Multifunctional CCA protein - Escherichia coli (strain K12)

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Reviewed, UniProtKB/Swiss-Prot P06961 (CCA_ECOLI)

Last modified June 16, 2009. Version 83. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    Multifunctional CCA protein
Including the following 4 domains:
    1- Recommended name:
            CCA-adding enzyme
              EC=2.7.7.25
              EC=2.7.7.21
        Alternative name(s):
            tRNA nucleotidyltransferase
            tRNA adenylyl-/cytidylyl-transferase
            tRNA CCA-pyrophosphorylase
            tRNA-NT
    2- Recommended name:
            2'-nucleotidase
              EC=3.1.3.-
    3- Recommended name:
            2',3'-cyclic phosphodiesterase
              EC=3.1.4.-
    4- Recommended name:
            Phosphatase
              EC=3.1.3.-

Gene names

Name:	cca
Ordered Locus Names:	b3056, JW3028

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

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Protein attributes

Sequence length	412 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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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	ATP + tRNA(n) = diphosphate + tRNA(n+1). HAMAP MF_01261 CTP + tRNA(n) = diphosphate + tRNA(n+1). HAMAP MF_01261
Cofactor	Magnesium for nucleotidyltransferase activity. HAMAP MF_01261 Nickel for phosphatase activity. HAMAP MF_01261
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.
Sequence similarities	Belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family. Bacterial CCA-adding enzyme type 1 subfamily.
Biophysicochemical properties	Kinetic parameters: K_M=0.33 mM for ATP (in the tRNA-NT activity assay) HAMAP MF_01261 K_M=0.03 mM for CTP (in the tRNA-NT activity assay) K_M=0.015 mM for tRNA-CC K_M=0.02 mM for tRNA-C K_M=6.2 mM for pNPP K_M=0.10 mM for PPi K_M=0.15 mM for NADP K_M=0.19 mM for ADP K_M=0.18 mM for ATP (in the phosphatase activity assay) K_M=0.53 mM for CDP K_M=0.13 mM for CTP (in the phosphatase activity assay) K_M=0.76 mM for 2'-AMP K_M=0.49 mM for 2',3'-cAMP K_M=1.60 mM for 2',3'-cGMP V_max=12.4 µmol/min/mg enzyme with pNPP as substrate V_max=3.01 µmol/min/mg enzyme with PPi as substrate V_max=17.9 µmol/min/mg enzyme with NADP as substrate V_max=1.49 µmol/min/mg enzyme with ADP as substrate V_max=4.53 µmol/min/mg enzyme with ATP as substrate (in the phosphatase activity assay) V_max=5.80 µmol/min/mg enzyme with CDP as substrate V_max=4.03 µmol/min/mg enzyme with CTP as substrate (in the phosphatase activity assay) V_max=3.71 µmol/min/mg enzyme with 2'-AMP as substrate V_max=3.21 µmol/min/mg enzyme with 2',3'-cAMP as substrate V_max=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.

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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
Gene Ontology (GO)
Biological process	RNA repair Inferred from electronic annotation. Source: UniProtKB-KW tRNA 3'-terminal CCA addition Inferred from electronic annotation. Source: HAMAP
Molecular function	ATP binding Inferred from electronic annotation. Source: HAMAP cyclic-nucleotide phosphodiesterase activity Inferred from electronic annotation. Source: HAMAP magnesium ion binding Inferred from electronic annotation. Source: HAMAP nickel ion binding Inferred from electronic annotation. Source: UniProtKB-KW phosphatase activity Inferred from electronic annotation. Source: HAMAP protein binding Inferred from physical interaction. Source: IntAct tRNA adenylyltransferase activity Inferred from electronic annotation. Source: HAMAP tRNA binding Inferred from electronic annotation. Source: HAMAP tRNA cytidylyltransferase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

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Binary interactions

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

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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

Magnesium By similarity

Metal binding

Magnesium By similarity

Binding site

ATP or CTP; via amide nitrogen By similarity

Binding site

ATP or CTP By similarity

Binding site

ATP or CTP By similarity

Binding site

137

ATP or CTP By similarity

Binding site

140

ATP or CTP By similarity

Experimental info

Mutagenesis

D → A: No effect on phosphodiesterase and phosphatase activities. Ref.6

Mutagenesis

D → A: No effect on phosphodiesterase and phosphatase activities. Ref.6

Mutagenesis

G → D: Lowered AMP incorporation. Ref.4

Mutagenesis

255

H → A: Loss of phosphodiesterase and phosphatase activities. Ref.6

Mutagenesis

256

D → A: Loss of phosphodiesterase and phosphatase activities. Ref.6

Mutagenesis

305

H → A: Loss of phosphodiesterase and phosphatase activities. Ref.6

Mutagenesis

306

D → A: Still possesses phosphodiesterase and phosphatase activities. Ref.6

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Sequences

Sequence

Length

Mass (Da)

Tools

P06961-1 [UniParc].

Last modified April 1, 1988. Version 1.
Checksum: 947182E6086220F7
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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

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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.

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Cross-references

Sequence databases
	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	AP_003606.1. NP_417528.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
DIP	DIP:9250N.
IntAct	P06961. 24 interactions.
Genome annotation databases
GeneID	947553.
GenomeReviews	Gene locus JW3028 in contig AP009048_GR. Gene locus b3056 in contig U00096_GR.
KEGG	ecj:JW3028. eco:b3056.
Organism-specific databases
EchoBASE	EB0134.
EcoGene	EG10136. cca.
CMR	Search...
Phylogenomic databases
HOGENOM	P06961.
OMA	P06961. KHHGHGQ.
Enzyme and pathway databases
BioCyc	EcoCyc:EG10136-MON.
BRENDA	3.1.4.16. 246. 3.1.4.37. 246.
Family and domain databases
HAMAP	MF_01261. [Tree]
InterPro	IPR012006. CCA_bact. IPR003607. Met-dep_phosphohydro_HD. IPR006674. Met-dep_phosphohydro_HD_sub. IPR002646. PolyA_pol_reg. [Graphical view]
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...

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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:	June 16, 2009
This is version 83 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

SIMILARITY comments

Index of protein domains and families

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Sites

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents