ZCHC4_RAT
ID ZCHC4_RAT Reviewed; 489 AA.
AC D3ZV31;
DT 16-MAY-2012, integrated into UniProtKB/Swiss-Prot.
DT 20-APR-2010, sequence version 1.
DT 03-AUG-2022, entry version 56.
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|RGD:1311414};
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Brown Norway;
RX PubMed=15057822; DOI=10.1038/nature02426;
RA Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J.,
RA Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G.,
RA Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G.,
RA Morgan M., Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G.,
RA Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S.,
RA Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T.,
RA Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D.,
RA Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L.,
RA Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D.,
RA Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M.,
RA Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C.,
RA Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J.,
RA Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H.,
RA Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X.,
RA Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q.,
RA Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P.,
RA Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A.,
RA Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C.,
RA Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J.,
RA Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J.,
RA Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F.,
RA Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A.,
RA Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A.,
RA Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J.,
RA Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E.,
RA Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M.,
RA Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C.,
RA Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L.,
RA Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W.,
RA Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y.,
RA Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V.,
RA Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M.,
RA Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S.,
RA Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B.,
RA Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R.,
RA Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J.,
RA Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D.,
RA Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S.,
RA Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S.,
RA Mockrin S., Collins F.S.;
RT "Genome sequence of the Brown Norway rat yields insights into mammalian
RT evolution.";
RL Nature 428:493-521(2004).
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 -!- 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 RefSeq; XP_017454783.1; XM_017599294.1.
DR AlphaFoldDB; D3ZV31; -.
DR SMR; D3ZV31; -.
DR STRING; 10116.ENSRNOP00000051233; -.
DR PaxDb; D3ZV31; -.
DR PRIDE; D3ZV31; -.
DR Ensembl; ENSRNOT00000042757; ENSRNOP00000051233; ENSRNOG00000029064.
DR GeneID; 360946; -.
DR CTD; 29063; -.
DR RGD; 1311414; Zcchc4.
DR eggNOG; KOG4399; Eukaryota.
DR InParanoid; D3ZV31; -.
DR OrthoDB; 709190at2759; -.
DR PhylomeDB; D3ZV31; -.
DR TreeFam; TF313872; -.
DR PRO; PR:D3ZV31; -.
DR Proteomes; UP000002494; Chromosome 14.
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 3: Inferred from homology;
KW Cytoplasm; Metal-binding; Methyltransferase; Nucleus; Reference proteome;
KW S-adenosyl-L-methionine; Transferase; Zinc; Zinc-finger.
FT CHAIN 1..489
FT /note="rRNA N6-adenosine-methyltransferase ZCCHC4"
FT /id="PRO_0000417069"
FT DOMAIN 393..443
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 REGION 467..489
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
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"
SQ SEQUENCE 489 AA; 56027 MW; 18BE71D07634CD02 CRC64;
MAAPMDCLES LEGEGSVGRR ASGVEVALPS NPGAPAPQCP HGPTLLFVKV SQGKEEPRKF
YACSACRDRK DCNFFQWEDE KLSEARLAAR EIHNQRCQPP LSRAQCIERY LSFIQLPLTQ
RKFCRSCQQL LLPADWREHG EHQLSADIST TQIARPSQLL YPLENKKTHA QYLFADRSCQ
FLAGLLATLG FRRVLCVGAP RLHEQIRLTA PGEKPDMRSL LLDIDFRYSQ FYLEESFCRY
NMFNHHFFDG KAALEVCKAF LQEEEGKGVI MVTDPPFGGL VEPLAVTFKK LIAMWKEGQS
QDDSHKELPI FWIFPYFFES RICQFFPSFC MLDYQVDYDN HALYKHGKTG RKQSPVRIFT
NIPPNKIILP SEEGYRFCSV CQRYVSRENQ HCVHCNSCTS KDGRKWSHCF FCKKCVKPSW
IHCNTCNRCA LPDHSCLGPK DGCFICGSLD HKRSNCPSIG ASQRANNAVR KQKQRKSNKI
RREALKDNP
