Reviewed, UniProtKB/Swiss-Prot P03842 (RNPH_ECOLI)

Names and origin

Protein names

Recommended name:
    Ribonuclease PH
      Short name=RNase PH
    EC=2.7.7.56
Alternative name(s):
    tRNA nucleotidyltransferase

Gene names

Name:	rph
Ordered Locus Names:	b3643

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	238 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Phosphorolytic exoribonuclease that removes nucleotide residues following the -CCA terminus of tRNA and adds nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates. Also acts to regulate the attenuation of pyrE. Ref.5
Catalytic activity	tRNA(n+1) + phosphate = tRNA(n) + a nucleoside diphosphate. HAMAP MF_00564
Miscellaneous	The gene in K12 strains MG1655 and W3110 (and also other derivatives of K12 W1485) has a frameshift mutation that leads to loss of activity, although the protein may be translated. Thus in those strains rph is a pseudogene. The sequence shown here is the functional one corresponding to K12 strains MC1000 and MC4100. HAMAP MF_00564
Sequence similarities	Belongs to the RNase PH family.

Ontologies

Keywords
Biological process	tRNA processing
Molecular function	Nucleotidyltransferase Transferase
Technical term	Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	tRNA processing Inferred from electronic annotation. Source: HAMAP
Molecular function	3'-5'-exoribonuclease activity Inferred from electronic annotation. Source: InterPro tRNA binding Inferred from electronic annotation. Source: HAMAP tRNA nucleotidyltransferase activity Inferred from electronic annotation. Source: HAMAP tRNA-specific ribonuclease activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 238	238	Ribonuclease PH HAMAP MF_00564		PRO_0000139889
Natural variations
	Natural variant	224 – 238	15	GIESI…AALAN → ESNPL in strain: K12 / MG1655 / ATCC 47076 and K12 / W3110 / ATCC 27325 / DSM 5911.
Experimental info
	Sequence conflict	123 – 124	2	GG → AW in CAA25357. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	P03842-1 [UniParc]. Last modified July 1, 1993. Version 2. Checksum: 7299C5C8F2364D34	FASTA	238	25,352
	10 20 30 40 50 60 MRPAGRSNNQ VRPVTLTRNY TKHAEGSVLV EFGDTKVLCT ASIEEGVPRF LKGQGQGWIT 70 80 90 100 110 120 AEYGMLPRST HTRNAREAAK GKQGGRTMEI QRLIARALRA AVDLKALGEF TITLDCDVLQ 130 140 150 160 170 180 ADGGTRTASI TGACVALVDA LQKLVENGKL KTNPMKGMVA AVSVGIVNGE AVCDLEYVED 190 200 210 220 230 SAAETDMNVV MTEDGRIIEV QGTAEGEPFT HEELLILLAL ARGGIESIVA TQKAALAN

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Structure of the Escherichia coli pyrE operon and control of pyrE expression by a UTP modulated intercistronic attentuation." Poulsen P., Bonekamp F., Jensen K.F. EMBO J. 3:1783-1790(1984) [PubMed: 6207018] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.
[2]	"DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication." Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R. Genomics 16:551-561(1993) [PubMed: 7686882] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"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.
[4]	"Three genes preceding pyrE on the Escherichia coli chromosome are essential for survival and normal cell morphology in stationary culture and at high temperature." Poulsen P., Jensen K.F. Res. Microbiol. 142:283-288(1991) [PubMed: 1925027] [Abstract] Cited for: IMPORTANCE AT HIGH TEMPERATURE. Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.
[5]	"Escherichia coli orfE (upstream of pyrE) encodes RNase PH." Ost K.A., Deutscher M.P. J. Bacteriol. 173:5589-5591(1991) [PubMed: 1885537] [Abstract] Cited for: FUNCTION, PARTIAL PROTEIN SEQUENCE OF 1-21.
[6]	"Overexpression and rapid purification of the orfE/rph gene product, RNase PH of Escherichia coli." Jensen K.F., Andersen J.T., Poulsen P. J. Biol. Chem. 267:17147-17152(1992) [PubMed: 1512252] [Abstract] Cited for: CHARACTERIZATION. Strain: K12 / MC1000 / ATCC 39531.
[7]	"Characterization of Escherichia coli RNase PH." Kelly K.O., Deutscher M.P. J. Biol. Chem. 267:17153-17158(1992) [PubMed: 1512253] [Abstract] Cited for: CHARACTERIZATION. Strain: K12 / MC1000 / ATCC 39531.
[8]	"The Escherichia coli K-12 'wild types' W3110 and MG1655 have an rph frameshift mutation that leads to pyrimidine starvation due to low pyrE expression levels." Jensen K.F. J. Bacteriol. 175:3401-3407(1993) [PubMed: 8501045] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 208-238 (STRAIN W3110), LOSS OF ACTIVITY IN SOME K12 STRAINS. Strain: K12 / MG1655 / ATCC 47076, K12 / W1485 and K12 / W3110 / ATCC 27325 / DSM 5911.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X00781 Genomic DNA. Translation: CAA25357.1. V01578 Genomic DNA. No translation available. L10328 Genomic DNA. Translation: AAA61996.1. U00096 Genomic DNA. Translation: ABV59576.1. Sequence problems. X72920 Genomic DNA. No translation available.
PIR	QQECPE. A04470.
3D structure databases
SMR	P03842. Positions 2-237.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-10738N.
STRING	P03842.
Genome annotation databases
GenomeReviews	Gene locus b3643 in contig U00096_GR.
KEGG	eco:b3643.
Organism-specific databases
EcoGene	EG10863. rph.
CMR	Search...
Phylogenomic databases
eggNOG	COG0689.
HOGENOM	HBG737187.
OMA	MLPRATG.
Enzyme and pathway databases
BioCyc	EcoCyc:EG10863-MONOMER. ECOL168927:B3643-MONOMER.
Gene expression databases
Genevestigator	P03842.
Family and domain databases
HAMAP	MF_00564. RNase_PH. [Tree]
InterPro	IPR001247. ExoRNase_PH_dom1. IPR015847. ExoRNase_PH_dom2. IPR020568. Ribosomal_S5_D2-typ_fold. IPR002381. RNase_PH_bac-type. IPR018336. RNase_PH_CS. [Graphical view]
Pfam	PF01138. RNase_PH. 1 hit. PF03725. RNase_PH_C. 1 hit. [Graphical view]
TIGRFAMs	TIGR01966. RNasePH. 1 hit.
PROSITE	PS01277. RIBONUCLEASE_PH. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RNPH_ECOLI

Accession

Primary (citable) accession number: P03842
Secondary accession number(s): A8DYQ0

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	July 1, 1993
Last modified:	February 9, 2010
This is version 87 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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