RNZ1_ARATH
ID RNZ1_ARATH Reviewed; 280 AA.
AC Q8LGU7; Q9CA48; Q9SSF6;
DT 16-JAN-2004, integrated into UniProtKB/Swiss-Prot.
DT 21-FEB-2006, sequence version 3.
DT 03-AUG-2022, entry version 117.
DE RecName: Full=tRNase Z TRZ1 {ECO:0000303|PubMed:16336119};
DE EC=3.1.26.11 {ECO:0000269|PubMed:16118225};
DE AltName: Full=Nuclear ribonuclease Z {ECO:0000303|PubMed:12032089};
DE Short=Nuclear RNase Z {ECO:0000303|PubMed:12032089};
DE AltName: Full=Short tRNase Z 1 {ECO:0000303|PubMed:16336119};
DE AltName: Full=Zinc phosphodiesterase NUZ {ECO:0000303|PubMed:12032089};
DE AltName: Full=tRNA 3 endonuclease;
DE AltName: Full=tRNase ZS1 {ECO:0000303|PubMed:16336119};
DE Short=AthTRZS1 {ECO:0000303|PubMed:16336119};
GN Name=TRZ1 {ECO:0000303|PubMed:16336119};
GN Synonyms=NUZ {ECO:0000303|PubMed:12032089};
GN OrderedLocusNames=At1g74700 {ECO:0000312|Araport:AT1G74700};
GN ORFNames=F1M20.38 {ECO:0000312|EMBL:AAG52354.1},
GN F25A4.32 {ECO:0000312|EMBL:AAD55271.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, AND HOMODIMERIZATION.
RC STRAIN=cv. Columbia; TISSUE=Leaf;
RX PubMed=12032089; DOI=10.1093/emboj/21.11.2769;
RA Schiffer S., Roesch S., Marchfelder A.;
RT "Assigning a function to a conserved group of proteins: the tRNA 3'
RT - processing enzymes.";
RL EMBO J. 21:2769-2777(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=16336119; DOI=10.1515/bc.2005.142;
RA Vogel A., Schilling O., Spaeth B., Marchfelder A.;
RT "The tRNase Z family of proteins: physiological functions, substrate
RT specificity and structural properties.";
RL Biol. Chem. 386:1253-1264(2005).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, COFACTOR, DOMAIN, AND MUTAGENESIS OF
RP CYS-25; CYS-40; 51-PHE--ILE-60; PHE-51; HIS-54; HIS-56; ASP-58; HIS-59;
RP GLY-62; PRO-64; PRO-83; HIS-133; TYR-140; PRO-178; GLY-184; ASP-185;
RP THR-186; LYS-203; LEU-205; GLU-208; THR-210; HIS-226; HIS-248; ARG-252;
RP TYR-253 AND 270-GLU--PHE-280.
RX PubMed=16118225; DOI=10.1074/jbc.m506418200;
RA Spaeth B., Kirchner S., Vogel A., Schubert S., Meinlschmidt P., Aymanns S.,
RA Nezzar J., Marchfelder A.;
RT "Analysis of the functional modules of the tRNA 3' endonuclease (tRNase
RT Z).";
RL J. Biol. Chem. 280:35440-35447(2005).
RN [6]
RP FUNCTION, SUBSTRATE SPECIFICITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES,
RP AND 3D-STRUCTURE MODELING.
RX PubMed=18052196; DOI=10.1021/bi7010459;
RA Spaeth B., Settele F., Schilling O., D'Angelo I., Vogel A., Feldmann I.,
RA Meyer-Klaucke W., Marchfelder A.;
RT "Metal requirements and phosphodiesterase activity of tRNase Z enzymes.";
RL Biochemistry 46:14742-14750(2007).
RN [7]
RP FUNCTION, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX PubMed=19411372; DOI=10.1104/pp.109.137950;
RA Canino G., Bocian E., Barbezier N., Echeverria M., Forner J., Binder S.,
RA Marchfelder A.;
RT "Arabidopsis encodes four tRNase Z enzymes.";
RL Plant Physiol. 150:1494-1502(2009).
RN [8]
RP FUNCTION.
RX PubMed=19420328; DOI=10.1104/pp.109.137968;
RA Barbezier N., Canino G., Rodor J., Jobet E., Saez-Vasquez J.,
RA Marchfelder A., Echeverria M.;
RT "Processing of a dicistronic tRNA-snoRNA precursor: combined analysis in
RT vitro and in vivo reveals alternate pathways and coupling to assembly of
RT snoRNP.";
RL Plant Physiol. 150:1598-1610(2009).
CC -!- FUNCTION: Zinc phosphodiesterase, which displays tRNA 3'-processing
CC endonuclease activity (PubMed:12032089, PubMed:16118225,
CC PubMed:18052196, PubMed:19411372). Involved in tRNA maturation, by
CC removing a 3'-trailer from precursor tRNA (PubMed:12032089,
CC PubMed:18052196, PubMed:19411372). Can use bis-(p-nitophenyl) phosphate
CC (bpNPP) as substrate (PubMed:18052196). Involved in the processing of
CC small nucleolar RNAs (snoRNAs) (PubMed:19420328).
CC {ECO:0000269|PubMed:12032089, ECO:0000269|PubMed:16118225,
CC ECO:0000269|PubMed:18052196, ECO:0000269|PubMed:19411372,
CC ECO:0000269|PubMed:19420328}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Endonucleolytic cleavage of RNA, removing extra 3' nucleotides
CC from tRNA precursor, generating 3' termini of tRNAs. A 3'-hydroxy
CC group is left at the tRNA terminus and a 5'-phosphoryl group is left
CC at the trailer molecule.; EC=3.1.26.11;
CC Evidence={ECO:0000269|PubMed:16118225};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:18052196};
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000269|PubMed:18052196};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:16118225, ECO:0000269|PubMed:18052196};
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:16118225, ECO:0000269|PubMed:18052196};
CC Note=Besides the tightly bound Zn(2+) ion, TRZ1 requires additional
CC Ca(2+), Mn(2+) or Mg(2+) for pre-tRNA processing, while bpNPP
CC hydrolysis occurs without addition of metal ions but is stimulated
CC 2- to 3-fold when free Mn(2+) or Zn(2+) ions are added.
CC {ECO:0000269|PubMed:18052196};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=8.5 mM for bpNPP {ECO:0000269|PubMed:18052196};
CC Note=kcat is 7.4 sec(-1) with bpNPP as substrate.
CC {ECO:0000269|PubMed:18052196};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:16118225,
CC ECO:0000305|PubMed:12032089}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:19411372}.
CC -!- DOMAIN: The C-terminus (270-280) is essential for tRNA binding and
CC processing activity. {ECO:0000269|PubMed:16118225}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype when grown under standard
CC conditions. {ECO:0000269|PubMed:19411372}.
CC -!- SIMILARITY: Belongs to the RNase Z family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAD55271.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=AAG52354.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AJ428989; CAD22100.1; -; mRNA.
DR EMBL; AC008263; AAD55271.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AC011765; AAG52354.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE35623.1; -; Genomic_DNA.
DR PIR; C96776; C96776.
DR RefSeq; NP_177608.2; NM_106128.3.
DR AlphaFoldDB; Q8LGU7; -.
DR SMR; Q8LGU7; -.
DR STRING; 3702.AT1G74700.1; -.
DR PaxDb; Q8LGU7; -.
DR PRIDE; Q8LGU7; -.
DR ProteomicsDB; 228000; -.
DR EnsemblPlants; AT1G74700.1; AT1G74700.1; AT1G74700.
DR GeneID; 843809; -.
DR Gramene; AT1G74700.1; AT1G74700.1; AT1G74700.
DR KEGG; ath:AT1G74700; -.
DR Araport; AT1G74700; -.
DR TAIR; locus:2019235; AT1G74700.
DR eggNOG; ENOG502QVD0; Eukaryota.
DR HOGENOM; CLU_054121_0_0_1; -.
DR InParanoid; Q8LGU7; -.
DR OMA; MESTFVD; -.
DR OrthoDB; 1387038at2759; -.
DR PhylomeDB; Q8LGU7; -.
DR BRENDA; 3.1.26.11; 399.
DR PRO; PR:Q8LGU7; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q8LGU7; baseline and differential.
DR Genevisible; Q8LGU7; AT.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; TAS:TAIR.
DR GO; GO:0042781; F:3'-tRNA processing endoribonuclease activity; IDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0042780; P:tRNA 3'-end processing; IDA:TAIR.
DR GO; GO:0008033; P:tRNA processing; TAS:TAIR.
DR Gene3D; 3.60.15.10; -; 1.
DR InterPro; IPR001279; Metallo-B-lactamas.
DR InterPro; IPR036866; RibonucZ/Hydroxyglut_hydro.
DR Pfam; PF12706; Lactamase_B_2; 1.
DR SUPFAM; SSF56281; SSF56281; 1.
PE 1: Evidence at protein level;
KW Calcium; Cytoplasm; Endonuclease; Hydrolase; Magnesium; Manganese;
KW Metal-binding; Nuclease; Reference proteome; tRNA processing; Zinc.
FT CHAIN 1..280
FT /note="tRNase Z TRZ1"
FT /id="PRO_0000155834"
FT MUTAGEN 25
FT /note="C->G: Reduced catalytic activity, but no effect on
FT dimerization and tRNA binding."
FT /evidence="ECO:0000269|PubMed:16118225"
FT MUTAGEN 40
FT /note="C->G: No effect."
FT /evidence="ECO:0000269|PubMed:16118225"
FT MUTAGEN 51..60
FT /note="Missing: Loss of tRNA binding, but no effect on
FT dimerization."
FT /evidence="ECO:0000269|PubMed:16118225"
FT MUTAGEN 51
FT /note="F->L: No effect."
FT /evidence="ECO:0000269|PubMed:16118225"
FT MUTAGEN 54
FT /note="H->L: Loss of catalytic activity, but no effect on
FT dimerization and tRNA binding."
FT /evidence="ECO:0000269|PubMed:16118225"
FT MUTAGEN 56
FT /note="H->L: Loss of catalytic activity, but no effect on
FT dimerization and tRNA binding."
FT /evidence="ECO:0000269|PubMed:16118225"
FT MUTAGEN 58
FT /note="D->A: Loss of catalytic activity, but no effect on
FT dimerization and tRNA binding."
FT /evidence="ECO:0000269|PubMed:16118225"
FT MUTAGEN 59
FT /note="H->L: Loss of dimerization and catalytic activity."
FT /evidence="ECO:0000269|PubMed:16118225"
FT MUTAGEN 62
FT /note="G->V: Reduced catalytic activity, but no effect on
FT dimerization and tRNA binding."
FT /evidence="ECO:0000269|PubMed:16118225"
FT MUTAGEN 64
FT /note="P->A: No effect."
FT /evidence="ECO:0000269|PubMed:16118225"
FT MUTAGEN 83
FT /note="P->L: Loss of dimerization and catalytic activity."
FT /evidence="ECO:0000269|PubMed:16118225"
FT MUTAGEN 133
FT /note="H->L: Loss of catalytic activity, but no effect on
FT dimerization and tRNA binding."
FT /evidence="ECO:0000269|PubMed:16118225"
FT MUTAGEN 140
FT /note="Y->L: Reduced catalytic activity, but no effect on
FT dimerization and tRNA binding."
FT /evidence="ECO:0000269|PubMed:16118225"
FT MUTAGEN 178
FT /note="P->A: Reduced catalytic activity, but no effect on
FT dimerization and tRNA binding."
FT /evidence="ECO:0000269|PubMed:16118225"
FT MUTAGEN 184
FT /note="G->V: Loss of tRNA binding, but no effect on
FT dimerization."
FT /evidence="ECO:0000269|PubMed:16118225"
FT MUTAGEN 185
FT /note="D->G: Loss of catalytic activity, but no effect on
FT dimerization and tRNA binding."
FT /evidence="ECO:0000269|PubMed:16118225"
FT MUTAGEN 186
FT /note="T->I: Loss of dimerization and catalytic activity."
FT /evidence="ECO:0000269|PubMed:16118225"
FT MUTAGEN 203
FT /note="K->I: Loss of dimerization and catalytic activity."
FT /evidence="ECO:0000269|PubMed:16118225"
FT MUTAGEN 205
FT /note="L->I: Reduced catalytic activity, but no effect on
FT dimerization and tRNA binding."
FT /evidence="ECO:0000269|PubMed:16118225"
FT MUTAGEN 208
FT /note="E->A: Reduced catalytic activity, but no effect on
FT dimerization and tRNA binding."
FT /evidence="ECO:0000269|PubMed:16118225"
FT MUTAGEN 210
FT /note="T->I: No effect."
FT /evidence="ECO:0000269|PubMed:16118225"
FT MUTAGEN 226
FT /note="H->L: Loss of catalytic activity, but no effect on
FT dimerization and tRNA binding."
FT /evidence="ECO:0000269|PubMed:16118225"
FT MUTAGEN 248
FT /note="H->L: Loss of dimerization and catalytic activity."
FT /evidence="ECO:0000269|PubMed:16118225"
FT MUTAGEN 252
FT /note="R->G: Reduced pre-tRNA processing, but increased
FT hydrolysis of bpNPP. No effect on dimerization and tRNA
FT binding."
FT /evidence="ECO:0000269|PubMed:16118225"
FT MUTAGEN 252
FT /note="Missing: Loss of catalytic activity, but no effect
FT on dimerization and tRNA binding."
FT /evidence="ECO:0000269|PubMed:16118225"
FT MUTAGEN 253
FT /note="Y->S: Reduced catalytic activity, but no effect on
FT dimerization and tRNA binding."
FT /evidence="ECO:0000269|PubMed:16118225"
FT MUTAGEN 270..280
FT /note="Missing: Loss of dimerization and catalytic
FT activity."
FT /evidence="ECO:0000269|PubMed:16118225"
SQ SEQUENCE 280 AA; 31333 MW; 10126C052C8BB94D CRC64;
MEKKKAMQIE GYPIEGLSIG GHETCIIFPS LRIAFDIGRC PHRAISQDFL FISHSHMDHI
GGLPMYVATR GLYKMKPPTI IVPASIKETV ESLFEVHRKL DSSELKHNLV GLDIGEEFII
RKDLKVKAFK TFHVIQSQGY VVYSTKYKLK KEYIGLSGNE IKNLKVSGVE ITDSIITPEV
AFTGDTTSDF VVDETNADAL KAKVLVMEST FLDDSVSVEH ARDYGHIHIS EIVNHAEKFE
NKAILLIHFS ARYTVKEIED AVSALPPPLE GRVFALTQGF
