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P46849 (RTCA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 118. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
RNA 3'-terminal phosphate cyclase

Short name=RNA cyclase
Short name=RNA-3'-phosphate cyclase
EC=6.5.1.4
Gene names
Name:rtcA
Synonyms:yhgJ, yhgK
Ordered Locus Names:b4475, JW5688
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length338 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the conversion of 3'-phosphate to a 2',3'-cyclic phosphodiester at the end of RNA. The mechanism of action of the enzyme occurs in 3 steps: (A) adenylation of the enzyme by ATP; (B) transfer of adenylate to an RNA-N3'P to produce RNA-N3'PP5'A; (C) and attack of the adjacent 2'-hydroxyl on the 3'-phosphorus in the diester linkage to produce the cyclic end product. The biological role of this enzyme is unknown but it is likely to function in some aspects of cellular RNA processing. Ref.6

Catalytic activity

ATP + RNA 3'-terminal-phosphate = AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate. Ref.6 Ref.8

Subcellular location

Cytoplasm HAMAP-Rule MF_00200.

Disruption phenotype

Disruption of the rtcA gene does not affect growth. Ref.6

Miscellaneous

RtcA (apo form) crystallized as a disulfide-linked homodimer via Cys-307 (Ref.7) but the covalent RtcA-AMP catalytic intermediate crystallized as a monomer with the shortest distance between Cys-307 side chains of neighboring protomers being 41 Angstroms (Ref.8).

Sequence similarities

Belongs to the RNA 3'-terminal cyclase family. Type 1 subfamily.

Biophysicochemical properties

Kinetic parameters:

KM=20 µM for ATP Ref.6

KM=100 µM for GTP

pH dependence:

Optimum pH is 8.0-8.5.

Sequence caution

The sequence AAA58217.1 differs from that shown. Reason: Frameshift at position 122. Produces two separate ORFs.

The sequence AAA58218.1 differs from that shown. Reason: Frameshift at position 122. Produces two separate ORFs.

Ontologies

Keywords
   Cellular componentCytoplasm
   LigandATP-binding
Nucleotide-binding
   Molecular functionLigase
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processRNA processing

Inferred from electronic annotation. Source: InterPro

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionATP binding

Inferred from electronic annotation. Source: UniProtKB-KW

RNA-3'-phosphate cyclase activity

Inferred from direct assay Ref.6. Source: EcoCyc

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 338338RNA 3'-terminal phosphate cyclase HAMAP-Rule MF_00200
PRO_0000156416

Regions

Nucleotide binding283 – 2875ATP HAMAP-Rule MF_00200

Sites

Active site3081Tele-AMP-histidine intermediate Ref.8
Binding site1031ATP

Experimental info

Mutagenesis1031Q → A: No effect on RNA cyclase activity and RtcA adenylation. Ref.8
Mutagenesis1281S → A: No effect on RNA cyclase activity and RtcA adenylation. Ref.8
Mutagenesis1301P → G: 33% of wild-type RNA cyclase activity and 13% of wild-type RtcA adenylation. Ref.8
Mutagenesis1341F → A: 3% of wild-type RNA cyclase activity and 2% of wild-type RtcA adenylation. Ref.8
Mutagenesis2501F → A: 28% of wild-type RNA cyclase activity and 38% of wild-type RtcA adenylation. Ref.8
Mutagenesis2691E → A: Nearly no effect on RNA cyclase activity and 2-fold decrease in RtcA adenylation. Ref.8
Mutagenesis2831Y → A: 12% of wild-type RNA cyclase activity and 2% of wild-type RtcA adenylation. Ref.8
Mutagenesis2861D → A: Loss of RNA cyclase activity and RtcA adenylation. Ref.8
Mutagenesis2871Q → A: Loss of RNA cyclase activity and RtcA adenylation. Ref.8
Mutagenesis3081H → A or G: Loss of RNA cyclase activity and RtcA adenylation. Ref.8

Secondary structure

.................................................................. 338
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P46849 [UniParc].

Last modified December 1, 2000. Version 3.
Checksum: 3450201CB8E40CE7

FASTA33835,903
        10         20         30         40         50         60 
MKRMIALDGA QGEGGGQILR SALSLSMITG QPFTITSIRA GRAKPGLLRQ HLTAVKAATE 

        70         80         90        100        110        120 
ICGATVEGAE LGSQRLLFRP GTVRGGDYRF AIGSAGSCTL VLQTVLPALW FADGPSRVEV 

       130        140        150        160        170        180 
SGGTDNPSAP PADFIRRVLE PLLAKIGIHQ QTTLLRHGFY PAGGGVVATE VSPVASFNTL 

       190        200        210        220        230        240 
QLGERGNIVQ MRGEVLLAGV PRHVAEREIA TLAGSFSLHE QNIHNLPRDQ GPGNTVSLEV 

       250        260        270        280        290        300 
ESENITERFF VVGEKRVSAE VVAAQLVKEV KRYLASTAAV GEYLADQLVL PMALAGAGEF 

       310        320        330 
TVAHPSCHLL TNIAVVERFL PVRFSLIETD GVTRVSIE 

« Hide

References

« Hide 'large scale' references
[1]"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 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[2]"Escherichia coli K-12: a cooperatively developed annotation snapshot -- 2005."
Riley M., Abe T., Arnaud M.B., Berlyn M.K.B., Blattner F.R., Chaudhuri R.R., Glasner J.D., Horiuchi T., Keseler I.M., Kosuge T., Mori H., Perna N.T., Plunkett G. III, Rudd K.E., Serres M.H., Thomas G.H., Thomson N.R., Wishart D., Wanner B.L.
Nucleic Acids Res. 34:1-9(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: SEQUENCE REVISION.
[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]"The nucleotide sequence of the malT gene encoding the positive regulator of the Escherichia coli maltose regulon."
Cole S.T., Raibaud O.
Gene 42:201-208(1986) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 149-338.
Strain: K12.
[5]"The human RNA 3'-terminal phosphate cyclase is a member of a new family of proteins conserved in Eucarya, Bacteria and Archaea."
Genschik P., Billy E., Swianiewicz M., Filipowicz W.
EMBO J. 16:2955-2967(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: SEQUENCE REVISION, CHARACTERIZATION.
[6]"Characterization of the Escherichia coli RNA 3'-terminal phosphate cyclase and its sigma54-regulated operon."
Genschik P., Drabikowski K., Filipowicz W.
J. Biol. Chem. 273:25516-25526(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, CHARACTERIZATION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, DISRUPTION PHENOTYPE.
[7]"Crystal structure of RNA 3'-terminal phosphate cyclase, a ubiquitous enzyme with unusual topology."
Palm G.J., Billy E., Filipowicz W., Wlodawer A.
Structure 8:13-23(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
Strain: K12.
[8]"Structure of the RNA 3'-phosphate cyclase-adenylate intermediate illuminates nucleotide specificity and covalent nucleotidyl transfer."
Tanaka N., Smith P., Shuman S.
Structure 18:449-457(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.68 ANGSTROMS) IN COMPLEX WITH AMP, CATALYTIC ACTIVITY, ACTIVE SITE, REACTION MECHANISM, MUTAGENESIS OF GLN-103; SER-128; PRO-130; PHE-134; PHE-250; GLU-269; TYR-283; ASP-286; GLN-287 AND HIS-308.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U18997 Genomic DNA. Translation: AAA58218.1. Frameshift.
U18997 Genomic DNA. Translation: AAA58217.1. Frameshift.
U00096 Genomic DNA. Translation: AAT48181.1.
AP009048 Genomic DNA. Translation: BAE77872.1.
M13585 Genomic DNA. Translation: AAA83889.1.
RefSeqYP_026219.1. NC_000913.3.
YP_492013.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1QMHX-ray2.10A/B2-338[»]
1QMIX-ray2.80A/B/C/D2-338[»]
3KGDX-ray1.68A/B/C/D1-338[»]
3TUTX-ray1.58A1-338[»]
3TUXX-ray1.85A1-338[»]
3TV1X-ray1.90A/B1-338[»]
3TW3X-ray2.10A1-338[»]
ProteinModelPortalP46849.
SMRP46849. Positions 2-338.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING511145.b4475.

Proteomic databases

PRIDEP46849.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAT48181; AAT48181; b4475.
BAE77872; BAE77872; BAE77872.
GeneID12932192.
2847707.
KEGGecj:Y75_p3757.
eco:b4475.
PATRIC32122276. VBIEscCol129921_3515.

Organism-specific databases

EchoBASEEB2773.
EcoGeneEG12938. rtcA.

Phylogenomic databases

eggNOGCOG0430.
HOGENOMHOG000015264.
KOK01974.
OMARRGHYPK.
OrthoDBEOG6RNQDX.
ProtClustDBPRK04204.

Enzyme and pathway databases

BioCycEcoCyc:G7750-MONOMER.
ECOL316407:JW5688-MONOMER.
MetaCyc:G7750-MONOMER.
BRENDA6.5.1.4. 2026.

Gene expression databases

GenevestigatorP46849.

Family and domain databases

Gene3D3.30.360.20. 1 hit.
3.65.10.20. 2 hits.
HAMAPMF_00200. RTC.
InterProIPR013791. RNA3'-term_phos_cycl_insert.
IPR023797. RNA3'_phos_cyclase_dom.
IPR000228. RNA3'_term_phos_cyc.
IPR017770. RNA3'_term_phos_cyc_type_1.
IPR020719. RNA3'_term_phos_cycl-like_CS.
IPR013792. RNA3'P_cycl/enolpyr_Trfase_a/b.
[Graphical view]
PANTHERPTHR11096. PTHR11096. 1 hit.
PfamPF01137. RTC. 1 hit.
PF05189. RTC_insert. 1 hit.
[Graphical view]
SUPFAMSSF52913. SSF52913. 1 hit.
SSF55205. SSF55205. 2 hits.
TIGRFAMsTIGR03399. RNA_3prim_cycl. 1 hit.
PROSITEPS01287. RTC. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP46849.
PROP46849.

Entry information

Entry nameRTCA_ECOLI
AccessionPrimary (citable) accession number: P46849
Secondary accession number(s): P46848, Q2M784, Q47349
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: December 1, 2000
Last modified: March 19, 2014
This is version 118 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

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