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Protein

Protein arginine N-methyltransferase 5

Gene

prmt-5

Organism
Caenorhabditis elegans
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the symmetrical dimethylation of arginine residues in targets such as small nuclear ribonucleoproteins, histone H2A/H4 and cbp-1 (PubMed:19521535, PubMed:23866019, PubMed:22143770). Dimethylation occurs in a distributive manner where the protein is released after the addition of the first methyl group prior to rebinding for the addition of the second methyl group (PubMed:23866019). Plays a role in the negative regulation of DNA damage-induced apoptosis (PubMed:19521535). By methylating cbp-1, may prevent apoptosis by repressing the capacity of cbp-1 to enhance cep-1 dependent transcription activation of the programmed cell death activator egl-1 (PubMed:19521535).1 Publication3 Publications

Catalytic activityi

2 S-adenosyl-L-methionine + [protein]-L-arginine = 2 S-adenosyl-L-homocysteine + [protein]-N(omega),N(omega')-dimethyl-L-arginine.1 Publication

Kineticsi

  1. KM=4.5 µM for histone H4 (at 37 degrees Celsius)1 Publication
  2. KM=22 µM for histone H4 (at 25 degrees Celsius)1 Publication
  1. Vmax=1.4 nmol/min/mg enzyme with histone H4 as substrate1 Publication

Temperature dependencei

Optimum temperature is about 25 degrees Celsius.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei356 – 3561Peptide substrateBy similarity
Binding sitei376 – 3761S-adenosyl-L-methionineBy similarity
Sitei379 – 3791Critical for specifying symmetric addition of methyl groups1 Publication
Binding sitei450 – 4501S-adenosyl-L-methionineBy similarity
Active sitei499 – 4991Proton donor/acceptor1 Publication
Active sitei508 – 5081Proton donor/acceptor1 Publication

GO - Molecular functioni

  • activating transcription factor binding Source: WormBase
  • histone methyltransferase activity (H4-R3 specific) Source: WormBase
  • p53 binding Source: WormBase
  • protein-arginine N-methyltransferase activity Source: WormBase

GO - Biological processi

  • histone arginine methylation Source: WormBase
  • histone H4-R3 methylation Source: GOC
  • intrinsic apoptotic signaling pathway in response to DNA damage Source: WormBase
  • locomotory behavior Source: WormBase
  • negative regulation of DNA damage response, signal transduction by p53 class mediator Source: WormBase
  • negative regulation of transcription, DNA-templated Source: WormBase
  • peptidyl-arginine N-methylation Source: WormBase
  • response to odorant Source: WormBase
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Methyltransferase, Transferase

Keywords - Biological processi

Apoptosis, DNA damage, Transcription, Transcription regulation

Keywords - Ligandi

S-adenosyl-L-methionine

Enzyme and pathway databases

BRENDAi2.1.1.125. 1045.
ReactomeiR-CEL-3214858. RMTs methylate histone arginines.

Names & Taxonomyi

Protein namesi
Recommended name:
Protein arginine N-methyltransferase 51 Publication (EC:2.1.1.3201 Publication)
Gene namesi
Name:prmt-5Imported
Synonyms:tag-251Imported
ORF Names:C34E10.5Imported
OrganismiCaenorhabditis elegans
Taxonomic identifieri6239 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
Proteomesi
  • UP000001940 Componenti: Chromosome III

Organism-specific databases

WormBaseiC34E10.5; CE29033; WBGene00016408; prmt-5.

Subcellular locationi

  • Nucleus 1 Publication

GO - Cellular componenti

  • nucleus Source: WormBase
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

Increased germ cell apoptosis following treatment with ionizing radiation (IR) or ethylnitrosourea and significantly enhanced IR-induced egl-1 levels.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi379 – 3791F → M: Significantly elevates methylase activity, and converts PRMT5 to an enzyme catalyzing both symmetric and asymmetric arginine dimethylation. 1 Publication
Mutagenesisi379 – 3791F → Y: Abolishes catalytic activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 734734Protein arginine N-methyltransferase 5PRO_0000212348Add
BLAST

Proteomic databases

EPDiP46580.
PaxDbiP46580.

PTM databases

iPTMnetiP46580.

Interactioni

Subunit structurei

Homodimer (PubMed:22143770). Interacts with cep-1 (via C-terminus domain); does not methylate cep-1 (PubMed:19521535). Interacts with cbp-1 (via N-terminus domain and HAT domain); the interaction results in methylation of cbp-1 (PubMed:19521535). Component of a complex that contains cep-1 and cbp-1 (PubMed:19521535).2 Publications

GO - Molecular functioni

  • activating transcription factor binding Source: WormBase
  • p53 binding Source: WormBase

Protein-protein interaction databases

BioGridi40948. 2 interactions.
DIPiDIP-25435N.
IntActiP46580. 1 interaction.
STRINGi6239.C34E10.5.3.

Structurei

Secondary structure

1
734
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi50 – 534Combined sources
Beta strandi56 – 583Combined sources
Turni61 – 666Combined sources
Helixi67 – 7610Combined sources
Beta strandi82 – 854Combined sources
Helixi89 – 924Combined sources
Helixi116 – 1216Combined sources
Beta strandi122 – 1265Combined sources
Helixi138 – 15720Combined sources
Beta strandi161 – 1666Combined sources
Helixi173 – 18513Combined sources
Beta strandi191 – 1955Combined sources
Helixi200 – 2023Combined sources
Turni208 – 2103Combined sources
Helixi216 – 22611Combined sources
Turni232 – 2343Combined sources
Beta strandi235 – 2417Combined sources
Helixi247 – 2493Combined sources
Helixi252 – 2554Combined sources
Helixi257 – 2604Combined sources
Beta strandi263 – 2708Combined sources
Turni277 – 2793Combined sources
Helixi285 – 2939Combined sources
Beta strandi301 – 3055Combined sources
Turni312 – 3143Combined sources
Helixi318 – 3269Combined sources
Turni327 – 3293Combined sources
Turni366 – 3683Combined sources
Helixi373 – 3819Combined sources
Helixi383 – 40119Combined sources
Beta strandi406 – 4149Combined sources
Helixi419 – 43517Combined sources
Beta strandi443 – 4508Combined sources
Helixi453 – 46513Combined sources
Turni466 – 4694Combined sources
Beta strandi471 – 4766Combined sources
Helixi478 – 4803Combined sources
Helixi481 – 4877Combined sources
Beta strandi494 – 4985Combined sources
Helixi506 – 5083Combined sources
Helixi510 – 5156Combined sources
Helixi516 – 5205Combined sources
Beta strandi526 – 5294Combined sources
Beta strandi531 – 54010Combined sources
Helixi542 – 5498Combined sources
Helixi555 – 5573Combined sources
Beta strandi563 – 5653Combined sources
Helixi584 – 5896Combined sources
Beta strandi593 – 5953Combined sources
Beta strandi601 – 6066Combined sources
Beta strandi608 – 6169Combined sources
Beta strandi625 – 6328Combined sources
Beta strandi635 – 65117Combined sources
Beta strandi654 – 6574Combined sources
Helixi660 – 6623Combined sources
Beta strandi673 – 68311Combined sources
Beta strandi688 – 69811Combined sources
Beta strandi701 – 71111Combined sources
Beta strandi717 – 7193Combined sources
Helixi725 – 7273Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3UA3X-ray3.00A/B1-734[»]
3UA4X-ray3.00A/B1-734[»]
ProteinModelPortaliP46580.
SMRiP46580. Positions 45-734.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini360 – 706347SAM-dependent MTase PRMT-typePROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni42 – 329288TIM barrel1 PublicationAdd
BLAST
Regioni385 – 3862S-adenosyl-L-methionine bindingBy similarity
Regioni477 – 4782S-adenosyl-L-methionine bindingBy similarity
Regioni529 – 734206Beta barrel1 PublicationAdd
BLAST
Regioni541 – 58949Dimerization1 PublicationAdd
BLAST

Sequence similaritiesi

Belongs to the class I-like SAM-binding methyltransferase superfamily. Protein arginine N-methyltransferase family.PROSITE-ProRule annotation
Contains 1 SAM-dependent MTase PRMT-type domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG0822. Eukaryota.
ENOG410XNZM. LUCA.
GeneTreeiENSGT00390000001141.
HOGENOMiHOG000022012.
InParanoidiP46580.
KOiK02516.
OMAiWFPAVIP.
OrthoDBiEOG7X6KZR.
PhylomeDBiP46580.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR025799. Arg_MeTrfase.
IPR007857. Arg_MeTrfase_PRMT5.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PANTHERiPTHR10738. PTHR10738. 2 hits.
PfamiPF05185. PRMT5. 1 hit.
[Graphical view]
SUPFAMiSSF53335. SSF53335. 1 hit.
PROSITEiPS51678. SAM_MT_PRMT. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P46580-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSNRTYADNL FPQQVAEQHE EQMSSGSSPK SNSPSRSISS VEAANSRIHI
60 70 80 90 100
GWMATTLDVA ENLDRHVATF CTRLGEFKYN FVVYPIGGVV RAFWTPNGSA
110 120 130 140 150
ENHPPVIDLP DVQLRNDLWE SYVVGKISPW IDCDSSDPAF ASLSEEHLLK
160 170 180 190 200
ELSYICYLGL QTMAIELTRI SSPRTAAILK KWIWTRNSRF TVWVQLPSAI
210 220 230 240 250
EKCKDYDAFT IEHVDLWTIW ADFRKNCGNF SGVYFQVALT ISSELPDELT
260 270 280 290 300
ELKLVDRWKA EPLAAFVIES GLFISGRNGE ASIPSAHINL LKHLWTTDAL
310 320 330 340 350
RIVLRATTDT FKYNTSIKSE YSQALRHAVR NVNYRSRPDV GEGSNDSTHY
360 370 380 390 400
LNVIEYKDVL QAPLQPLSEN LDSGVYNTFE QDQIKYDVYG EAVVGALKDL
410 420 430 440 450
GADGRKTVVI YLLGGGRGPI GTKILKSERE YNNTFRQGQE SLKVKLYIVE
460 470 480 490 500
KNPNAIVTLK YMNVRTWKRR VTIIESDMRS LPGIAKDRGF EQPDIIVSEL
510 520 530 540 550
LGSFGDNELS PECLDGVTGF LKPTTISIPQ KYTSYVKPIM STHIHQTIKA
560 570 580 590 600
QSIPYLSRAI PSHGRGEPEL DEDEMWIQKY PQGHVRNNMD QIYVVYLSKY
610 620 630 640 650
IPLAETTKPV FTFEHPNFMN SSNERSDSIE FVMDRNADLM GFAGYFDLQL
660 670 680 690 700
YKTVMLSIEP STHTPGMVSW FPAVIPLRDQ LRVGEGDRIS LKIDRKVDNT
710 720 730
GVWYEWHVEK KKTNGESVST PIQNPNGESY YMRM
Length:734
Mass (Da):83,292
Last modified:March 1, 2004 - v2
Checksum:i415AAC571206DB2C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FO080774 Genomic DNA. Translation: CCD66649.1.
PIRiT15762.
RefSeqiNP_498112.1. NM_065711.6.
UniGeneiCel.16951.

Genome annotation databases

EnsemblMetazoaiC34E10.5.1; C34E10.5.1; WBGene00016408.
C34E10.5.2; C34E10.5.2; WBGene00016408.
C34E10.5.3; C34E10.5.3; WBGene00016408.
GeneIDi175717.
KEGGicel:CELE_C34E10.5.
UCSCiC34E10.5.3. c. elegans.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FO080774 Genomic DNA. Translation: CCD66649.1.
PIRiT15762.
RefSeqiNP_498112.1. NM_065711.6.
UniGeneiCel.16951.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3UA3X-ray3.00A/B1-734[»]
3UA4X-ray3.00A/B1-734[»]
ProteinModelPortaliP46580.
SMRiP46580. Positions 45-734.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi40948. 2 interactions.
DIPiDIP-25435N.
IntActiP46580. 1 interaction.
STRINGi6239.C34E10.5.3.

PTM databases

iPTMnetiP46580.

Proteomic databases

EPDiP46580.
PaxDbiP46580.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiC34E10.5.1; C34E10.5.1; WBGene00016408.
C34E10.5.2; C34E10.5.2; WBGene00016408.
C34E10.5.3; C34E10.5.3; WBGene00016408.
GeneIDi175717.
KEGGicel:CELE_C34E10.5.
UCSCiC34E10.5.3. c. elegans.

Organism-specific databases

CTDi175717.
WormBaseiC34E10.5; CE29033; WBGene00016408; prmt-5.

Phylogenomic databases

eggNOGiKOG0822. Eukaryota.
ENOG410XNZM. LUCA.
GeneTreeiENSGT00390000001141.
HOGENOMiHOG000022012.
InParanoidiP46580.
KOiK02516.
OMAiWFPAVIP.
OrthoDBiEOG7X6KZR.
PhylomeDBiP46580.

Enzyme and pathway databases

BRENDAi2.1.1.125. 1045.
ReactomeiR-CEL-3214858. RMTs methylate histone arginines.

Miscellaneous databases

PROiP46580.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR025799. Arg_MeTrfase.
IPR007857. Arg_MeTrfase_PRMT5.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PANTHERiPTHR10738. PTHR10738. 2 hits.
PfamiPF05185. PRMT5. 1 hit.
[Graphical view]
SUPFAMiSSF53335. SSF53335. 1 hit.
PROSITEiPS51678. SAM_MT_PRMT. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Genome sequence of the nematode C. elegans: a platform for investigating biology."
    The C. elegans sequencing consortium
    Science 282:2012-2018(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Bristol N2.
  2. "Caenorhabditis elegans protein arginine methyltransferase PRMT-5 negatively regulates DNA damage-induced apoptosis."
    Yang M., Sun J., Sun X., Shen Q., Gao Z., Yang C.
    PLoS Genet. 5:E1000514-E1000514(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH CEP-1 AND CBP-1, DISRUPTION PHENOTYPE.
  3. "Substrate specificity, processivity, and kinetic mechanism of protein arginine methyltransferase 5."
    Wang M., Xu R.M., Thompson P.R.
    Biochemistry 52:5430-5440(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, CATALYTIC ACTIVITY.
  4. "Structural insights into protein arginine symmetric dimethylation by PRMT5."
    Sun L., Wang M., Lv Z., Yang N., Liu Y., Bao S., Gong W., Xu R.M.
    Proc. Natl. Acad. Sci. U.S.A. 108:20538-20543(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS), FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVE SITE, SUBUNIT, MUTAGENESIS OF PHE-379.

Entry informationi

Entry nameiANM5_CAEEL
AccessioniPrimary (citable) accession number: P46580
Secondary accession number(s): Q8T8N5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: March 1, 2004
Last modified: June 8, 2016
This is version 117 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programCaenorhabditis annotation project

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Caenorhabditis elegans
    Caenorhabditis elegans: entries, gene names and cross-references to WormBase
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.