ZCHC4_MOUSE
ID ZCHC4_MOUSE Reviewed; 512 AA.
AC Q8BKW4; Q3UTX6; Q9D2I1;
DT 31-AUG-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 125.
DE RecName: Full=rRNA N6-adenosine-methyltransferase ZCCHC4 {ECO:0000305};
DE EC=2.1.1.- {ECO:0000250|UniProtKB:Q9H5U6};
DE AltName: Full=Zinc finger CCHC domain-containing protein 4 {ECO:0000305};
GN Name=Zcchc4 {ECO:0000312|MGI:MGI:1926046};
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
RC STRAIN=C57BL/6J; TISSUE=Aorta, and Vein;
RX PubMed=16141072; DOI=10.1126/science.1112014;
RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT "The transcriptional landscape of the mammalian genome.";
RL Science 309:1559-1563(2005).
CC -!- FUNCTION: rRNA N6-methyltransferase that specifically methylates the
CC adenine in position 4220 of 28S rRNA. N6-methylation of adenine(4220)
CC in 28S rRNA is required for translation.
CC {ECO:0000250|UniProtKB:Q9H5U6}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=adenosine(4220) in 28S rRNA + S-adenosyl-L-methionine = H(+) +
CC N(6)-methyladenosine(4220) in 28S rRNA + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:58724, Rhea:RHEA-COMP:16142, Rhea:RHEA-COMP:16143,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74411, ChEBI:CHEBI:74449;
CC Evidence={ECO:0000250|UniProtKB:Q9H5U6};
CC -!- SUBUNIT: Interacts with components of the ASC-1 complex TRIP4, ASCC1,
CC ASCC2 and ASCC3. Interact with AHCYL1 and AHCYL2. Interact with YTHDC2.
CC {ECO:0000250|UniProtKB:Q9H5U6}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:Q9H5U6}.
CC Nucleus, nucleolus {ECO:0000250|UniProtKB:Q9H5U6}. Note=Accumulates in
CC the nucleolus, where ribosome biogenesis takes place.
CC {ECO:0000250|UniProtKB:Q9H5U6}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q8BKW4-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8BKW4-2; Sequence=VSP_017013;
CC -!- DOMAIN: The regulatory loop blocks the catalytic center by bridging the
CC methyltransferase domain and the C-terminal CCHC-type zinc finger,
CC resulting in an autoinhibitory conformation.
CC {ECO:0000250|UniProtKB:Q9H5U6}.
CC -!- SIMILARITY: Belongs to the ZCCHC4 family. {ECO:0000305}.
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DR EMBL; AK019621; BAB31816.1; -; mRNA.
DR EMBL; AK049511; BAC33785.1; -; mRNA.
DR EMBL; AK138997; BAE23854.1; -; mRNA.
DR CCDS; CCDS39087.1; -. [Q8BKW4-1]
DR CCDS; CCDS80282.1; -. [Q8BKW4-2]
DR RefSeq; NP_001295073.1; NM_001308144.1. [Q8BKW4-2]
DR RefSeq; NP_001296374.1; NM_001309445.1.
DR RefSeq; NP_084461.1; NM_030185.3. [Q8BKW4-1]
DR AlphaFoldDB; Q8BKW4; -.
DR SMR; Q8BKW4; -.
DR BioGRID; 219639; 1.
DR STRING; 10090.ENSMUSP00000031077; -.
DR PhosphoSitePlus; Q8BKW4; -.
DR EPD; Q8BKW4; -.
DR MaxQB; Q8BKW4; -.
DR PaxDb; Q8BKW4; -.
DR PeptideAtlas; Q8BKW4; -.
DR PRIDE; Q8BKW4; -.
DR ProteomicsDB; 275058; -. [Q8BKW4-1]
DR ProteomicsDB; 275059; -. [Q8BKW4-2]
DR Antibodypedia; 23199; 83 antibodies from 14 providers.
DR Ensembl; ENSMUST00000031077; ENSMUSP00000031077; ENSMUSG00000029179. [Q8BKW4-1]
DR Ensembl; ENSMUST00000113904; ENSMUSP00000109537; ENSMUSG00000029179. [Q8BKW4-2]
DR GeneID; 78796; -.
DR KEGG; mmu:78796; -.
DR UCSC; uc008xku.1; mouse. [Q8BKW4-1]
DR UCSC; uc008xkv.1; mouse. [Q8BKW4-2]
DR CTD; 29063; -.
DR MGI; MGI:1926046; Zcchc4.
DR VEuPathDB; HostDB:ENSMUSG00000029179; -.
DR eggNOG; KOG4399; Eukaryota.
DR GeneTree; ENSGT00390000012556; -.
DR HOGENOM; CLU_034589_0_0_1; -.
DR InParanoid; Q8BKW4; -.
DR OMA; EFCLYNM; -.
DR OrthoDB; 709190at2759; -.
DR PhylomeDB; Q8BKW4; -.
DR TreeFam; TF313872; -.
DR BioGRID-ORCS; 78796; 3 hits in 68 CRISPR screens.
DR ChiTaRS; Zcchc4; mouse.
DR PRO; PR:Q8BKW4; -.
DR Proteomes; UP000000589; Chromosome 5.
DR RNAct; Q8BKW4; protein.
DR Bgee; ENSMUSG00000029179; Expressed in ectoplacental cone and 184 other tissues.
DR ExpressionAtlas; Q8BKW4; baseline and differential.
DR Genevisible; Q8BKW4; MM.
DR GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR GO; GO:0005730; C:nucleolus; ISS:UniProtKB.
DR GO; GO:0003676; F:nucleic acid binding; IEA:InterPro.
DR GO; GO:0008988; F:rRNA (adenine-N6-)-methyltransferase activity; ISS:UniProtKB.
DR GO; GO:1904047; F:S-adenosyl-L-methionine binding; ISS:UniProtKB.
DR GO; GO:0008270; F:zinc ion binding; ISS:UniProtKB.
DR GO; GO:0045727; P:positive regulation of translation; ISS:UniProtKB.
DR GO; GO:0031167; P:rRNA methylation; ISS:UniProtKB.
DR InterPro; IPR002052; DNA_methylase_N6_adenine_CS.
DR InterPro; IPR041370; Mlase_EEF1AKMT1/ZCCHC4.
DR InterPro; IPR039846; ZCCHC4.
DR InterPro; IPR010666; Znf_GRF.
DR PANTHER; PTHR13493; PTHR13493; 1.
DR Pfam; PF10237; N6-adenineMlase; 1.
DR Pfam; PF06839; zf-GRF; 1.
DR PROSITE; PS50216; DHHC; 1.
DR PROSITE; PS00092; N6_MTASE; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Cytoplasm; Metal-binding; Methyltransferase; Nucleus;
KW Reference proteome; S-adenosyl-L-methionine; Transferase; Zinc;
KW Zinc-finger.
FT CHAIN 1..512
FT /note="rRNA N6-adenosine-methyltransferase ZCCHC4"
FT /id="PRO_0000150953"
FT DOMAIN 393..445
FT /note="DHHC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00067"
FT ZN_FING 37..81
FT /note="GRF-type"
FT /evidence="ECO:0000255"
FT ZN_FING 441..458
FT /note="CCHC-type"
FT REGION 335..355
FT /note="Regulatory loop"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 39
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 41
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 63
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 72
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 124
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 127
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 139
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 142
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 171..174
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 201
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 223
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 241..242
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 274
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 378
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 381
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 391
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 392
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="4"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 395
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="4"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 398
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 408
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="4"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 409
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="5"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 412
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="5"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 415
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="4"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 422
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="5"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 423
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="6"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 426
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="6"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 429
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="5"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 434
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="6"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT BINDING 436
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="6"
FT /evidence="ECO:0000250|UniProtKB:Q9H5U6"
FT VAR_SEQ 468..512
FT /note="LVEFFGFLEKRLLMSSFLGAIYRSTKLSEDSEFFRVLNRSSHHYV -> AVR
FT KQKQRKRNKIRREALKDNP (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:16141072"
FT /id="VSP_017013"
SQ SEQUENCE 512 AA; 58567 MW; 8BBE0912790005C8 CRC64;
MAAPMDCLES LEGDGDAGRR ASGVEVALPS NPTAPAPLCP HGPTLLFVKV NQGKEETRKF
YACSACRDRK DCNFFQWEDE KLSEARLAAR EIHNQKCQPP LSRAQCIERY LSFIQLPLAQ
RKFCQSCQQL LLPADWREHG THQLSADISV AQLGRPSQLL YPLENKKTHA QYLFADRSCQ
FLAGLLATLG FSRVLCVGAP RLHEQIRLTA SGERSGMRSL LLDIDFRYSQ FYLEGSFCRY
NMFNHHFFDG KAALEVCKEF LQEEEGKGVI MVTDPPFGGL VEPLAITFKK LIAMWKEGQS
QDDSHKELPI FWIFPYFFES RICQFFPSFC MLDYQVDYDN HALYKHGKTG RKQSPVRIFT
NVPPNKIILP SEEGYRFCSL CQRYVSRENQ HCVHCNSCTS KDGRKWSHCF LCKKCVKPSW
IHCNTCNRCA LPDHSCLGPK DGCFICGALD HKRSNCPNIG TSWRANKLVE FFGFLEKRLL
MSSFLGAIYR STKLSEDSEF FRVLNRSSHH YV
