P06961 (CCA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Multifunctional CCA protein

Including the following 4 domains:

1. 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. 2'-nucleotidase
   EC=3.1.3.-
3. 2',3'-cyclic phosphodiesterase
   EC=3.1.4.-
4. Phosphatase
   EC=3.1.3.-

Gene names

Name:	cca
Ordered Locus Names:	b3056, JW3028

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	412 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.5
Catalytic activity	A tRNA precursor + 2 CTP + ATP = a tRNA with a 3' CCA end + 3 diphosphate. HAMAP MF_01261
Cofactor	Magnesium for nucleotidyltransferase activity. Nickel for phosphatase activity.
Enzyme regulation	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+. HAMAP MF_01261
Subunit structure	Monomer. Can also form homodimers and oligomers, but with low levels. Ref.6
Domain	Comprises two domains: an N-terminal domain containing the nucleotidyltransferase activity and a C-terminal HD domain associated with both phosphodiesterase and phosphatase activities. HAMAP MF_01261
Miscellaneous	A single active site specifically recognizes both ATP and CTP and is responsible for their addition By similarity. HAMAP MF_01261
Sequence similarities	Belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family. Bacterial CCA-adding enzyme type 1 subfamily.
Biophysicochemical properties	Kinetic parameters: KM=0.33 mM for ATP (in the tRNA-NT activity assay) Ref.5 Ref.6 KM=0.03 mM for CTP (in the tRNA-NT activity assay) KM=0.015 mM for tRNA-CC KM=0.02 mM for tRNA-C KM=6.2 mM for pNPP KM=0.10 mM for PPi KM=0.15 mM for NADP KM=0.19 mM for ADP KM=0.18 mM for ATP (in the phosphatase activity assay) KM=0.53 mM for CDP KM=0.13 mM for CTP (in the phosphatase activity assay) KM=0.76 mM for 2'-AMP KM=0.49 mM for 2',3'-cAMP KM=1.60 mM for 2',3'-cGMP Vmax=12.4 µmol/min/mg enzyme with pNPP as substrate Vmax=3.01 µmol/min/mg enzyme with PPi as substrate Vmax=17.9 µmol/min/mg enzyme with NADP as substrate Vmax=1.49 µmol/min/mg enzyme with ADP as substrate Vmax=4.53 µmol/min/mg enzyme with ATP as substrate (in the phosphatase activity assay) Vmax=5.80 µmol/min/mg enzyme with CDP as substrate Vmax=4.03 µmol/min/mg enzyme with CTP as substrate (in the phosphatase activity assay) Vmax=3.71 µmol/min/mg enzyme with 2'-AMP as substrate Vmax=3.21 µmol/min/mg enzyme with 2',3'-cAMP as substrate Vmax=2.36 µmol/min/mg enzyme with 2',3'-cGMP as substrate pH dependence: Optimum pH is 9.4 for AMP incorporation, 10.0 for CMP incorporation, and 7.0 for the phosphatase and phosphodiesterase activities.

Ontologies

Keywords
Biological process	RNA repair tRNA processing
Ligand	ATP-binding Magnesium Metal-binding Nickel Nucleotide-binding RNA-binding
Molecular function	Hydrolase Nucleotidyltransferase Transferase
Technical term	Complete proteome Multifunctional enzyme Reference proteome
Gene Ontology (GO)
Biological process	RNA repair Inferred from electronic annotation. Source: UniProtKB-KW tRNA 3'-terminal CCA addition Inferred from electronic annotation. Source: InterPro
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW RNA binding Inferred from electronic annotation. Source: UniProtKB-KW metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW phosphoric diester hydrolase activity Inferred from electronic annotation. Source: InterPro tRNA adenylyltransferase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
dtd	P0A6M4	1	EBI-545256,EBI-562575

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 412	412	Multifunctional CCA protein HAMAP MF_01261		PRO_0000138975
Sites
	Metal binding	21	1	Magnesium By similarity
	Metal binding	23	1	Magnesium By similarity
	Binding site	8	1	ATP or CTP; via amide nitrogen By similarity
	Binding site	11	1	ATP or CTP By similarity
	Binding site	91	1	ATP or CTP By similarity
	Binding site	137	1	ATP or CTP By similarity
	Binding site	140	1	ATP or CTP By similarity
Experimental info
	Mutagenesis	21	1	D → A: No effect on phosphodiesterase and phosphatase activities. Ref.6
	Mutagenesis	23	1	D → A: No effect on phosphodiesterase and phosphatase activities. Ref.6
	Mutagenesis	70	1	G → D: Lowered AMP incorporation. Ref.4
	Mutagenesis	255	1	H → A: Loss of phosphodiesterase and phosphatase activities. Ref.6
	Mutagenesis	256	1	D → A: Loss of phosphodiesterase and phosphatase activities. Ref.6
	Mutagenesis	305	1	H → A: Loss of phosphodiesterase and phosphatase activities. Ref.6
	Mutagenesis	306	1	D → A: Still possesses phosphodiesterase and phosphatase activities. Ref.6

Sequences

	Sequence		Length	Mass (Da)
	P06961 [UniParc]. Last modified April 1, 1988. Version 1. Checksum: 947182E6086220F7	FASTA	412	46,467
	10 20 30 40 50 60 MKIYLVGGAV RDALLGLPVK DRDWVVVGST PQEMLDAGYQ QVGRDFPVFL HPQTHEEYAL 70 80 90 100 110 120 ARTERKSGSG YTGFTCYAAP DVTLEDDLKR RDLTINALAQ DDNGEIIDPY NGLGDLQNRL 130 140 150 160 170 180 LRHVSPAFGE DPLRVLRVAR FAARYAHLGF RIADETLALM REMTHAGELE HLTPERVWKE 190 200 210 220 230 240 TESALTTRNP QVFFQVLRDC GALRVLFPEI DALFGVPAPA KWHPEIDTGI HTLMTLSMAA 250 260 270 280 290 300 MLSPQVDVRF ATLCHDLGKG LTPPELWPRH HGHGPAGVKL VEQLCQRLRV PNEIRDLARL 310 320 330 340 350 360 VAEFHDLIHT FPMLNPKTIV KLFDSIDAWR KPQRVEQLAL TSEADVRGRT GFESADYPQG 370 380 390 400 410 RWLREAWEVA QSVPTKAVVE AGFKGVEIRE ELTRRRIAAV ASWKEQRCPK PE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 3009457] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] 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: 16738553] [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: 3533927] [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: 3516995] [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: 15210699] [Abstract] Cited for: PHOSPHOHYDROLASE ACTIVITIES, CHARACTERIZATION, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF ASP-21; ASP-23; HIS-255; ASP-256; HIS-305 AND ASP-306.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	M12788 Genomic DNA. Translation: AAA23541.1. U28379 Genomic DNA. Translation: AAA89136.1. U00096 Genomic DNA. Translation: AAC76092.1. AP009048 Genomic DNA. Translation: BAE77107.1.
PIR	RNECTA. A25215.
RefSeq	NP_417528.1. NC_000913.2.
3D structure databases
ProteinModelPortal	P06961.
SMR	P06961. Positions 1-400.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-9250N.
IntAct	P06961. 24 interactions.
MINT	MINT-1263446.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	EBESCT00000002337; EBESCP00000002337; EBESCG00000001907. EBESCT00000017105; EBESCP00000016396; EBESCG00000016164.
GeneID	947553.
GenomeReviews	Gene locus JW3028 in contig AP009048_GR. Gene locus b3056 in contig U00096_GR.
KEGG	ecj:JW3028. eco:b3056.
PATRIC	32121524. VBIEscCol129921_3149.
Organism-specific databases
EchoBASE	EB0134.
EcoGene	EG10136. cca.
Phylogenomic databases
eggNOG	COG0617.
GeneTree	EBGT00050000009869.
HOGENOM	HBG635063.
OMA	GHGQKGL.
PhylomeDB	P06961.
ProtClustDB	PRK10885.
Enzyme and pathway databases
BioCyc	EcoCyc:EG10136-MONOMER. MetaCyc:EG10136-MONOMER.
BRENDA	3.1.4.16. 2026.
Gene expression databases
Genevestigator	P06961.
Family and domain databases
HAMAP	MF_01261. CCA_bact_type1. [Tree]
InterPro	IPR012006. CCA_bact. IPR003607. Metal-dep_PHydrolase_HD_dom. IPR006674. Metal-dep_PHydrolase_HD_sub. IPR002646. PolA_pol_head_dom. [Graphical view]
KO	K00974.
Pfam	PF01966. HD. 1 hit. PF01743. PolyA_pol. 1 hit. [Graphical view]
PIRSF	PIRSF000813. CCA_bact. 1 hit.
SMART	SM00471. HDc. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

CCA_ECOLI

Accession

Primary (citable) accession number: P06961
Secondary accession number(s): Q2M9E9

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1988
Last sequence update:	April 1, 1988
Last modified:	January 25, 2012
This is version 109 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program