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Protein

N-terminal Xaa-Pro-Lys N-methyltransferase 1

Gene

NTMT1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Distributive alpha-N-methyltransferase that methylates the N-terminus of target proteins containing the N-terminal motif [Ala/Gly/Pro/Ser]-Pro-Lys when the initiator Met is cleaved. Specifically catalyzes mono-, di- or tri-methylation of the exposed alpha-amino group of the Ala, Gly or Ser residue in the [Ala/Gly/Ser]-Pro-Lys motif and mono- or di-methylation of Pro in the Pro-Pro-Lys motif. Some of the substrates may be primed by METTL11B-mediated monomethylation (PubMed:24090352). Catalyzes the trimethylation of the N-terminal Gly in CENPA (after removal of Met-1). Responsible for the N-terminal methylation of KLHL31, MYL2, MYL3, RB1, RCC1, RPL23A and SET. Required during mitosis for normal bipolar spindle formation and chromosome segregation via its action on RCC1.4 Publications

Catalytic activityi

3 S-adenosyl-L-methionine + N-terminal-(A,S)PK-[protein] = 3 S-adenosyl-L-homocysteine + N-terminal-N,N,N-trimethyl-N-(A,S)PK-[protein].2 Publications
2 S-adenosyl-L-methionine + N-terminal-PPK-[protein] = 2 S-adenosyl-L-homocysteine + N-terminal-N,N-dimethyl-N-PPK-[protein].2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei69S-adenosyl-L-methionine; via carbonyl oxygenCombined sources2 Publications1
Binding sitei74S-adenosyl-L-methionineCombined sources2 Publications1
Binding sitei135S-adenosyl-L-methionine; via carbonyl oxygenCombined sources2 Publications1

GO - Molecular functioni

  • histone methyltransferase activity Source: UniProtKB
  • N-terminal protein N-methyltransferase activity Source: UniProtKB
  • protein methyltransferase activity Source: UniProtKB

GO - Biological processi

  • chromosome segregation Source: UniProtKB
  • histone methylation Source: UniProtKB
  • N-terminal peptidyl-alanine methylation Source: GO_Central
  • N-terminal peptidyl-alanine trimethylation Source: Ensembl
  • N-terminal peptidyl-glycine methylation Source: UniProtKB
  • N-terminal peptidyl-proline dimethylation Source: UniProtKB
  • N-terminal peptidyl-serine dimethylation Source: UniProtKB
  • N-terminal peptidyl-serine trimethylation Source: UniProtKB
  • spindle organization Source: UniProtKB

Keywordsi

Molecular functionMethyltransferase, Transferase
LigandS-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciMetaCyc:ENSG00000148335-MONOMER.
BRENDAi2.1.1.244. 2681.

Names & Taxonomyi

Protein namesi
Recommended name:
N-terminal Xaa-Pro-Lys N-methyltransferase 1 (EC:2.1.1.2441 Publication)
Alternative name(s):
Alpha N-terminal protein methyltransferase 1A
Methyltransferase-like protein 11A
N-terminal RCC1 methyltransferase
X-Pro-Lys N-terminal protein methyltransferase 1A
Short name:
NTM1A
Cleaved into the following chain:
Gene namesi
Name:NTMT1
Synonyms:C9orf32, METTL11A, NRMT, NRMT1
ORF Names:AD-003
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 9

Organism-specific databases

EuPathDBiHostDB:ENSG00000148335.14.
HGNCiHGNC:23373. NTMT1.

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi19Y → A or F: Decreased methyltransferase activity with CENPA. 1 Publication1
Mutagenesisi19Y → A: Reduced methyltransferase activity with CENPA. 1 Publication1
Mutagenesisi20W → A, M or Y: Nearly abolishes methyltransferase activity with CENPA. 1 Publication1
Mutagenesisi136W → L: Strongly reduces methyltransferase activity with CENPA. 1 Publication1
Mutagenesisi167D → A: Does not affect methyltransferase activity. 1 Publication1
Mutagenesisi167D → N or Q: Abolishes methyltransferase activity with CENPA. 1 Publication1
Mutagenesisi168N → A: Decreased methyltransferase activity. 2 Publications1
Mutagenesisi168N → K: Loss of methyltransferase activity. 1 Publication1
Mutagenesisi177D → A: Induces a slight decrease in methyltransferase activity. 1 Publication1
Mutagenesisi177D → K: Induces a strong decrease in methyltransferase activity. 1 Publication1
Mutagenesisi177D → N: Strongly reduces methyltransferase activity with CENPA. 1 Publication1
Mutagenesisi180D → A: Induces a decrease in methyltransferase activity. 1 Publication1
Mutagenesisi180D → K: Induces a strong decrease in methyltransferase activity. 1 Publication1
Mutagenesisi180D → N: Reduced methyltransferase activity with CENPA. 1 Publication1
Mutagenesisi182S → A: Induces a slight decrease in methyltransferase activity. 1 Publication1
Mutagenesisi182S → K: Induces a strong decrease in methyltransferase activity. 1 Publication1

Organism-specific databases

OpenTargetsiENSG00000148335.
PharmGKBiPA162395788.

Polymorphism and mutation databases

DMDMi74761281.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004232281 – 223N-terminal Xaa-Pro-Lys N-methyltransferase 1Add BLAST223
Initiator methionineiRemoved; alternateCombined sources1 Publication
ChainiPRO_00001192882 – 223N-terminal Xaa-Pro-Lys N-methyltransferase 1, N-terminally processedAdd BLAST222

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionineCombined sources1
Modified residuei2N-acetylthreonine; in N-terminal Xaa-Pro-Lys N-methyltransferase 1, N-terminally processedCombined sources1 Publication1

Keywords - PTMi

Acetylation

Proteomic databases

EPDiQ9BV86.
MaxQBiQ9BV86.
PaxDbiQ9BV86.
PeptideAtlasiQ9BV86.
PRIDEiQ9BV86.
TopDownProteomicsiQ9BV86-1. [Q9BV86-1]

PTM databases

iPTMnetiQ9BV86.
PhosphoSitePlusiQ9BV86.

Expressioni

Gene expression databases

BgeeiENSG00000148335.
CleanExiHS_METTL11A.
ExpressionAtlasiQ9BV86. baseline and differential.
GenevisibleiQ9BV86. HS.

Organism-specific databases

HPAiHPA020092.
HPA058420.

Interactioni

Protein-protein interaction databases

BioGridi118810. 24 interactors.
DIPiDIP-31241N.
IntActiQ9BV86. 4 interactors.
STRINGi9606.ENSP00000361558.

Structurei

Secondary structure

1223
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi2 – 4Combined sources3
Helixi9 – 21Combined sources13
Helixi27 – 30Combined sources4
Turni31 – 33Combined sources3
Helixi35 – 37Combined sources3
Helixi38 – 54Combined sources17
Beta strandi55 – 58Combined sources4
Beta strandi63 – 68Combined sources6
Turni71 – 73Combined sources3
Helixi74 – 78Combined sources5
Turni79 – 83Combined sources5
Beta strandi85 – 92Combined sources8
Helixi94 – 103Combined sources10
Helixi105 – 110Combined sources6
Beta strandi111 – 116Combined sources6
Helixi119 – 121Combined sources3
Beta strandi129 – 136Combined sources8
Helixi138 – 140Combined sources3
Helixi143 – 156Combined sources14
Beta strandi157 – 177Combined sources21
Turni178 – 181Combined sources4
Beta strandi182 – 186Combined sources5
Helixi187 – 196Combined sources10
Beta strandi200 – 206Combined sources7
Beta strandi216 – 223Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2EX4X-ray1.75A/B2-222[»]
5CVDX-ray1.30A/B1-223[»]
5CVEX-ray1.50A/B1-223[»]
5E1BX-ray1.65A/B2-223[»]
5E1DX-ray1.45A/B2-223[»]
5E1MX-ray1.75A/B2-223[»]
5E1OX-ray2.00A/B2-223[»]
5E2AX-ray1.75A/B2-223[»]
5E2BX-ray1.95A/B2-223[»]
ProteinModelPortaliQ9BV86.
SMRiQ9BV86.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9BV86.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni91 – 93S-adenosyl-L-methionine bindingCombined sources2 Publications3
Regioni119 – 120S-adenosyl-L-methionine bindingCombined sources2 Publications2

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG3178. Eukaryota.
ENOG410XS7T. LUCA.
GeneTreeiENSGT00390000008371.
HOGENOMiHOG000161910.
HOVERGENiHBG054992.
InParanoidiQ9BV86.
KOiK16219.
OMAiPVYMIAC.
OrthoDBiEOG091G0NA7.
PhylomeDBiQ9BV86.
TreeFamiTF314174.

Family and domain databases

InterProiView protein in InterPro
IPR008576. MeTrfase_NTM1.
IPR029063. SAM-dependent_MTases.
PANTHERiPTHR12753. PTHR12753. 1 hit.
PfamiView protein in Pfam
PF05891. Methyltransf_PK. 1 hit.
PIRSFiPIRSF016958. DUF858_MeTrfase_lik. 1 hit.
SUPFAMiSSF53335. SSF53335. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9BV86-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MTSEVIEDEK QFYSKAKTYW KQIPPTVDGM LGGYGHISSI DINSSRKFLQ
60 70 80 90 100
RFLREGPNKT GTSCALDCGA GIGRITKRLL LPLFREVDMV DITEDFLVQA
110 120 130 140 150
KTYLGEEGKR VRNYFCCGLQ DFTPEPDSYD VIWIQWVIGH LTDQHLAEFL
160 170 180 190 200
RRCKGSLRPN GIIVIKDNMA QEGVILDDVD SSVCRDLDVV RRIICSAGLS
210 220
LLAEERQENL PDEIYHVYSF ALR
Length:223
Mass (Da):25,387
Last modified:January 23, 2007 - v3
Checksum:i4A0EC492D9B52C49
GO
Isoform 2 (identifier: Q9BV86-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     111-223: VRNYFCCGLQ...IYHVYSFALR → ATSPISTWPSSCGAARAASAPTASSSSKTTWPRRA

Note: No experimental confirmation available.
Show »
Length:145
Mass (Da):15,896
Checksum:i4D5E90507357F03B
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti25P → L in BAF85021 (PubMed:14702039).Curated1
Sequence conflicti39S → SS in AAF14859 (PubMed:10931946).Curated1
Sequence conflicti131V → A in BAF83646 (PubMed:14702039).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_039886111 – 223VRNYF…SFALR → ATSPISTWPSSCGAARAASA PTASSSSKTTWPRRA in isoform 2. 1 PublicationAdd BLAST113

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF110776 mRNA. Translation: AAF14859.1.
AK290957 mRNA. Translation: BAF83646.1.
AK292332 mRNA. Translation: BAF85021.1.
AK298840 mRNA. Translation: BAG60968.1.
AL590369 Genomic DNA. Translation: CAI14507.1.
AL590369 Genomic DNA. Translation: CAI14508.1.
BC001396 mRNA. Translation: AAH01396.1.
BC033234 mRNA. Translation: AAH33234.1.
CCDSiCCDS35160.1. [Q9BV86-1]
CCDS69682.1. [Q9BV86-2]
RefSeqiNP_001273725.1. NM_001286796.1. [Q9BV86-1]
NP_001273726.1. NM_001286797.1. [Q9BV86-1]
NP_001273727.1. NM_001286798.1. [Q9BV86-1]
NP_001273728.1. NM_001286799.1. [Q9BV86-1]
NP_001273729.1. NM_001286800.1. [Q9BV86-2]
NP_001273730.1. NM_001286801.1. [Q9BV86-2]
NP_001273731.1. NM_001286802.1.
NP_001273732.1. NM_001286803.1.
NP_054783.2. NM_014064.3. [Q9BV86-1]
UniGeneiHs.744027.

Genome annotation databases

EnsembliENST00000372480; ENSP00000361558; ENSG00000148335. [Q9BV86-1]
ENST00000372481; ENSP00000361559; ENSG00000148335. [Q9BV86-2]
ENST00000372483; ENSP00000361561; ENSG00000148335. [Q9BV86-1]
ENST00000372486; ENSP00000361564; ENSG00000148335. [Q9BV86-1]
ENST00000611055; ENSP00000483489; ENSG00000148335. [Q9BV86-1]
ENST00000613644; ENSP00000478521; ENSG00000148335. [Q9BV86-1]
GeneIDi28989.
KEGGihsa:28989.
UCSCiuc004byd.3. human. [Q9BV86-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiNTM1A_HUMAN
AccessioniPrimary (citable) accession number: Q9BV86
Secondary accession number(s): A8K4J2
, A8K8G7, Q5SZB9, Q9UI28
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 8, 2005
Last sequence update: January 23, 2007
Last modified: September 27, 2017
This is version 150 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 9
    Human chromosome 9: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families