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Protein

Multifunctional CCA protein

Gene

cca

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the addition and repair of the essential 3'-terminal CCA sequence in tRNAs without using a nucleic acid template. Adds these three nucleotides in the order of C, C, and A to the tRNA nucleotide-73, using CTP and ATP as substrates and producing inorganic pyrophosphate. Also shows highest phosphatase activity in the presence of Ni2+ and hydrolyzes pyrophosphate, canonical 5'-nucleoside tri- and diphosphates, NADP, and 2'-AMP with the production of Pi. Displays a metal-independent phosphodiesterase activity toward 2',3'-cAMP, 2',3'-cGMP, and 2',3'-cCMP. Without metal or in the presence of Mg2+, this protein hydrolyzes 2',3'-cyclic substrates with the formation of 2'-nucleotides, whereas in the presence of Ni2+, it also produces some 3'-nucleotides. These phosphohydrolase activities are probably involved in the repair of the tRNA 3'-CCA terminus degraded by intracellular RNases.1 Publication

Catalytic activityi

A tRNA precursor + 2 CTP + ATP = a tRNA with a 3' CCA end + 3 diphosphate.

Cofactori

Protein has several cofactor binding sites:
  • Mg2+Note: Magnesium is required for nucleotidyltransferase activity.
  • Ni2+Note: Nickel for phosphatase activity.

Enzyme regulationi

Both phosphatase and phosphodiesterase activities are competitively inhibited by low concentrations of the E.coli tRNA (10 nM). Cu2+ stimulates the hydrolysis of pyrophosphate and ATP and completely inhibits the hydrolysis of 2'-AMP. The phosphodiesterase activity is inhibited by Zn2+, Cu2+ and Co2+.

Kineticsi

  1. KM=0.33 mM for ATP (in the tRNA-NT activity assay)2 Publications
  2. KM=0.03 mM for CTP (in the tRNA-NT activity assay)2 Publications
  3. KM=0.015 mM for tRNA-CC2 Publications
  4. KM=0.02 mM for tRNA-C2 Publications
  5. KM=6.2 mM for pNPP2 Publications
  6. KM=0.10 mM for PPi2 Publications
  7. KM=0.15 mM for NADP2 Publications
  8. KM=0.19 mM for ADP2 Publications
  9. KM=0.18 mM for ATP (in the phosphatase activity assay)2 Publications
  10. KM=0.53 mM for CDP2 Publications
  11. KM=0.13 mM for CTP (in the phosphatase activity assay)2 Publications
  12. KM=0.76 mM for 2'-AMP2 Publications
  13. KM=0.49 mM for 2',3'-cAMP2 Publications
  14. KM=1.60 mM for 2',3'-cGMP2 Publications
  1. Vmax=12.4 µmol/min/mg enzyme with pNPP as substrate2 Publications
  2. Vmax=3.01 µmol/min/mg enzyme with PPi as substrate2 Publications
  3. Vmax=17.9 µmol/min/mg enzyme with NADP as substrate2 Publications
  4. Vmax=1.49 µmol/min/mg enzyme with ADP as substrate2 Publications
  5. Vmax=4.53 µmol/min/mg enzyme with ATP as substrate (in the phosphatase activity assay)2 Publications
  6. Vmax=5.80 µmol/min/mg enzyme with CDP as substrate2 Publications
  7. Vmax=4.03 µmol/min/mg enzyme with CTP as substrate (in the phosphatase activity assay)2 Publications
  8. Vmax=3.71 µmol/min/mg enzyme with 2'-AMP as substrate2 Publications
  9. Vmax=3.21 µmol/min/mg enzyme with 2',3'-cAMP as substrate2 Publications
  10. Vmax=2.36 µmol/min/mg enzyme with 2',3'-cGMP as substrate2 Publications

pH dependencei

Optimum pH is 9.4 for AMP incorporation, 10.0 for CMP incorporation, and 7.0 for the phosphatase and phosphodiesterase activities.2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei8 – 81ATP or CTP; via amide nitrogenBy similarity
Binding sitei11 – 111ATP or CTPBy similarity
Metal bindingi21 – 211MagnesiumBy similarity
Metal bindingi23 – 231MagnesiumBy similarity
Binding sitei91 – 911ATP or CTPBy similarity
Binding sitei137 – 1371ATP or CTPBy similarity
Binding sitei140 – 1401ATP or CTPBy similarity

GO - Molecular functioni

GO - Biological processi

  • RNA repair Source: EcoCyc
  • tRNA 3'-terminal CCA addition Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Nucleotidyltransferase, Transferase

Keywords - Biological processi

RNA repair, tRNA processing

Keywords - Ligandi

ATP-binding, Magnesium, Metal-binding, Nickel, Nucleotide-binding, RNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG10136-MONOMER.
ECOL316407:JW3028-MONOMER.
MetaCyc:EG10136-MONOMER.
BRENDAi2.7.7.72. 2026.
3.1.4.16. 2026.
3.1.4.37. 2026.
SABIO-RKP06961.

Names & Taxonomyi

Protein namesi
Recommended name:
Multifunctional CCA protein
Including the following 4 domains:
CCA-adding enzyme (EC:2.7.7.72)
Alternative name(s):
CCA tRNA nucleotidyltransferase
tRNA CCA-pyrophosphorylase
tRNA adenylyl-/cytidylyl-transferase
tRNA nucleotidyltransferase
tRNA-NT
2'-nucleotidase (EC:3.1.3.-)
2',3'-cyclic phosphodiesterase (EC:3.1.4.-)
Phosphatase (EC:3.1.3.-)
Gene namesi
Name:cca
Ordered Locus Names:b3056, JW3028
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10136. cca.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi21 – 211D → A: No effect on phosphodiesterase and phosphatase activities. 1 Publication
Mutagenesisi23 – 231D → A: No effect on phosphodiesterase and phosphatase activities. 1 Publication
Mutagenesisi70 – 701G → D: Lowered AMP incorporation. 1 Publication
Mutagenesisi255 – 2551H → A: Loss of phosphodiesterase and phosphatase activities. 1 Publication
Mutagenesisi256 – 2561D → A: Loss of phosphodiesterase and phosphatase activities. 1 Publication
Mutagenesisi305 – 3051H → A: Loss of phosphodiesterase and phosphatase activities. 1 Publication
Mutagenesisi306 – 3061D → A: Still possesses phosphodiesterase and phosphatase activities. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 412412Multifunctional CCA proteinPRO_0000138975Add
BLAST

Proteomic databases

PaxDbiP06961.

Interactioni

Subunit structurei

Monomer. Can also form homodimers and oligomers, but with low levels.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
dtdP0A6M41EBI-545256,EBI-562575

Protein-protein interaction databases

BioGridi4259255. 13 interactions.
DIPiDIP-9250N.
IntActiP06961. 24 interactions.
MINTiMINT-1263446.
STRINGi511145.b3056.

Structurei

3D structure databases

ProteinModelPortaliP06961.
SMRiP06961. Positions 2-299.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domaini

Comprises two domains: an N-terminal domain containing the nucleotidyltransferase activity and a C-terminal HD domain associated with both phosphodiesterase and phosphatase activities.

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105D4J. Bacteria.
COG0617. LUCA.
HOGENOMiHOG000007368.
InParanoidiP06961.
KOiK00974.
OMAiSEWPSHK.
OrthoDBiEOG651SRP.
PhylomeDBiP06961.

Family and domain databases

HAMAPiMF_01261. CCA_bact_type1.
MF_01262. CCA_bact_type2.
InterProiIPR012006. CCA_bact.
IPR006674. HD_domain.
IPR002646. PolA_pol_head_dom.
IPR032828. PolyA_RNA-bd.
[Graphical view]
PfamiPF01966. HD. 1 hit.
PF01743. PolyA_pol. 1 hit.
PF12627. PolyA_pol_RNAbd. 1 hit.
[Graphical view]
PIRSFiPIRSF000813. CCA_bact. 1 hit.

Sequencei

Sequence statusi: Complete.

P06961-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKIYLVGGAV RDALLGLPVK DRDWVVVGST PQEMLDAGYQ QVGRDFPVFL
60 70 80 90 100
HPQTHEEYAL ARTERKSGSG YTGFTCYAAP DVTLEDDLKR RDLTINALAQ
110 120 130 140 150
DDNGEIIDPY NGLGDLQNRL LRHVSPAFGE DPLRVLRVAR FAARYAHLGF
160 170 180 190 200
RIADETLALM REMTHAGELE HLTPERVWKE TESALTTRNP QVFFQVLRDC
210 220 230 240 250
GALRVLFPEI DALFGVPAPA KWHPEIDTGI HTLMTLSMAA MLSPQVDVRF
260 270 280 290 300
ATLCHDLGKG LTPPELWPRH HGHGPAGVKL VEQLCQRLRV PNEIRDLARL
310 320 330 340 350
VAEFHDLIHT FPMLNPKTIV KLFDSIDAWR KPQRVEQLAL TSEADVRGRT
360 370 380 390 400
GFESADYPQG RWLREAWEVA QSVPTKAVVE AGFKGVEIRE ELTRRRIAAV
410
ASWKEQRCPK PE
Length:412
Mass (Da):46,467
Last modified:April 1, 1988 - v1
Checksum:i947182E6086220F7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M12788 Genomic DNA. Translation: AAA23541.1.
U28379 Genomic DNA. Translation: AAA89136.1.
U00096 Genomic DNA. Translation: AAC76092.1.
AP009048 Genomic DNA. Translation: BAE77107.1.
PIRiA25215. RNECTA.
RefSeqiNP_417528.1. NC_000913.3.
WP_000708487.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76092; AAC76092; b3056.
BAE77107; BAE77107; BAE77107.
GeneIDi947553.
KEGGiecj:JW3028.
eco:b3056.
PATRICi32121524. VBIEscCol129921_3149.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M12788 Genomic DNA. Translation: AAA23541.1.
U28379 Genomic DNA. Translation: AAA89136.1.
U00096 Genomic DNA. Translation: AAC76092.1.
AP009048 Genomic DNA. Translation: BAE77107.1.
PIRiA25215. RNECTA.
RefSeqiNP_417528.1. NC_000913.3.
WP_000708487.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP06961.
SMRiP06961. Positions 2-299.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259255. 13 interactions.
DIPiDIP-9250N.
IntActiP06961. 24 interactions.
MINTiMINT-1263446.
STRINGi511145.b3056.

Proteomic databases

PaxDbiP06961.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76092; AAC76092; b3056.
BAE77107; BAE77107; BAE77107.
GeneIDi947553.
KEGGiecj:JW3028.
eco:b3056.
PATRICi32121524. VBIEscCol129921_3149.

Organism-specific databases

EchoBASEiEB0134.
EcoGeneiEG10136. cca.

Phylogenomic databases

eggNOGiENOG4105D4J. Bacteria.
COG0617. LUCA.
HOGENOMiHOG000007368.
InParanoidiP06961.
KOiK00974.
OMAiSEWPSHK.
OrthoDBiEOG651SRP.
PhylomeDBiP06961.

Enzyme and pathway databases

BioCyciEcoCyc:EG10136-MONOMER.
ECOL316407:JW3028-MONOMER.
MetaCyc:EG10136-MONOMER.
BRENDAi2.7.7.72. 2026.
3.1.4.16. 2026.
3.1.4.37. 2026.
SABIO-RKP06961.

Miscellaneous databases

PROiP06961.

Family and domain databases

HAMAPiMF_01261. CCA_bact_type1.
MF_01262. CCA_bact_type2.
InterProiIPR012006. CCA_bact.
IPR006674. HD_domain.
IPR002646. PolA_pol_head_dom.
IPR032828. PolyA_RNA-bd.
[Graphical view]
PfamiPF01966. HD. 1 hit.
PF01743. PolyA_pol. 1 hit.
PF12627. PolyA_pol_RNAbd. 1 hit.
[Graphical view]
PIRSFiPIRSF000813. CCA_bact. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning, sequencing, and species relatedness of the Escherichia coli cca gene encoding the enzyme tRNA nucleotidyltransferase."
    Cudny H., Lupski J.R., Godson G.N., Deutscher M.P.
    J. Biol. Chem. 261:6444-6449(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "A mutation in Escherichia coli tRNA nucleotidyltransferase that affects only AMP incorporation is in a sequence often associated with nucleotide-binding proteins."
    Zhu L.Q., Cudny H., Deutscher M.P.
    J. Biol. Chem. 261:14875-14877(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 65-76, MUTAGENESIS OF GLY-70.
  5. "High-level overexpression, rapid purification, and properties of Escherichia coli tRNA nucleotidyltransferase."
    Cudny H., Deutscher M.P.
    J. Biol. Chem. 261:6450-6453(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, NUCLEOTIDYLTRANSFERASE ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES.
  6. "The HD domain of the Escherichia coli tRNA nucleotidyltransferase has 2',3'-cyclic phosphodiesterase, 2'-nucleotidase, and phosphatase activities."
    Yakunin A.F., Proudfoot M., Kuznetsova E., Savchenko A., Brown G., Arrowsmith C.H., Edwards A.M.
    J. Biol. Chem. 279:36819-36827(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHOHYDROLASE ACTIVITIES, CHARACTERIZATION, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF ASP-21; ASP-23; HIS-255; ASP-256; HIS-305 AND ASP-306.

Entry informationi

Entry nameiCCA_ECOLI
AccessioniPrimary (citable) accession number: P06961
Secondary accession number(s): Q2M9E9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: April 1, 1988
Last modified: May 11, 2016
This is version 142 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

A single active site specifically recognizes both ATP and CTP and is responsible for their addition.By similarity

Keywords - Technical termi

Complete proteome, Multifunctional enzyme, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.