PRRP2_ARATH
ID PRRP2_ARATH Reviewed; 528 AA.
AC Q680B9; Q9SLF2;
DT 28-NOV-2012, integrated into UniProtKB/Swiss-Prot.
DT 11-OCT-2004, sequence version 1.
DT 03-AUG-2022, entry version 108.
DE RecName: Full=Proteinaceous RNase P 2;
DE EC=3.1.26.5 {ECO:0000269|PubMed:22549728, ECO:0000269|PubMed:26655022};
GN Name=PRORP2; OrderedLocusNames=At2g16650; ORFNames=T24I21.6;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
RN [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (SEP-2004) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP IDENTIFICATION, AND SUBCELLULAR LOCATION.
RX PubMed=20473316; DOI=10.1038/nsmb.1812;
RA Gobert A., Gutmann B., Taschner A., Goessringer M., Holzmann J.,
RA Hartmann R.K., Rossmanith W., Giege P.;
RT "A single Arabidopsis organellar protein has RNase P activity.";
RL Nat. Struct. Mol. Biol. 17:740-744(2010).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF
RP 421-ASP-ASP-422.
RX PubMed=22549728; DOI=10.1101/gad.189514.112;
RA Gutmann B., Gobert A., Giege P.;
RT "PRORP proteins support RNase P activity in both organelles and the nucleus
RT in Arabidopsis.";
RL Genes Dev. 26:1022-1027(2012).
RN [6] {ECO:0007744|PDB:5DIZ}
RP X-RAY CRYSTALLOGRAPHY (3.20 ANGSTROMS) IN COMPLEX WITH ZINC, FUNCTION,
RP CATALYTIC ACTIVITY, COFACTOR, SUBUNIT, AND MUTAGENESIS OF ASP-343; ASP-421;
RP ASP-422; ASP-440 AND HIS-445.
RX PubMed=26655022; DOI=10.1016/j.jmb.2015.11.025;
RA Karasik A., Shanmuganathan A., Howard M.J., Fierke C.A., Koutmos M.;
RT "Nuclear protein-only ribonuclease P2 structure and Biochemical
RT characterization provide insight into the conserved properties of tRNA 5'
RT End processing enzymes.";
RL J. Mol. Biol. 428:26-40(2016).
CC -!- FUNCTION: Endonuclease RNase P responsible for the 5' maturation of
CC tRNA precursors (PubMed:22549728, PubMed:26655022). Preferentially
CC binds precursor tRNAs containing short 5' leaders and 3' trailers
CC (PubMed:26655022). Also involved in the maturation of mRNA and small
CC nucleolar RNA (snoRNA) (PubMed:22549728). {ECO:0000269|PubMed:22549728,
CC ECO:0000269|PubMed:26655022}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Endonucleolytic cleavage of RNA, removing 5'-extranucleotides
CC from tRNA precursor.; EC=3.1.26.5;
CC Evidence={ECO:0000269|PubMed:22549728, ECO:0000269|PubMed:26655022};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:26655022};
CC Note=Binds 2 Mg(2+) ions per subunit. {ECO:0000269|PubMed:26655022};
CC -!- SUBUNIT: Monomer; forms dimers in crystallo but monomers in solution
CC (PubMed:26655022). {ECO:0000269|PubMed:26655022}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:20473316}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype; due to the redundancy with
CC PRORP3. Prorp2 and prorp3 double mutant is lethal.
CC {ECO:0000269|PubMed:22549728}.
CC -!- SIMILARITY: Belongs to the PPR family. P subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAD24622.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC005825; AAD24622.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002685; AEC06522.1; -; Genomic_DNA.
DR EMBL; AK175948; BAD43711.1; -; mRNA.
DR PIR; E84542; E84542.
DR RefSeq; NP_179256.3; NM_127217.4.
DR PDB; 5DIZ; X-ray; 3.20 A; A/B=1-528.
DR PDB; 5FT9; X-ray; 3.05 A; A/B=2-528.
DR PDBsum; 5DIZ; -.
DR PDBsum; 5FT9; -.
DR AlphaFoldDB; Q680B9; -.
DR SMR; Q680B9; -.
DR STRING; 3702.AT2G16650.1; -.
DR iPTMnet; Q680B9; -.
DR PaxDb; Q680B9; -.
DR PRIDE; Q680B9; -.
DR ProteomicsDB; 226476; -.
DR EnsemblPlants; AT2G16650.1; AT2G16650.1; AT2G16650.
DR GeneID; 816166; -.
DR Gramene; AT2G16650.1; AT2G16650.1; AT2G16650.
DR KEGG; ath:AT2G16650; -.
DR Araport; AT2G16650; -.
DR TAIR; locus:2059824; AT2G16650.
DR eggNOG; KOG1347; Eukaryota.
DR HOGENOM; CLU_014066_2_0_1; -.
DR InParanoid; Q680B9; -.
DR OMA; YAVETHM; -.
DR OrthoDB; 1247650at2759; -.
DR PhylomeDB; Q680B9; -.
DR BRENDA; 3.1.26.5; 399.
DR PRO; PR:Q680B9; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q680B9; baseline and differential.
DR Genevisible; Q680B9; AT.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004526; F:ribonuclease P activity; IDA:TAIR.
DR GO; GO:0006397; P:mRNA processing; IMP:TAIR.
DR GO; GO:0043144; P:sno(s)RNA processing; IMP:TAIR.
DR GO; GO:0001682; P:tRNA 5'-leader removal; IDA:TAIR.
DR Gene3D; 1.25.40.10; -; 1.
DR InterPro; IPR033443; PPR_long.
DR InterPro; IPR031595; PRORP_C.
DR InterPro; IPR011990; TPR-like_helical_dom_sf.
DR Pfam; PF17177; PPR_long; 1.
DR Pfam; PF16953; PRORP; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Magnesium; Manganese; Metal-binding; Nuclease;
KW Nucleus; Reference proteome; Repeat; tRNA processing; Zinc.
FT CHAIN 1..528
FT /note="Proteinaceous RNase P 2"
FT /id="PRO_0000420273"
FT REPEAT 29..64
FT /note="PPR 1"
FT REPEAT 72..107
FT /note="PPR 2"
FT REPEAT 108..142
FT /note="PPR 3"
FT REPEAT 145..179
FT /note="PPR 4"
FT DOMAIN 275..511
FT /note="PRORP"
FT REGION 1..28
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 281
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:26655022,
FT ECO:0007744|PDB:5DIZ"
FT BINDING 284
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:26655022,
FT ECO:0007744|PDB:5DIZ"
FT BINDING 343
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000305|PubMed:26655022"
FT BINDING 421
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000305|PubMed:26655022"
FT BINDING 422
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000305|PubMed:26655022"
FT BINDING 440
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000305|PubMed:26655022"
FT BINDING 494
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:26655022,
FT ECO:0007744|PDB:5DIZ"
FT BINDING 511
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:26655022,
FT ECO:0007744|PDB:5DIZ"
FT MUTAGEN 343
FT /note="D->A: Abolishes ribonuclease activity."
FT /evidence="ECO:0000269|PubMed:26655022"
FT MUTAGEN 421..422
FT /note="DD->AA: Loss of activity."
FT /evidence="ECO:0000269|PubMed:22549728"
FT MUTAGEN 421
FT /note="D->A: Abolishes ribonuclease activity."
FT /evidence="ECO:0000269|PubMed:26655022"
FT MUTAGEN 422
FT /note="D->A: Abolishes ribonuclease activity."
FT /evidence="ECO:0000269|PubMed:26655022"
FT MUTAGEN 440
FT /note="D->A: Abolishes ribonuclease activity."
FT /evidence="ECO:0000269|PubMed:26655022"
FT MUTAGEN 445
FT /note="H->A: Abolishes ribonuclease activity."
FT /evidence="ECO:0000269|PubMed:26655022"
FT HELIX 29..43
FT /evidence="ECO:0007829|PDB:5FT9"
FT HELIX 46..59
FT /evidence="ECO:0007829|PDB:5FT9"
FT HELIX 67..81
FT /evidence="ECO:0007829|PDB:5FT9"
FT TURN 83..85
FT /evidence="ECO:0007829|PDB:5DIZ"
FT HELIX 86..101
FT /evidence="ECO:0007829|PDB:5FT9"
FT TURN 102..104
FT /evidence="ECO:0007829|PDB:5FT9"
FT HELIX 109..121
FT /evidence="ECO:0007829|PDB:5FT9"
FT HELIX 125..138
FT /evidence="ECO:0007829|PDB:5FT9"
FT HELIX 146..158
FT /evidence="ECO:0007829|PDB:5FT9"
FT HELIX 162..175
FT /evidence="ECO:0007829|PDB:5FT9"
FT HELIX 181..193
FT /evidence="ECO:0007829|PDB:5FT9"
FT HELIX 197..210
FT /evidence="ECO:0007829|PDB:5FT9"
FT STRAND 212..214
FT /evidence="ECO:0007829|PDB:5FT9"
FT HELIX 216..226
FT /evidence="ECO:0007829|PDB:5FT9"
FT HELIX 229..234
FT /evidence="ECO:0007829|PDB:5FT9"
FT HELIX 243..252
FT /evidence="ECO:0007829|PDB:5FT9"
FT STRAND 264..266
FT /evidence="ECO:0007829|PDB:5DIZ"
FT STRAND 269..273
FT /evidence="ECO:0007829|PDB:5FT9"
FT STRAND 279..281
FT /evidence="ECO:0007829|PDB:5DIZ"
FT TURN 282..284
FT /evidence="ECO:0007829|PDB:5FT9"
FT HELIX 295..310
FT /evidence="ECO:0007829|PDB:5FT9"
FT HELIX 323..335
FT /evidence="ECO:0007829|PDB:5FT9"
FT STRAND 339..343
FT /evidence="ECO:0007829|PDB:5FT9"
FT HELIX 344..349
FT /evidence="ECO:0007829|PDB:5FT9"
FT STRAND 350..352
FT /evidence="ECO:0007829|PDB:5FT9"
FT STRAND 354..356
FT /evidence="ECO:0007829|PDB:5FT9"
FT HELIX 361..375
FT /evidence="ECO:0007829|PDB:5FT9"
FT STRAND 382..386
FT /evidence="ECO:0007829|PDB:5FT9"
FT HELIX 387..395
FT /evidence="ECO:0007829|PDB:5FT9"
FT HELIX 397..409
FT /evidence="ECO:0007829|PDB:5FT9"
FT STRAND 411..415
FT /evidence="ECO:0007829|PDB:5FT9"
FT STRAND 417..419
FT /evidence="ECO:0007829|PDB:5DIZ"
FT HELIX 423..431
FT /evidence="ECO:0007829|PDB:5FT9"
FT STRAND 435..437
FT /evidence="ECO:0007829|PDB:5FT9"
FT HELIX 445..450
FT /evidence="ECO:0007829|PDB:5FT9"
FT HELIX 453..462
FT /evidence="ECO:0007829|PDB:5FT9"
FT STRAND 463..467
FT /evidence="ECO:0007829|PDB:5FT9"
FT STRAND 469..471
FT /evidence="ECO:0007829|PDB:5FT9"
FT STRAND 474..476
FT /evidence="ECO:0007829|PDB:5FT9"
FT STRAND 489..491
FT /evidence="ECO:0007829|PDB:5FT9"
FT STRAND 493..497
FT /evidence="ECO:0007829|PDB:5FT9"
FT STRAND 509..513
FT /evidence="ECO:0007829|PDB:5FT9"
SQ SEQUENCE 528 AA; 59228 MW; E9CE36AE22686ABF CRC64;
MAASDQHRSR RHDESSSRPN KKKKVSRNPE TNLLFNLNSC SKSKDLSAAL ALYDAAITSS
EVRLSQQHFQ TLLYLCSASI TDISLQYLAI DRGFEIFDRM VSSGISPNEA SVTSVARLAA
AKGNGDYAFK VVKEFVSVGG VSIPRLRTYA PALLCFCEKL EAEKGYEVEE HMEAAGIALE
EAEISALLKV SAATGRENKV YRYLHKLREY VGCVSEETLK IIEEWFCGEK AGEVGDNGIG
SDVGMLREAV LNNGGGWHGH GWVGEGKWTV KKGNVSSTGR CLSCSEQLAC VDTNEVETQK
FVDSLVALAM DRKTKMNSCE TNVVFSEFQD WLEKHGDYEA IVDGANIGLY QQNFVDGSFS
LSQLESVMKE LYRESGNNKW PLILLHKRRV KTLLENPTHR NLVEEWISNG VLYATPPGSN
DDWYWLYAAA KLKCLLVTND EMRDHIFELL GSTFFQKWKE RHQVRYTFVK GNLKLEMPSP
FSVVIQESEK GSWHFPVSCE NNEESSRTWM CISRQSILDS PKSNGKIP
