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Histone-lysine N-methyltransferase, H3 lysine-9 specific dim-5 (EC 2.1.1.43) (Histone H3-K9 methyltransferase dim-5) (H3-K9-HMTase dim-5) (HKMT)

 DIM5_NEUCR              Reviewed;         331 AA.
Q8X225; Q1K5Y7;
01-FEB-2005, integrated into UniProtKB/Swiss-Prot.
04-DEC-2007, sequence version 2.
08-MAY-2019, entry version 112.
RecName: Full=Histone-lysine N-methyltransferase, H3 lysine-9 specific dim-5;
EC=2.1.1.43;
AltName: Full=Histone H3-K9 methyltransferase dim-5;
Short=H3-K9-HMTase dim-5;
Short=HKMT;
Name=dim-5; ORFNames=29E8.110, NCU04402;
Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM
1257 / FGSC 987).
Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina;
Sordariomycetes; Sordariomycetidae; Sordariales; Sordariaceae;
Neurospora.
NCBI_TaxID=367110;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
STRAIN=ATCC 18889 / 74-OR8-1a / 40-21 / DSM 1258 / FGSC 988;
PubMed=11713521; DOI=10.1038/35104508;
Tamaru H., Selker E.U.;
"A histone H3 methyltransferase controls DNA methylation in Neurospora
crassa.";
Nature 414:277-283(2001).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987;
PubMed=12655011; DOI=10.1093/nar/gkg293;
Mannhaupt G., Montrone C., Haase D., Mewes H.-W., Aign V.,
Hoheisel J.D., Fartmann B., Nyakatura G., Kempken F., Maier J.,
Schulte U.;
"What's in the genome of a filamentous fungus? Analysis of the
Neurospora genome sequence.";
Nucleic Acids Res. 31:1944-1954(2003).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987;
PubMed=12712197; DOI=10.1038/nature01554;
Galagan J.E., Calvo S.E., Borkovich K.A., Selker E.U., Read N.D.,
Jaffe D.B., FitzHugh W., Ma L.-J., Smirnov S., Purcell S., Rehman B.,
Elkins T., Engels R., Wang S., Nielsen C.B., Butler J., Endrizzi M.,
Qui D., Ianakiev P., Bell-Pedersen D., Nelson M.A.,
Werner-Washburne M., Selitrennikoff C.P., Kinsey J.A., Braun E.L.,
Zelter A., Schulte U., Kothe G.O., Jedd G., Mewes H.-W., Staben C.,
Marcotte E., Greenberg D., Roy A., Foley K., Naylor J.,
Stange-Thomann N., Barrett R., Gnerre S., Kamal M., Kamvysselis M.,
Mauceli E.W., Bielke C., Rudd S., Frishman D., Krystofova S.,
Rasmussen C., Metzenberg R.L., Perkins D.D., Kroken S., Cogoni C.,
Macino G., Catcheside D.E.A., Li W., Pratt R.J., Osmani S.A.,
DeSouza C.P.C., Glass N.L., Orbach M.J., Berglund J.A., Voelker R.,
Yarden O., Plamann M., Seiler S., Dunlap J.C., Radford A., Aramayo R.,
Natvig D.O., Alex L.A., Mannhaupt G., Ebbole D.J., Freitag M.,
Paulsen I., Sachs M.S., Lander E.S., Nusbaum C., Birren B.W.;
"The genome sequence of the filamentous fungus Neurospora crassa.";
Nature 422:859-868(2003).
[4]
FUNCTION, AND METHYLATION OF HISTONE H3.
PubMed=12679815; DOI=10.1038/ng1143;
Tamaru H., Zhang X., McMillen D., Singh P.B., Nakayama J.,
Grewal S.I., Allis C.D., Cheng X., Selker E.U.;
"Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in
Neurospora crassa.";
Nat. Genet. 34:75-79(2003).
[5]
X-RAY CRYSTALLOGRAPHY (1.98 ANGSTROMS) OF 30-331 IN COMPLEX WITH ZINC
IONS, FUNCTION, CATALYTIC ACTIVITY, AND MUTAGENESIS OF ARG-251;
ASN-254; HIS-255 AND TYR-296.
PubMed=12372305; DOI=10.1016/S0092-8674(02)00999-6;
Zhang X., Tamaru H., Khan S.I., Horton J.R., Keefe L.J., Selker E.U.,
Cheng X.;
"Structure of the Neurospora SET domain protein DIM-5, a histone H3
lysine methyltransferase.";
Cell 111:117-127(2002).
[6]
X-RAY CRYSTALLOGRAPHY (2.59 ANGSTROMS) OF 30-331 IN COMPLEX WITH
HISTONE H3; S-ADENOSYL-L-HOMOCYSTEINE AND ZINC IONS, FUNCTION,
CATALYTIC ACTIVITY, AND MUTAGENESIS OF TYR-191; ASP-222; PHE-294;
LEU-330 AND TRP-331.
PubMed=12887903; DOI=10.1016/S1097-2765(03)00224-7;
Zhang X., Yang Z., Khan S.I., Horton J.R., Tamaru H., Selker E.U.,
Cheng X.;
"Structural basis for the product specificity of histone lysine
methyltransferases.";
Mol. Cell 12:177-185(2003).
-!- FUNCTION: Histone methyltransferase that specifically
trimethylates histone H3 to form H3K9me3. H3K9me3 marks chromatin
regions for DNA methylation. {ECO:0000269|PubMed:11713521,
ECO:0000269|PubMed:12372305, ECO:0000269|PubMed:12679815,
ECO:0000269|PubMed:12887903}.
-!- CATALYTIC ACTIVITY:
Reaction=L-lysyl-[histone] + S-adenosyl-L-methionine = H(+) +
N(6)-methyl-L-lysyl-[histone] + S-adenosyl-L-homocysteine;
Xref=Rhea:RHEA:10024, Rhea:RHEA-COMP:9845, Rhea:RHEA-COMP:9846,
ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856,
ChEBI:CHEBI:59789, ChEBI:CHEBI:61929; EC=2.1.1.43;
Evidence={ECO:0000269|PubMed:12372305,
ECO:0000269|PubMed:12887903};
-!- INTERACTION:
Q96UA9:9G6.050 (xeno); NbExp=2; IntAct=EBI-1268994, EBI-15849296;
P07041:hh3; NbExp=2; IntAct=EBI-1268994, EBI-1270655;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}. Chromosome
{ECO:0000250}.
-!- DOMAIN: In the pre-SET domain, Cys residues bind 3 zinc ions that
are arranged in a triangular cluster; some of these Cys residues
contribute to the binding of two zinc ions within the cluster.
{ECO:0000269|PubMed:12372305}.
-!- SIMILARITY: Belongs to the class V-like SAM-binding
methyltransferase superfamily. Histone-lysine methyltransferase
family. Suvar3-9 subfamily. {ECO:0000255|PROSITE-
ProRule:PRU00190}.
-!- SEQUENCE CAUTION:
Sequence=AAL35215.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
Sequence=CAF06044.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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EMBL; AF419248; AAL35215.1; ALT_SEQ; Genomic_DNA.
EMBL; BX908809; CAF06044.1; ALT_SEQ; Genomic_DNA.
EMBL; CM002239; EAA28243.2; -; Genomic_DNA.
RefSeq; XP_957479.2; XM_952386.3.
PDB; 1ML9; X-ray; 1.98 A; A=30-331.
PDB; 1PEG; X-ray; 2.59 A; A/B=30-331.
PDBsum; 1ML9; -.
PDBsum; 1PEG; -.
SMR; Q8X225; -.
DIP; DIP-39600N; -.
IntAct; Q8X225; 2.
ChEMBL; CHEMBL3309062; -.
PRIDE; Q8X225; -.
EnsemblFungi; EAA28243; EAA28243; NCU04402.
GeneID; 3873656; -.
KEGG; ncr:NCU04402; -.
EuPathDB; FungiDB:NCU04402; -.
InParanoid; Q8X225; -.
KO; K11419; -.
OMA; KRIRVEC; -.
EvolutionaryTrace; Q8X225; -.
Proteomes; UP000001805; Chromosome 4, Linkage Group IV.
GO; GO:0005694; C:chromosome; IEA:UniProtKB-SubCell.
GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
GO; GO:0018024; F:histone-lysine N-methyltransferase activity; IEA:UniProtKB-EC.
GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
InterPro; IPR003616; Post-SET_dom.
InterPro; IPR007728; Pre-SET_dom.
InterPro; IPR001214; SET_dom.
Pfam; PF05033; Pre-SET; 1.
Pfam; PF00856; SET; 1.
SMART; SM00468; PreSET; 1.
SMART; SM00317; SET; 1.
PROSITE; PS50868; POST_SET; 1.
PROSITE; PS50867; PRE_SET; 1.
PROSITE; PS50280; SET; 1.
1: Evidence at protein level;
3D-structure; Chromosome; Complete proteome; Metal-binding;
Methyltransferase; Nucleus; Reference proteome;
S-adenosyl-L-methionine; Transferase; Zinc.
CHAIN 1 331 Histone-lysine N-methyltransferase, H3
lysine-9 specific dim-5.
/FTId=PRO_0000186062.
DOMAIN 77 159 Pre-SET. {ECO:0000255|PROSITE-
ProRule:PRU00157}.
DOMAIN 162 297 SET. {ECO:0000255|PROSITE-
ProRule:PRU00190}.
DOMAIN 315 331 Post-SET. {ECO:0000255|PROSITE-
ProRule:PRU00155}.
REGION 172 174 S-adenosyl-L-methionine binding.
REGION 254 255 S-adenosyl-L-methionine binding.
METAL 79 79 Zinc 1.
METAL 79 79 Zinc 2.
METAL 81 81 Zinc 1.
METAL 87 87 Zinc 1.
METAL 87 87 Zinc 3.
METAL 92 92 Zinc 1.
METAL 94 94 Zinc 2.
METAL 141 141 Zinc 2.
METAL 141 141 Zinc 3.
METAL 145 145 Zinc 2.
METAL 147 147 Zinc 3.
METAL 151 151 Zinc 3.
METAL 257 257 Zinc 4.
METAL 319 319 Zinc 4.
METAL 321 321 Zinc 4.
METAL 326 326 Zinc 4.
BINDING 215 215 S-adenosyl-L-methionine.
BINDING 217 217 S-adenosyl-L-methionine.
BINDING 251 251 S-adenosyl-L-methionine.
MUTAGEN 191 191 Y->F: Reduces enzyme activity by 97%.
{ECO:0000269|PubMed:12887903}.
MUTAGEN 191 191 Y->V: Reduces enzyme activity by over
99%. {ECO:0000269|PubMed:12887903}.
MUTAGEN 222 222 D->E: Reduces enzyme activity by over
99%. {ECO:0000269|PubMed:12887903}.
MUTAGEN 222 222 D->K: Reduces enzyme activity by 97%.
{ECO:0000269|PubMed:12887903}.
MUTAGEN 222 222 D->Q: Reduces enzyme activity by 97%.
{ECO:0000269|PubMed:12887903}.
MUTAGEN 251 251 R->H: Reduces enzyme activity by over
99%. {ECO:0000269|PubMed:12372305}.
MUTAGEN 254 254 N->Q: Reduces enzyme activity by over
99%. {ECO:0000269|PubMed:12372305}.
MUTAGEN 255 255 H->K: Reduces enzyme activity by over
99%. {ECO:0000269|PubMed:12372305}.
MUTAGEN 294 294 F->W: Reduces enzyme activity by over
99%. {ECO:0000269|PubMed:12887903}.
MUTAGEN 294 294 F->Y: Reduces enzyme activity by 20%.
{ECO:0000269|PubMed:12887903}.
MUTAGEN 296 296 Y->F: Reduces enzyme activity by over
99%. {ECO:0000269|PubMed:12372305}.
MUTAGEN 330 330 L->A: Reduces enzyme activity by over
99%. {ECO:0000269|PubMed:12887903}.
MUTAGEN 331 331 W->A: Reduces enzyme activity by 97%.
{ECO:0000269|PubMed:12887903}.
STRAND 41 44 {ECO:0000244|PDB:1ML9}.
STRAND 46 49 {ECO:0000244|PDB:1ML9}.
HELIX 73 75 {ECO:0000244|PDB:1ML9}.
HELIX 86 88 {ECO:0000244|PDB:1ML9}.
HELIX 93 95 {ECO:0000244|PDB:1ML9}.
STRAND 96 98 {ECO:0000244|PDB:1PEG}.
STRAND 115 118 {ECO:0000244|PDB:1ML9}.
STRAND 119 121 {ECO:0000244|PDB:1PEG}.
TURN 122 125 {ECO:0000244|PDB:1PEG}.
HELIX 129 134 {ECO:0000244|PDB:1ML9}.
HELIX 155 158 {ECO:0000244|PDB:1ML9}.
STRAND 164 168 {ECO:0000244|PDB:1ML9}.
STRAND 170 172 {ECO:0000244|PDB:1ML9}.
STRAND 174 177 {ECO:0000244|PDB:1ML9}.
STRAND 187 190 {ECO:0000244|PDB:1ML9}.
STRAND 194 196 {ECO:0000244|PDB:1ML9}.
HELIX 198 207 {ECO:0000244|PDB:1ML9}.
HELIX 210 212 {ECO:0000244|PDB:1ML9}.
HELIX 214 217 {ECO:0000244|PDB:1ML9}.
STRAND 218 220 {ECO:0000244|PDB:1ML9}.
STRAND 227 230 {ECO:0000244|PDB:1ML9}.
HELIX 232 235 {ECO:0000244|PDB:1ML9}.
STRAND 240 242 {ECO:0000244|PDB:1ML9}.
STRAND 244 247 {ECO:0000244|PDB:1ML9}.
HELIX 249 252 {ECO:0000244|PDB:1ML9}.
STRAND 260 269 {ECO:0000244|PDB:1ML9}.
HELIX 270 275 {ECO:0000244|PDB:1ML9}.
STRAND 277 284 {ECO:0000244|PDB:1ML9}.
STRAND 291 294 {ECO:0000244|PDB:1ML9}.
SEQUENCE 331 AA; 37572 MW; 2C97AB4B5E582D88 CRC64;
MEKAFRPHFF NHGKPDANPK EKKNCHWCQI RSFATHAQLP ISIVNREDDA FLNPNFRFID
HSIIGKNVPV ADQSFRVGCS CASDEECMYS TCQCLDEMAP DSDEEADPYT RKKRFAYYSQ
GAKKGLLRDR VLQSQEPIYE CHQGCACSKD CPNRVVERGR TVPLQIFRTK DRGWGVKCPV
NIKRGQFVDR YLGEIITSEE ADRRRAESTI ARRKDVYLFA LDKFSDPDSL DPLLAGQPLE
VDGEYMSGPT RFINHSCDPN MAIFARVGDH ADKHIHDLAL FAIKDIPKGT ELTFDYVNGL
TGLESDAHDP SKISEMTKCL CGTAKCRGYL W


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