis-Menten model, steady-state kinetic analysis and mechanism
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0067
(E)-hex-2-en-5-ynyl-S-adenosyl-L-methionine
with RCC1, pH and temperature not specified in the publication
0.0075
S-adenosyl-L-methionine
with RCC1, pH and temperature not specified in the publication
0.0098
N-terminal-dimethyl-SPKRIAKRRS-[RCC1]
-
recombinant detagged enzyme, pH 7.5, 37°C
0.0097
N-terminal-methyl-SPKRIAKRRS-[RCC1]
-
recombinant detagged enzyme, pH 7.5, 37°C
0.0087
N-terminal-[RCC1]
with (E)-hex-2-en-5-ynyl-S-adenosyl-L-methionine, pH and temperature not specified in the publication
-
0.0097
N-terminal-[RCC1]
with S-adenosyl-L-methionine, pH and temperature not specified in the publication
-
0.0095
N-terminal-SPKRIAKRRSPP-[RCC1]
-
recombinant detagged enzyme, pH 7.5, 37°C
0.013
N-terminal-SPKRIAKRRSPP-[RCC1]
-
recombinant His6-tagged enzyme, pH 7.5, 37°C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
4.79
(E)-hex-2-en-5-ynyl-S-adenosyl-L-methionine
with RCC1, pH and temperature not specified in the publication
19.74
S-adenosyl-L-methionine
with RCC1, pH and temperature not specified in the publication
2.28
N-terminal-dimethyl-SPKRIAKRRS-[RCC1]
-
recombinant detagged enzyme, pH 7.5, 37°C
6.93
N-terminal-methyl-SPKRIAKRRS-[RCC1]
-
recombinant detagged enzyme, pH 7.5, 37°C
4.16
N-terminal-[RCC1]
with (E)-hex-2-en-5-ynyl-S-adenosyl-L-methionine, pH and temperature not specified in the publication
-
4.95
N-terminal-[RCC1]
with S-adenosyl-L-methionine, pH and temperature not specified in the publication
-
2.65
N-terminal-SPKRIAKRRSPP-[RCC1]
-
recombinant His6-tagged enzyme, pH 7.5, 37°C
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
steady-state inhibition of NTMT1 by NAM-TZ-SPKRIA, kinetic analysis
-
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.00094
NAM-C3-GPRRRS
Homo sapiens
pH and temperature not specified in the publication
0.00081
NAM-TZ-SPKRIA
Homo sapiens
pH and temperature not specified in the publication
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
additional information
FEAT is observed in the cytoplasm, mitochondria, and nucleus of HeLa cells, as well as in the blood of cancer patients
additional information
NRMT1 is a ubiquitously expressed distributive trimethylase
additional information
the NTMT1 gene is expressed in all tissues, and the protein is expressed in most tissues, except spleen, liver, and fallopian tube tissue. NTMT1 is overexpressed in tumor tissues of patients, including colorectal, melanoma, carcinoid, lung, and liver
additional information
the NTMT1 gene is expressed in all tissues, and the protein is expressed in most tissues, except spleen, liver, and fallopian tube tissue. NTMT1 is overexpressed in tumor tissues of patients, including colorectal, melanoma, carcinoid, lung, and liver
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
metabolism
protein alpha-N-terminal methylation is catalyzed by prokaryotic and eukaryotic protein N-terminal methyltransferases. The prevalent occurrence of this methylation in ribosomes, myosin, and histones implies its function in protein-protein interactions. Functions of methylated glycine, alanine, and serine, overview
physiological function
evolution
malfunction
metabolism
protein alpha-N-terminal methylation is catalyzed by prokaryotic and eukaryotic protein N-terminal methyltransferases. The prevalent occurrence of this methylation in ribosomes, myosin, and histones implies its function in protein-protein interactions. Functions of methylated glycine, alanine, and serine, overview
physiological function
additional information
evolution
enzymatic functional conservation of NRMT1 across species, evolutionary conservation of histone alpha-N-modification. Coevolution of NRMT1 recognition motifs in RCC1, CENP-A, and CENP-B, in which sequences 1SPKRIA6 of RCC1, 1GPRRRS6 of CENP-A, and 1GPKRRQ6 of CENP-B co-occur in mammals but are all missing in lower organisms. In contrast, the NRMT1 recognition motif of histone H2B is conserved from ciliates to insects but is lost in mammals. Remarkably, yeast and chicken orthologues of the above proteins do not harbor an NRMT1 recognition motif, suggesting that NRMT1 may exert its cellular function in these organisms through other protein substrates
evolution
structural comparison of isozymes NTMT1 and NTMT2 (EC 2.1.1.299), overview. NTMT1 and NTMT2 employ a similar substrate recognition mode
evolution
the enzyme belongs to the methyltransferase like (METTL) family of class I methyltransferases containing seven-beta-strand methyltransferase motifs and Rossman folds for binding SAM. The N-terminal methyltransferase homologs NRMT1 (N-terminal RCC1 methyltransferase 1) and NRMT2 (N-terminal RCC1 methyltransferase 2), which following cleavage of the initiating methionine, methylate the alpha-amine of the first N-terminal residue of their substrates. NRMT1 and NRMT2 are 50% identical and 75% similar and share an N-terminal X-P-K consensus sequence. Although structurally similar, they differ in their catalytic activities
malfunction
aberrant N-terminal methylation has been implicated in several cancers and developmental diseases
malfunction
in vivo, complete knockout of NRMT1 via homologous recombination or CRISPR/Cas9 abolishes N-terminal trimethylation
malfunction
knockdown of NTMT1 results in hypersensitivity of breast cancer cell lines to doublestranded DNA breaks (DSBs) and increased proliferation of estrogen receptor positive breast cancer cells MCF-7 and LCC9
malfunction
knockdown of NTMT1 results in mitotic defects and sensitizes etoposide and gamma irradiation in breast cancer cell lines such as MCF-7 and LCC9
physiological function
protein X-Pro-Lys N-terminal methylation reactions catalyzed by the enzyme may be widespread in nature
physiological function
biological significances of NTMT1 in cell mitosis, chromatin segregation, and damaged DNA repair, along with its implications in cancer and aging
physiological function
N-terminal methylation is a regulator of protein-DNA and protein-protein interactions for a number of proteins, such as RCC1, CENPA/B, DDB2, PARP3, an MYL9, playing important roles in cell mitotic progression, DNA damage repair, and regulation of protein function. N-terminal methyltransferase 1 (NTMT1) catalyzes the N-terminal methylation of proteins with a specific N-terminal motif after methionine removal. Obg-like ATPase 1 (OLA1) protein, a protein involved in many critical cellular functions, is methylated in vivo by NTMT1, NTMT1 is responsible for OLA1 methylation in vivo
physiological function
NRMT1 is a ubiquitously expressed distributive trimethylase
physiological function
NRMT1 is an N-terminal methyltransferase that methylates histone CENP-A as well as nonhistone substrates
physiological function
protein lysine/arginine methylation, the addition of a methyl group at the free alpha-N-termini of proteins represents a unique mode of post-translational modification. NTMT1 is an S-adenosyl-L-methionine (SAM)-dependent methyltransferase. During the enzymatic reaction, NTMT1 transfers a methyl group from SAM to the alpha-amino group of the protein substrates, resulting in the production of S-adenosyl-L-homocysteine (SAH) and alpha-N-methylated proteins. NTMT1 recognizes proteins bearing an N-terminal X-P-K/R consensus sequence, including RCC1, RB1, DDB2, CENP-A/B, PARP3, etc.
physiological function
protein N-terminal methyltransferase 1 (NTMT1) plays an important role in regulating mitosis and DNA repair
evolution
-
METTL11a, i.e. NRMT, encodes a 25 kDa protein in the methyltransferase 11 family, most members of which methylate metabolites or other small molecules. alpha-N-methyltransferase is a conserved member of a superfamily of non-SET domain enzymes
evolution
the enzyme is a distinct type of eukaryotic N-terminal methyltransferase as, unlike the three other known eukaryotic N-terminal methyltransferases, its substrate does not have an N-terminal [A/P/S]-P-K motif. The N-terminal methylation of eEF1A is also present in yeast catalyzed by enzymes Efm5 and Efm7, this conservation over a large evolutionary distance suggests it to be of functional importance. The trimethylation of Lys79 in eEF1A is conserved from yeast to human. Human enzyme N6AMT2 is the direct orthologue of the yeast Efm5, and Efm5 and N6AMT2 can methylate eEF1A from either species in vitro. Methyltransferases that act on lysine 79 in eEF1A are conserved from yeast to human
malfunction
-
methylation-defective mutants of RCC1 have reduced affinity for DNA and cause mitotic defects, and non-methylatable mutants of RCC1 are defective in chromatin association, and their expression in a wild-type background produces supernumerary spindle poles and missegregation of mitotic chromosomes, most likely due to the disruption of the Ran gradient
malfunction
-
loss of the N-terminal methyltransferase NRMT1 increases sensitivity to DNA damage and promotes mammary oncogenesis. Enzyme NRMT1 knockdown significantly enhances the sensitivity of breast cancer cell lines to both etoposide treatment and gamma-irradiation, as well as, increases proliferation rate, invasive potential, anchorage-independent growth, xenograft tumor size, and tamoxifen sensitivity, e.g. in MCF-7 cells. NRMT1 knockdown promotes growth of excision repair positive breast cancer cell lines, but has no effect on the normally low NRMT1-expressing SKBR-3 and MDA-MB-231 cells. Phenotype, overview
malfunction
-
NTMT1 is upregulated in a variety of cancers and knockdown of NTMT1 results in cell mitotic defects
malfunction
the activity of the D577A mutant decreases the enzymatic activity by about half
physiological function
-
importance of alpha-N-methylation for normal bipolar spindle formation and chromosome segregation. Function of the alpha-N-methylation is not solely to stabilize chromatin associations, but may have a more general role in the regulation of electrostatic interactions
physiological function
-
alpha-N-terminal methylation seems to regulate protein stability via N-end rule pathways or mediate proteinprotein interactions. The enzyme also mediates protein-DNA interactions between chromatin and regulator of chromatin condensation
physiological function
-
enzyme NRMT1 acts as a tumor suppressor protein involved in multiple DNA repair pathways, role of N-terminal methylation in DNA repair. N-terminal methylation of DDB2 by NRMT1 is necessary for its recruitment to UV-induced DNA damage and proper execution of nucleotide excision repai. Additional NRMT1 targets, BRCA1 associated protein 1 (BAP1) and poly-ADP-ribosylase 3 (PARP3), are involved in DNA double strand break repair. BAP1 is a deubiquitinating enzyme recruited to DNA and required for appropriate assembly of homologous recombination factors during DSB. PARP3 poly-ADP-ribosylates proteins at DSBs and promotes NHEJ
physiological function
METTL13/FEAT is implicated in tumorigenesis in vivo by suppressing apoptosis. METTL13/FEAT protein is also implied as a tumor suppressor in bladder carcinoma by negatively regulating cell proliferation, migration, and invasion in bladder cancer cells
additional information
analysis of crystal structures of NRMT1 and NRMT2 (PDB IDs 2EX4 and 5UBB, determined to 1.75 and 2.0 A, respectively), homology modeling. Modeling of NRMT1 and NRMT2 heterotrimer, interaction analysis, overview
additional information
substrate and ligand binding structures of NTMT1 and NTMT2 (EC 2.1.1.299), overview
additional information
-
substrate and ligand binding structures of NTMT1 and NTMT2 (EC 2.1.1.299), overview
additional information
substrate recognition and catalytic mechanisms, overview. Ligand binding structures are analyzed. NTMT1-catalyzed methylation follows a random sequential Bi Bi mechanism, which involves the formation of a ternary complex with either substrate binding to NTMT1 first. Two highly conserved Asp180 and His140 act as general bases to facilitate deprotonation of the alpha-amino group of the N-terminus to attack SAM to transfer the methyl group
additional information
substrate recognition and catalytic mechanisms, overview. Ligand binding structures are analyzed. NTMT1-catalyzed methylation follows a random sequential Bi Bi mechanism, which involves the formation of a ternary complex with either substrate binding to NTMT1 first. Two highly conserved Asp180 and His140 act as general bases to facilitate deprotonation of the alpha-amino group of the N-terminus to attack SAM to transfer the methyl group
additional information
ternary structures of human NRMT1 bound to alpha-N-methylated peptides of human histone CENP-A or fruit fly histone H2B in the presence of SAH, NRMT1 adopts a core methyltransferase fold that resembles DOT1L and PRMT but not SET domain family histone methyltransferases, key substrate recognition and catalytic residues, NTMT1 structure-function analysis, overview. NRMT1 harbors a canonical SAM-dependent methyltransferase (SAM-MTase) core fold consisting of a seven-stranded beta-sheet (beta1-beta7) sandwiched by five flanking alpha-helices. Active site structure and catalytic mechanism analysis
additional information
-
ternary structures of human NRMT1 bound to alpha-N-methylated peptides of human histone CENP-A or fruit fly histone H2B in the presence of SAH, NRMT1 adopts a core methyltransferase fold that resembles DOT1L and PRMT but not SET domain family histone methyltransferases, key substrate recognition and catalytic residues, NTMT1 structure-function analysis, overview. NRMT1 harbors a canonical SAM-dependent methyltransferase (SAM-MTase) core fold consisting of a seven-stranded beta-sheet (beta1-beta7) sandwiched by five flanking alpha-helices. Active site structure and catalytic mechanism analysis
additional information
-
the enzyme contains two characteristic structural elements, a beta hairpin and an N-terminal extension, that contribute to its substrate specificity. Identification of key elements involved in locking the consensus substrate motif XPK (X indicates any residue type other than D/E) into the catalytic pocket for alpha-N-terminal methylation, NTMT1 prefers an XPK sequence motif, catalytic mechanism for alpha-N-terminal methylation and overall structure of the NTMT1 ternary complexes, verview
additional information
substrate recognition and catalytic mechanisms, overview. METTL13 has two distinct MTase domains: N- and C-terminal domains that appear to have different recognition preferences. The C-terminal domain of dual MTase METTL13 is responsible for the a-N-terminal methylation of eEF1A. The unique interaction of Asp577 with the alpha-amino group of Gly1 is required for enzymatic activity
additional information
substrate recognition and catalytic mechanisms, overview. METTL13 has two distinct MTase domains: N- and C-terminal domains that appear to have different recognition preferences. The C-terminal domain of dual MTase METTL13 is responsible for the a-N-terminal methylation of eEF1A. The unique interaction of Asp577 with the alpha-amino group of Gly1 is required for enzymatic activity
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). NTM1A_HUMAN
223
0
25387
Swiss-Prot
other Location (Reliability: 1)
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
2 * 33000, recombinant isozyme NRMT1, SDS-PAGE and analytical ultracentrifugation
additional information
additional information
isozyme NRMT1 primarily exists as a dimer. Isozymes NRMT1 and NRMT2, when co-expressed, form a heterotrimer, interaction analysis, overview. When NRMT2 monomer is present the NRMT1 dimer will bind it and the pool of NRMT1 dimer is completely depleted
additional information
-
NRMT lacks a SET domain but possesses a Rossman-like alpha/beta fold
additional information
-
the structure of enzyme NTMT1 includes a typical methyltransferase Rossmann fold that consists of a seven-strand beta sheet and five alpha helixes, of which two alpha helixes (alpha6 and alpha7) pack on one side of the beta sheet, and the other three alpha helixes (alpha3, alpha4, and alpha5) pack on the other side of the beta sheet. In addition to the highly conserved Rossmann fold, enzyme NTMT1contains two unique structural elements distinct from other methyltransferases: a beta hairpin inserted between strand beta5 and helix alpha7 and an N-terminal extension consisting of two alpha helixes (alpha1 and alpha2) and one 310 helix. These two unique structural elements are extensively involved in substrate binding, suggesting their potential contributions to substrate specificity
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
analysis of crystal structures of NRMT1 and NRMT2 (PDB IDs 2EX4 and 5UBB, determined to 1.75 and 2.0 A, respectively), homology modeling
crystal structures with PDB IDs 2EX4, 5E1B, 5E1M, 5E1O, 5E1D, 5E2B, 5E2A, 5CVD, and 5CVE
purified recombinant His-tagged enzyme in complex with inhibitor NAM-C3-PKRIA-NH2 , hanging drop vapor diffusion method, mixing of 30 mg/ml protein and 2 mM ligand, with 1.5 M lithium sulfate and 0.1 M Na-HEPES, pH 7.5, 20°C, X-ray diffraction structure determination and analysis at 1.47 A resolution, molecular replacement using the structure PDB ID 6DTN as template, and modelling
purified recombinant NRMT1 bound to CENP-A peptide and to the fruit fly H2B peptide in presence of S-adenosyl-L-homocysteine, vapor diffusion method, X-ray diffraction structure determination and analysis at 1.3 A and 1.5 A resolution, respectively
recombinant purified full-length wild-type NTMT1 in complex with S-adenosyl-L-homocysteine and a peptide derived from either human (SPKRIA) or mouse (PPKRIA) RCC1, or crystals of NTMT1 in complex with S-adenosyl-L-homocysteine and either the RPK or YPK substrate peptide, sitting drop vapor diffusion method, mixing of 0.001 ml of 37 mg/ml protein and ligand in 20 mM Tris-HCl, pH 7.5, 150 mM NaCl, and 0.5 mM TECP, with 0.001 ml of reservoir solution containing 23-28% PET 3350 and 14-18% Tacsimate, pH 6.0, X-ray diffraction structure determination and analysis, molecular replacement
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D180N
site-directed mutagenesis, the mutant shows highly reduced activity compared to wild-type
D212N
site-directed mutagenesis, the mutant shows reduced activity compared to wild-type
E213A
site-directed mutagenesis, the mutant shows 15% reduced activity compared to wild-type
H140A
the mutant loses the catalytic activity, but retains binding affinity to the peptide substrate
N168A
site-directed mutagenesis, the mutant shows highly reduced activity compared to wild-type
W136L
site-directed mutagenesis, the mutant shows 92% reduced activity compared to wild-type
Y19A
site-directed mutagenesis, the mutant shows highly reduced activity compared to wild-type
Y19F
site-directed mutagenesis, the mutant shows highly reduced activity compared to wild-type
Y215A
site-directed mutagenesis, the mutant shows reduced activity compared to wild-type
Y215I
site-directed mutagenesis, the mutant shows reduced activity compared to wild-type
D178A/D181A
-
site-directed mutagenesis, mutating the residues Asp178 and Asp181 at the lip of the active site to Ala decreases enzyme activity, which is further decreased by reverse-charge mutagenesis to Lys
N168K
-
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
S183K
-
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
additional information
additional information
generation of NTMT1 knockout HEK-293FT cells by CRISPR-Cas9
additional information
NRMT1 co-expression with NRMT2 increases the trimethylation rate of NRMT1. Generation of truncation constructs of NRMT1. Full-length FLAG-tagged NRMT1 only weakly interacts with the first 112 aa of NRMT2, though strongly interacts with a GFP-tagged NRMT2 fragment (amino acids 77-223) that is missing the 59 aa tail that is also lacking from the crystal structure and subsequent model. Full-length FLAG-tagged NRMT2 strongly interacts with the first 59 aa of NRMT1, as well as, amino acids 52-172. There is a decreased interaction of FLAG-tagged NRMT2-FLAG with the C-terminal fragment of NRMT1 (amino acids 178-223). Generation of NRMT1 knockout mutant, NRMT2 overexpression cannot rescue NRMT1 knockout phenotypes
additional information
-
depleting NRMT in 293LT cells, using lentivirus, significantly decreases methylation of endogenous RCC1, while not affecting overall RCC1 level, depleting NRMT in HeLa cells using short interfering RNAs causing the same effects, RCC1 methylation is rescued by expression of murine NRMT-FLAG, which is not targeted by the human shRNA
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
45
SAH-saturated NRMT1 displays a melting temperature (Tm) of 45°C, and the incubation with CENP-A (1-9) peptide further elevates the Tm by 3°C
additional information
additional information
all of the mutant peptides that lost methylation capacity display no or negligible stabilization effect of NRMT1, suggesting loss of peptide binding due to residue substitution. In contrast, G1A and G1P CENP-A mutants stabilize NRMT1 by 1.5°C and 5.5°C compared with that of the NRMT1-SAH binary complex, consistent with their retained methylation capacity
additional information
-
all of the mutant peptides that lost methylation capacity display no or negligible stabilization effect of NRMT1, suggesting loss of peptide binding due to residue substitution. In contrast, G1A and G1P CENP-A mutants stabilize NRMT1 by 1.5°C and 5.5°C compared with that of the NRMT1-SAH binary complex, consistent with their retained methylation capacity
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
the experimentally calculated half-life for endogenous NRMT1 is approximately 8.8 h. NRMT2 expression stabilizes NRMT1 in HCT-116 cells
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged enzyme from Escherichia coli strain BL21-CodonPlus(DE3)-RIL by nickel affinity chromatography
recombinant His-tagged METTL11A from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
recombinant N-terminally His6-tagged wild-type and mutant enzymes NTMT1 from Escherichia coli strain BL21(DE3) codon plus RIL by nickel affinity and anion exchange chromatography followed by gel filtration
-
recombinant N-terminally His6-tagged wild-type and mutant enzymes NTMT1 from Escherichia coli strain BL21(DE3) codon plus RIL by nickel affinity chromatography, tag cleavage through thrombin, another 3 steps of nickel affinity chromatography and dialysis
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene METTL11A, cloning of the His-tagged human enzyme using vector pET-100/DTOPO that carries a His6 tag in the linker region MRGSHHHHHHGMASMTGGQQMGRDLYDDDDKDHPFT, which is incorporated before the initiator methionine residue of the cloned protein, and expression in Escherichia coli strain BL21(DE3)
gene NTMT1, recombinant expression of His-tagged NRMT1 in Escherichia coli and of FLAG-tagged wild-type and mutant NRMT1s in HEK-293 cells, recombinant expression of GFP-tagged enzyme in HCT-116 cells
recombinant expression of His-tagged enzyme in Escherichia coli strain BL21-CodonPlus(DE3)-RIL
recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli
gene EEF1AKMT1, sequence comparisons, recombinant expression of N-terminally His6-tagged enzyme in Escherichia coli strain Rosetta DE3
N-terminally tagged FLAG-NRMT overexpression in HEK 293LT cell nuceli, that show 3fold increased RCC1 alpha-N-methyltransferase activity
-
recombinant expression of N-terminally His6-tagged wild-type and mutant enzymes NTMT1 with a thrombin cleavage site at the N-terminus in Escherichia coli strain BL21(DE3) codon plus RIL
-
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
drug development
drug development
-
design and synthesis of the inhibitors targeting NTMT1 as potential therapeutics in cancer treatment
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Webb, K.J.; Lipson, R.S.; Al-Hadid, Q.; Whitelegge, J.P.; Clarke, S.G.
Identification of protein N-terminal methyltransferases in yeast and humans
Biochemistry
49
5225-5235
2010
Homo sapiens (Q9BV86), Homo sapiens, Mus musculus, Saccharomyces cerevisiae
Richon, V.M.; Johnston, D.; Sneeringer, C.J.; Jin, L.; Majer, C.R.; Elliston, K.; Jerva, L.F.; Scott, M.P.; Copeland, R.A.
Chemogenetic analysis of human protein methyltransferases
Chem. Biol. Drug Des.
78
199-210
2011
Homo sapiens
Tooley, C.E.; Petkowski, J.J.; Muratore-Schroeder, T.L.; Balsbaugh, J.L.; Shabanowitz, J.; Sabat, M.; Minor, W.; Hunt, D.F.; Macara, I.G.
NRMT is an alpha-N-methyltransferase that methylates RCC1 and retinoblastoma protein
Nature
466
1125-1128
2010
Homo sapiens
Dong, C.; Mao, Y.; Tempel, W.; Qin, S.; Li, L.; Loppnau, P.; Huang, R.; Min, J.
Structural basis for substrate recognition by the human N-terminal methyltransferase 1
Genes Dev.
29
2343-2348
2015
Homo sapiens
Richardson, S.L.; Mao, Y.; Zhang, G.; Hanjra, P.; Peterson, D.L.; Huang, R.
Kinetic mechanism of protein N-terminal methyltransferase 1
J. Biol. Chem.
290
11601-11610
2015
Homo sapiens
Bonsignore, L.A.; Butler, J.S.; Klinge, C.M.; Schaner Tooley, C.E.
Loss of the N-terminal methyltransferase NRMT1 increases sensitivity to DNA damage and promotes mammary oncogenesis
Oncotarget
6
12248-12263
2015
Homo sapiens
Zhang, G.; Richardson, S.L.; Mao, Y.; Huang, R.
Design, synthesis, and kinetic analysis of potent protein N-terminal methyltransferase 1 inhibitors
Org. Biomol. Chem.
13
4149-4154
2015
Homo sapiens
Jia, K.; Huang, G.; Wu, W.; Shrestha, R.; Wu, B.; Xiong, Y.; Li, P.
In vivo methylation of OLA1 revealed by activity-based target profiling of NTMT1
Chem. Sci.
10
8094-8099
2019
Homo sapiens (Q9BV86)
Huang, R.
Chemical biology of protein N-terminal methyltransferases
ChemBioChem
20
976-984
2019
Drosophila melanogaster (Q6NN40), Escherichia coli (P0A8T1), Homo sapiens (Q8N6R0), Homo sapiens (Q9BV86), Saccharomyces cerevisiae (P38340), Saccharomyces cerevisiae (Q05874), Saccharomyces cerevisiae ATCC 204508 (P38340), Saccharomyces cerevisiae ATCC 204508 (Q05874), Thermus thermophilus (Q84BQ9), Thermus thermophilus ATCC 27634 (Q84BQ9), Thermus thermophilus DSM 579 (Q84BQ9)
Dong, C.; Dong, G.; Li, L.; Zhu, L.; Tempel, W.; Liu, Y.; Huang, R.; Min, J.
An asparagine/glycine switch governs product specificity of human N-terminal methyltransferase NTMT2
Commun. Biol.
1
183
2018
Homo sapiens (Q9BV86), Homo sapiens
Wu, R.; Yue, Y.; Zheng, X.; Li, H.
Molecular basis for histone N-terminal methylation by NRMT1
Genes Dev.
29
2337-2342
2015
Homo sapiens (Q9BV86), Homo sapiens
Chen, D.; Dong, G.; Noinaj, N.; Huang, R.
Discovery of bisubstrate inhibitors for protein N-terminal methyltransferase 1
J. Med. Chem.
62
3773-3779
2019
Homo sapiens (Q9BV86)
Hamey, J.J.; Winter, D.L.; Yagoub, D.; Overall, C.M.; Hart-Smith, G.; Wilkins, M.R.
Novel N-terminal and lysine methyltransferases that target translation elongation factor 1A in yeast and human
Mol. Cell. Proteomics
15
164-176
2016
Homo sapiens (Q8WVE0), Homo sapiens, Saccharomyces cerevisiae (P53200), Saccharomyces cerevisiae (Q05874), Saccharomyces cerevisiae, Saccharomyces cerevisiae ATCC 204508 (P53200), Saccharomyces cerevisiae ATCC 204508 (Q05874)
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