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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)DescriptionActionsGraphical viewLength
Binding sitei356Peptide substrateBy similarity1
Binding sitei376S-adenosyl-L-methionineBy similarity1
Sitei379Critical for specifying symmetric addition of methyl groups1 Publication1
Binding sitei450S-adenosyl-L-methionineBy similarity1
Active sitei499Proton donor/acceptor1 Publication1
Active sitei508Proton donor/acceptor1 Publication1

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
  • 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 methylation, to symmetrical-dimethyl arginine Source: GO_Central
  • 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

  • cytosol Source: GO_Central
  • 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)DescriptionActionsGraphical viewLength
Mutagenesisi379F → M: Significantly elevates methylase activity, and converts PRMT5 to an enzyme catalyzing both symmetric and asymmetric arginine dimethylation. 1 Publication1
Mutagenesisi379F → Y: Abolishes catalytic activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002123481 – 734Protein arginine N-methyltransferase 5Add BLAST734

Proteomic databases

EPDiP46580.
PaxDbiP46580.
PeptideAtlasiP46580.
PRIDEiP46580.

PTM databases

iPTMnetiP46580.

Expressioni

Gene expression databases

BgeeiWBGene00016408.

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 interactors.
DIPiDIP-25435N.
IntActiP46580. 1 interactor.
STRINGi6239.C34E10.5.3.

Structurei

Secondary structure

1734
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi50 – 53Combined sources4
Beta strandi56 – 58Combined sources3
Turni61 – 66Combined sources6
Helixi67 – 76Combined sources10
Beta strandi82 – 85Combined sources4
Helixi89 – 92Combined sources4
Helixi116 – 121Combined sources6
Beta strandi122 – 126Combined sources5
Helixi138 – 157Combined sources20
Beta strandi161 – 166Combined sources6
Helixi173 – 185Combined sources13
Beta strandi191 – 195Combined sources5
Helixi200 – 202Combined sources3
Turni208 – 210Combined sources3
Helixi216 – 226Combined sources11
Turni232 – 234Combined sources3
Beta strandi235 – 241Combined sources7
Helixi247 – 249Combined sources3
Helixi252 – 255Combined sources4
Helixi257 – 260Combined sources4
Beta strandi263 – 270Combined sources8
Turni277 – 279Combined sources3
Helixi285 – 293Combined sources9
Beta strandi301 – 305Combined sources5
Turni312 – 314Combined sources3
Helixi318 – 326Combined sources9
Turni327 – 329Combined sources3
Turni366 – 368Combined sources3
Helixi373 – 381Combined sources9
Helixi383 – 401Combined sources19
Beta strandi406 – 414Combined sources9
Helixi419 – 435Combined sources17
Beta strandi443 – 450Combined sources8
Helixi453 – 465Combined sources13
Turni466 – 469Combined sources4
Beta strandi471 – 476Combined sources6
Helixi478 – 480Combined sources3
Helixi481 – 487Combined sources7
Beta strandi494 – 498Combined sources5
Helixi506 – 508Combined sources3
Helixi510 – 515Combined sources6
Helixi516 – 520Combined sources5
Beta strandi526 – 529Combined sources4
Beta strandi531 – 540Combined sources10
Helixi542 – 549Combined sources8
Helixi555 – 557Combined sources3
Beta strandi563 – 565Combined sources3
Helixi584 – 589Combined sources6
Beta strandi593 – 595Combined sources3
Beta strandi601 – 606Combined sources6
Beta strandi608 – 616Combined sources9
Beta strandi625 – 632Combined sources8
Beta strandi635 – 651Combined sources17
Beta strandi654 – 657Combined sources4
Helixi660 – 662Combined sources3
Beta strandi673 – 683Combined sources11
Beta strandi688 – 698Combined sources11
Beta strandi701 – 711Combined sources11
Beta strandi717 – 719Combined sources3
Helixi725 – 727Combined sources3

3D structure databases

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

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini360 – 706SAM-dependent MTase PRMT-typePROSITE-ProRule annotationAdd BLAST347

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni42 – 329TIM barrel1 PublicationAdd BLAST288
Regioni385 – 386S-adenosyl-L-methionine bindingBy similarity2
Regioni477 – 478S-adenosyl-L-methionine bindingBy similarity2
Regioni529 – 734Beta barrel1 PublicationAdd BLAST206
Regioni541 – 589Dimerization1 PublicationAdd BLAST49

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.
OMAiRLAFPTQ.
OrthoDBiEOG091G03PD.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3UA3X-ray3.00A/B1-734[»]
3UA4X-ray3.00A/B1-734[»]
ProteinModelPortaliP46580.
SMRiP46580.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi40948. 2 interactors.
DIPiDIP-25435N.
IntActiP46580. 1 interactor.
STRINGi6239.C34E10.5.3.

PTM databases

iPTMnetiP46580.

Proteomic databases

EPDiP46580.
PaxDbiP46580.
PeptideAtlasiP46580.
PRIDEiP46580.

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.
OMAiRLAFPTQ.
OrthoDBiEOG091G03PD.
PhylomeDBiP46580.

Enzyme and pathway databases

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

Miscellaneous databases

PROiP46580.

Gene expression databases

BgeeiWBGene00016408.

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...

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: November 2, 2016
This is version 121 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.