ID CCA_ECOLI Reviewed; 412 AA.
AC P06961; Q2M9E9;
DT 01-APR-1988, integrated into UniProtKB/Swiss-Prot.
DT 01-APR-1988, sequence version 1.
DT 27-MAR-2024, entry version 188.
DE RecName: Full=Multifunctional CCA protein;
DE Includes:
DE RecName: Full=CCA-adding enzyme;
DE EC=2.7.7.72 {ECO:0000269|PubMed:3516995};
DE AltName: Full=CCA tRNA nucleotidyltransferase;
DE AltName: Full=tRNA CCA-pyrophosphorylase;
DE AltName: Full=tRNA adenylyl-/cytidylyl-transferase;
DE AltName: Full=tRNA nucleotidyltransferase;
DE AltName: Full=tRNA-NT;
DE Includes:
DE RecName: Full=2'-nucleotidase;
DE EC=3.1.3.-;
DE Includes:
DE RecName: Full=2',3'-cyclic phosphodiesterase;
DE EC=3.1.4.-;
DE Includes:
DE RecName: Full=Phosphatase;
DE EC=3.1.3.-;
GN Name=cca; OrderedLocusNames=b3056, JW3028;
OS Escherichia coli (strain K12).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=3009457; DOI=10.1016/s0021-9258(19)84582-9;
RA Cudny H., Lupski J.R., Godson G.N., Deutscher M.P.;
RT "Cloning, sequencing, and species relatedness of the Escherichia coli cca
RT gene encoding the enzyme tRNA nucleotidyltransferase.";
RL J. Biol. Chem. 261:6444-6449(1986).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 65-76, AND MUTAGENESIS OF GLY-70.
RX PubMed=3533927; DOI=10.1016/s0021-9258(18)66797-3;
RA Zhu L.Q., Cudny H., Deutscher M.P.;
RT "A mutation in Escherichia coli tRNA nucleotidyltransferase that affects
RT only AMP incorporation is in a sequence often associated with nucleotide-
RT binding proteins.";
RL J. Biol. Chem. 261:14875-14877(1986).
RN [5]
RP FUNCTION, NUCLEOTIDYLTRANSFERASE ACTIVITY, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
RX PubMed=3516995; DOI=10.1016/s0021-9258(19)84583-0;
RA Cudny H., Deutscher M.P.;
RT "High-level overexpression, rapid purification, and properties of
RT Escherichia coli tRNA nucleotidyltransferase.";
RL J. Biol. Chem. 261:6450-6453(1986).
RN [6]
RP PHOSPHOHYDROLASE ACTIVITIES, FUNCTION, COFACTOR, SUBUNIT,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF ASP-21; ASP-23; HIS-255;
RP ASP-256; HIS-305 AND ASP-306.
RX PubMed=15210699; DOI=10.1074/jbc.m405120200;
RA Yakunin A.F., Proudfoot M., Kuznetsova E., Savchenko A., Brown G.,
RA Arrowsmith C.H., Edwards A.M.;
RT "The HD domain of the Escherichia coli tRNA nucleotidyltransferase has
RT 2',3'-cyclic phosphodiesterase, 2'-nucleotidase, and phosphatase
RT activities.";
RL J. Biol. Chem. 279:36819-36827(2004).
RN [7]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=22076379; DOI=10.1126/science.1213671;
RA Wilusz J.E., Whipple J.M., Phizicky E.M., Sharp P.A.;
RT "tRNAs marked with CCACCA are targeted for degradation.";
RL Science 334:817-821(2011).
CC -!- FUNCTION: Catalyzes the addition and repair of the essential 3'-
CC terminal CCA sequence in tRNAs without using a nucleic acid template
CC (PubMed:3516995). Adds these three nucleotides in the order of C, C,
CC and A to the tRNA nucleotide-73, using CTP and ATP as substrates and
CC producing inorganic pyrophosphate (PubMed:3516995). tRNA 3'-terminal
CC CCA addition is required both for tRNA processing and repair
CC (PubMed:22076379). Also involved in tRNA surveillance by mediating
CC tandem CCA addition to generate a CCACCA at the 3' terminus of unstable
CC tRNAs (PubMed:22076379). While stable tRNAs receive only 3'-terminal
CC CCA, unstable tRNAs are marked with CCACCA and rapidly degraded
CC (PubMed:22076379). The structural flexibility of RNA controls the
CC choice between CCA versus CCACCA addition: following the first CCA
CC addition cycle, nucleotide-binding to the active site triggers a
CC clockwise screw motion, producing torque on the RNA (By similarity).
CC This ejects stable RNAs, whereas unstable RNAs are refolded while bound
CC to the enzyme and subjected to a second CCA catalytic cycle (By
CC similarity). Also shows highest phosphatase activity in the presence of
CC Ni(2+) and hydrolyzes pyrophosphate, canonical 5'-nucleoside tri- and
CC diphosphates, NADP, and 2'-AMP with the production of Pi
CC (PubMed:15210699). Displays a metal-independent phosphodiesterase
CC activity toward 2',3'-cAMP, 2',3'-cGMP, and 2',3'-cCMP
CC (PubMed:15210699). Without metal or in the presence of Mg(2+), this
CC protein hydrolyzes 2',3'-cyclic substrates with the formation of 2'-
CC nucleotides, whereas in the presence of Ni(2+), it also produces some
CC 3'-nucleotides (PubMed:15210699). These phosphohydrolase activities are
CC probably involved in the repair of the tRNA 3'-CCA terminus degraded by
CC intracellular RNases (PubMed:15210699). {ECO:0000250|UniProtKB:O28126,
CC ECO:0000269|PubMed:15210699, ECO:0000269|PubMed:22076379,
CC ECO:0000269|PubMed:3516995}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a tRNA precursor + ATP + 2 CTP = a tRNA with a 3' CCA end + 3
CC diphosphate; Xref=Rhea:RHEA:14433, Rhea:RHEA-COMP:10465, Rhea:RHEA-
CC COMP:10468, ChEBI:CHEBI:30616, ChEBI:CHEBI:33019, ChEBI:CHEBI:37563,
CC ChEBI:CHEBI:74896, ChEBI:CHEBI:83071; EC=2.7.7.72;
CC Evidence={ECO:0000269|PubMed:3516995};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a tRNA with a 3' CCA end + ATP + 2 CTP = a tRNA with a 3'
CC CCACCA end + 3 diphosphate; Xref=Rhea:RHEA:76235, Rhea:RHEA-
CC COMP:10468, Rhea:RHEA-COMP:18655, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:37563, ChEBI:CHEBI:83071,
CC ChEBI:CHEBI:195187; Evidence={ECO:0000269|PubMed:22076379};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:76236;
CC Evidence={ECO:0000269|PubMed:22076379};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:O28126};
CC Note=Magnesium is required for nucleotidyltransferase activity.
CC {ECO:0000250|UniProtKB:O28126};
CC -!- COFACTOR:
CC Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC Note=Nickel for phosphatase activity. {ECO:0000269|PubMed:15210699};
CC -!- ACTIVITY REGULATION: Both phosphatase and phosphodiesterase activities
CC are competitively inhibited by low concentrations of the E.coli tRNA
CC (10 nM). Cu(2+) stimulates the hydrolysis of pyrophosphate and ATP and
CC completely inhibits the hydrolysis of 2'-AMP. The phosphodiesterase
CC activity is inhibited by Zn(2+), Cu(2+) and Co(2+).
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.33 mM for ATP (in the tRNA-NT activity assay)
CC {ECO:0000269|PubMed:15210699, ECO:0000269|PubMed:3516995};
CC KM=0.03 mM for CTP (in the tRNA-NT activity assay)
CC {ECO:0000269|PubMed:15210699, ECO:0000269|PubMed:3516995};
CC KM=0.015 mM for tRNA-CC {ECO:0000269|PubMed:15210699,
CC ECO:0000269|PubMed:3516995};
CC KM=0.02 mM for tRNA-C {ECO:0000269|PubMed:15210699,
CC ECO:0000269|PubMed:3516995};
CC KM=6.2 mM for pNPP {ECO:0000269|PubMed:15210699,
CC ECO:0000269|PubMed:3516995};
CC KM=0.10 mM for PPi {ECO:0000269|PubMed:15210699,
CC ECO:0000269|PubMed:3516995};
CC KM=0.15 mM for NADP {ECO:0000269|PubMed:15210699,
CC ECO:0000269|PubMed:3516995};
CC KM=0.19 mM for ADP {ECO:0000269|PubMed:15210699,
CC ECO:0000269|PubMed:3516995};
CC KM=0.18 mM for ATP (in the phosphatase activity assay)
CC {ECO:0000269|PubMed:15210699, ECO:0000269|PubMed:3516995};
CC KM=0.53 mM for CDP {ECO:0000269|PubMed:15210699,
CC ECO:0000269|PubMed:3516995};
CC KM=0.13 mM for CTP (in the phosphatase activity assay)
CC {ECO:0000269|PubMed:15210699, ECO:0000269|PubMed:3516995};
CC KM=0.76 mM for 2'-AMP {ECO:0000269|PubMed:15210699,
CC ECO:0000269|PubMed:3516995};
CC KM=0.49 mM for 2',3'-cAMP {ECO:0000269|PubMed:15210699,
CC ECO:0000269|PubMed:3516995};
CC KM=1.60 mM for 2',3'-cGMP {ECO:0000269|PubMed:15210699,
CC ECO:0000269|PubMed:3516995};
CC Vmax=12.4 umol/min/mg enzyme with pNPP as substrate
CC {ECO:0000269|PubMed:15210699, ECO:0000269|PubMed:3516995};
CC Vmax=3.01 umol/min/mg enzyme with PPi as substrate
CC {ECO:0000269|PubMed:15210699, ECO:0000269|PubMed:3516995};
CC Vmax=17.9 umol/min/mg enzyme with NADP as substrate
CC {ECO:0000269|PubMed:15210699, ECO:0000269|PubMed:3516995};
CC Vmax=1.49 umol/min/mg enzyme with ADP as substrate
CC {ECO:0000269|PubMed:15210699, ECO:0000269|PubMed:3516995};
CC Vmax=4.53 umol/min/mg enzyme with ATP as substrate (in the
CC phosphatase activity assay) {ECO:0000269|PubMed:15210699,
CC ECO:0000269|PubMed:3516995};
CC Vmax=5.80 umol/min/mg enzyme with CDP as substrate
CC {ECO:0000269|PubMed:15210699, ECO:0000269|PubMed:3516995};
CC Vmax=4.03 umol/min/mg enzyme with CTP as substrate (in the
CC phosphatase activity assay) {ECO:0000269|PubMed:15210699,
CC ECO:0000269|PubMed:3516995};
CC Vmax=3.71 umol/min/mg enzyme with 2'-AMP as substrate
CC {ECO:0000269|PubMed:15210699, ECO:0000269|PubMed:3516995};
CC Vmax=3.21 umol/min/mg enzyme with 2',3'-cAMP as substrate
CC {ECO:0000269|PubMed:15210699, ECO:0000269|PubMed:3516995};
CC Vmax=2.36 umol/min/mg enzyme with 2',3'-cGMP as substrate
CC {ECO:0000269|PubMed:15210699, ECO:0000269|PubMed:3516995};
CC pH dependence:
CC Optimum pH is 9.4 for AMP incorporation, 10.0 for CMP incorporation,
CC and 7.0 for the phosphatase and phosphodiesterase activities.
CC {ECO:0000269|PubMed:15210699, ECO:0000269|PubMed:3516995};
CC -!- SUBUNIT: Monomer. Can also form homodimers and oligomers, but with low
CC levels. {ECO:0000269|PubMed:15210699}.
CC -!- INTERACTION:
CC P06961; P0A6M4: dtd; NbExp=2; IntAct=EBI-545256, EBI-562575;
CC -!- DOMAIN: Comprises two domains: an N-terminal domain containing the
CC nucleotidyltransferase activity and a C-terminal HD domain associated
CC with both phosphodiesterase and phosphatase activities.
CC -!- MISCELLANEOUS: A single active site specifically recognizes both ATP
CC and CTP and is responsible for their addition. {ECO:0000255|HAMAP-
CC Rule:MF_01261}.
CC -!- SIMILARITY: Belongs to the tRNA nucleotidyltransferase/poly(A)
CC polymerase family. Bacterial CCA-adding enzyme type 1 subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_01261, ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; M12788; AAA23541.1; -; Genomic_DNA.
DR EMBL; U28379; AAA89136.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76092.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77107.1; -; Genomic_DNA.
DR PIR; A25215; RNECTA.
DR RefSeq; NP_417528.1; NC_000913.3.
DR RefSeq; WP_000708487.1; NZ_STEB01000001.1.
DR AlphaFoldDB; P06961; -.
DR SMR; P06961; -.
DR BioGRID; 4259255; 71.
DR DIP; DIP-9250N; -.
DR IntAct; P06961; 25.
DR STRING; 511145.b3056; -.
DR ChEMBL; CHEMBL3309020; -.
DR jPOST; P06961; -.
DR PaxDb; 511145-b3056; -.
DR EnsemblBacteria; AAC76092; AAC76092; b3056.
DR GeneID; 947553; -.
DR KEGG; ecj:JW3028; -.
DR KEGG; eco:b3056; -.
DR PATRIC; fig|1411691.4.peg.3675; -.
DR EchoBASE; EB0134; -.
DR eggNOG; COG0617; Bacteria.
DR HOGENOM; CLU_015961_1_1_6; -.
DR InParanoid; P06961; -.
DR OMA; HRHKDVY; -.
DR OrthoDB; 9805698at2; -.
DR PhylomeDB; P06961; -.
DR BioCyc; EcoCyc:EG10136-MONOMER; -.
DR BioCyc; MetaCyc:EG10136-MONOMER; -.
DR BRENDA; 2.7.7.72; 2026.
DR BRENDA; 3.1.4.16; 2026.
DR BRENDA; 3.1.4.37; 2026.
DR SABIO-RK; P06961; -.
DR PRO; PR:P06961; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004810; F:CCA tRNA nucleotidyltransferase activity; IDA:EcoCyc.
DR GO; GO:0160016; F:CCACCA tRNA nucleotidyltransferase activity; IDA:UniProtKB.
DR GO; GO:0004112; F:cyclic-nucleotide phosphodiesterase activity; IDA:EcoCyc.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016791; F:phosphatase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0042245; P:RNA repair; IMP:EcoCyc.
DR GO; GO:0001680; P:tRNA 3'-terminal CCA addition; IDA:EcoCyc.
DR GO; GO:0106354; P:tRNA surveillance; IDA:UniProtKB.
DR CDD; cd00077; HDc; 1.
DR CDD; cd05398; NT_ClassII-CCAase; 1.
DR Gene3D; 3.30.460.10; Beta Polymerase, domain 2; 1.
DR Gene3D; 1.10.3090.10; cca-adding enzyme, domain 2; 1.
DR HAMAP; MF_01261; CCA_bact_type1; 1.
DR HAMAP; MF_01262; CCA_bact_type2; 1.
DR InterPro; IPR012006; CCA_bact.
DR InterPro; IPR003607; HD/PDEase_dom.
DR InterPro; IPR006674; HD_domain.
DR InterPro; IPR043519; NT_sf.
DR InterPro; IPR002646; PolA_pol_head_dom.
DR InterPro; IPR032828; PolyA_RNA-bd.
DR PANTHER; PTHR47545; MULTIFUNCTIONAL CCA PROTEIN; 1.
DR PANTHER; PTHR47545:SF1; MULTIFUNCTIONAL CCA PROTEIN; 1.
DR Pfam; PF01966; HD; 1.
DR Pfam; PF01743; PolyA_pol; 1.
DR Pfam; PF12627; PolyA_pol_RNAbd; 1.
DR PIRSF; PIRSF000813; CCA_bact; 1.
DR SUPFAM; SSF81301; Nucleotidyltransferase; 1.
DR SUPFAM; SSF81891; Poly A polymerase C-terminal region-like; 1.
DR PROSITE; PS51831; HD; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Hydrolase; Magnesium; Metal-binding; Multifunctional enzyme;
KW Nickel; Nucleotide-binding; Nucleotidyltransferase; Reference proteome;
KW RNA repair; RNA-binding; Transferase; tRNA processing.
FT CHAIN 1..412
FT /note="Multifunctional CCA protein"
FT /id="PRO_0000138975"
FT DOMAIN 228..329
FT /note="HD"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01261"
FT BINDING 8
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01261"
FT BINDING 8
FT /ligand="CTP"
FT /ligand_id="ChEBI:CHEBI:37563"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01261"
FT BINDING 11
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01261"
FT BINDING 11
FT /ligand="CTP"
FT /ligand_id="ChEBI:CHEBI:37563"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01261"
FT BINDING 21
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:O66728"
FT BINDING 23
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:O66728"
FT BINDING 91
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01261"
FT BINDING 91
FT /ligand="CTP"
FT /ligand_id="ChEBI:CHEBI:37563"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01261"
FT BINDING 137
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01261"
FT BINDING 137
FT /ligand="CTP"
FT /ligand_id="ChEBI:CHEBI:37563"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01261"
FT BINDING 140
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01261"
FT BINDING 140
FT /ligand="CTP"
FT /ligand_id="ChEBI:CHEBI:37563"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01261"
FT MUTAGEN 21
FT /note="D->A: No effect on phosphodiesterase and phosphatase
FT activities."
FT /evidence="ECO:0000269|PubMed:15210699"
FT MUTAGEN 23
FT /note="D->A: No effect on phosphodiesterase and phosphatase
FT activities."
FT /evidence="ECO:0000269|PubMed:15210699"
FT MUTAGEN 70
FT /note="G->D: Lowered AMP incorporation."
FT /evidence="ECO:0000269|PubMed:3533927"
FT MUTAGEN 255
FT /note="H->A: Loss of phosphodiesterase and phosphatase
FT activities."
FT /evidence="ECO:0000269|PubMed:15210699"
FT MUTAGEN 256
FT /note="D->A: Loss of phosphodiesterase and phosphatase
FT activities."
FT /evidence="ECO:0000269|PubMed:15210699"
FT MUTAGEN 305
FT /note="H->A: Loss of phosphodiesterase and phosphatase
FT activities."
FT /evidence="ECO:0000269|PubMed:15210699"
FT MUTAGEN 306
FT /note="D->A: Still possesses phosphodiesterase and
FT phosphatase activities."
FT /evidence="ECO:0000269|PubMed:15210699"
SQ SEQUENCE 412 AA; 46467 MW; 947182E6086220F7 CRC64;
MKIYLVGGAV RDALLGLPVK DRDWVVVGST PQEMLDAGYQ QVGRDFPVFL HPQTHEEYAL
ARTERKSGSG YTGFTCYAAP DVTLEDDLKR RDLTINALAQ DDNGEIIDPY NGLGDLQNRL
LRHVSPAFGE DPLRVLRVAR FAARYAHLGF RIADETLALM REMTHAGELE HLTPERVWKE
TESALTTRNP QVFFQVLRDC GALRVLFPEI DALFGVPAPA KWHPEIDTGI HTLMTLSMAA
MLSPQVDVRF ATLCHDLGKG LTPPELWPRH HGHGPAGVKL VEQLCQRLRV PNEIRDLARL
VAEFHDLIHT FPMLNPKTIV KLFDSIDAWR KPQRVEQLAL TSEADVRGRT GFESADYPQG
RWLREAWEVA QSVPTKAVVE AGFKGVEIRE ELTRRRIAAV ASWKEQRCPK PE
//
