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Chlamydia pneumoniae Search Results

Record: 1 of 1  
MiniMap IGR457 IGR460 IGR456 IGR455 IGR459 IGR458 CPn0581 CPn0573 prfB, - CPn0576 murA, - CPn0571 CPn0577 CPn0582 truA, - CPn0580 CPn0578 CPn0572 CPn0581 CPn0573 prfB, - CPn0576 murA, - CPn0571 CPn0577 CPn0582 truA, - CPn0580 CPn0578 CPn0572 CPn0581 CPn0573 prfB, - CPn0576 murA, - CPn0571 CPn0575 CPn0574 CPn0574 CPn0575 CPn0577 CPn0582 truA, - CPn0580 CPn0578 CPn0572 ygbP,yacM, - CPn0579 ygbP,yacM, - CPn0579
* Calculated from Protein Sequence

Gene ID: CPn0576

DNA Molecule Name:
1  

Genbank ID:


Gene Name:
prfB  

Definition:
peptide chain release factor 2 (a natural UGA frameshift)

Gene Start:
667598

Gene Stop:
666491

Gene Length:
1105

Molecular Weight*:
0

pI*:
5.00

Net Charge*:
-13.31

EC:
 

Functional Class:
translation; translation factors  

Pathway: pathway table

Comment:
For review on E. coli release factor 2 UGA frameshifting, see the chapter by Atkins and Gesteland, 1996 (In "Translational Control" pp. 657-662. Eds. Hershey, Mathews, Sonenberg. CSH Laboratory Press).
In E. coli the first 25 aa are encoded by frame 0. Just before encountering the UGA stop codon the frame shifts to frame +1 for re-pairing and continues for another 340 aa. The framshifting in RF2 decoding may be autoregualtory (high levels of RF2, low levels of UGA frameshifting). It is believed that the recognition sites for RF2 may be quadruplets (i.e., UGAN with UGAC being the poorest termination signal in E. coli).

This region was originally part of the IGR458 sequence. However,
upon nucleotide sequence comparision to the Berkeley C.
pneumoniae database and
to the C. trachomatis genome database, IGR458 was divided into
two regions: CPn0576 and IGR458. IGR458 had some homology to the record for release factor 2 from C. trachomatis (CT459). Upon examination of the sequence,
IGR458 could encode one long open reading frame of 348 residues
(frame -1, with predicted start at position 667543 and predicted
stop at 666491, at the 'A', 1 nt upstream of the of CPn0575 'ATG'
start codon). This 348 aa protein starts with a Leucine. The
14 bases upstream of Leu start are: GGAAAtAtctttag, with capital
letters being possible SD contributors.

Upon analysis of the 6 translational frames obtained from the
original IGR458 nucleotide sequence (nt 666495-667894), there is
a potential coding region downstream from the potential
ORF mentioned above, starting at nt position 667598 (frame -3)
and ending at 667527. It starts with Met and the 10 bp upstream
of the start looks like: GGtAAGAGtA(ATG start). This ORF (frame -3)
ends at nt position 667527 with a TGA codon.

The UGA shift, characteristic of RF2 from E. coli, is believed to occur at nt position 667527 and to take
up frame -1 at this point, at the D residue at nt position 667528
(as indicated by lower case 'd' in the gene protein sequence field of this record).
According to BLAST protein comparison with CT459, the shift may include the F residue upstream of the D at nt 667531, it all depends on where the actual frameshift occurs.

Potential protein sequence for CPn0576:
start frame -3:
MQENLDKRLEALRTEISLAARSL
start frame -1 (truncated to pick up at the D residue):
dLDKKQKELQVLEEESSEENFWQDSVHAGKISEQIVSLRRQIQEYQELKSKIDAIEFFLED
ADALEDPAICEDLEKEFLFCEKKLAVWETQRLLSGEADKNSCFLTINAGAGGTESCDWVEMLFRMY
SRWATKHQWALEVVDRLDGEVVGIKHVTVKFSGMYAYGYAKAERGVHRLVRISPFDSNGKRHTSFA
SVDVFPEIDDQIKIEIRPNDLRIDTFRSSGAGGQHVNVTESAVRITHLPSGVVVSCQNERSQIQNR
ESCMKMLQAKLYQQVLQERLEKQSLDRKDKKEIAWGSQIRNYVFQPYTLVKDVRTGHETGNVQAML
DGELLDEFIKAYLAEFGEVS$

Blast Summary:  PSI-Blast Search
CPn0576 is orthologously related to CT459, a potential peptide release factor 2 (RF-2) and they share 35% similarity.

COGS Summary:  COGS Search
BeTs to 11 clades of COG1186
COG name: Protein chain release factor B
Functional Class:  J
The phylogenetic pattern of COG1186 is -----qvcebrhuj--olinx
Number of proteins in this genome belonging to this COG is 1

Blocks Summary:  Blocks Search


ProDom Summary:  Protein Domain Search


Paralogs:  Local Blast Search
No evidence of paralogs in C. pneumoniae.

Pfam Summary:  Pfam Search
Residues 83 to 193 (E-value = 9.3e-55) place CPn0576 in the PCRF family which is described as PCRF domain (PF03462)
Residues 225 to 336 (E-value = 1.7e-71) place CPn0576 in the RF-1 family which is described as Peptidyl-tRNA hydrolase domain (PF00472)

PDB Hit:


Gene Protein Sequence:
MQENLDKRLEALRTEISLAARSLdLDKKQKELQVLEEESSEENFWQDSVH
AGKISEQIVSLRRQIQEYQELKSKIDAIEFFLEDADALEDPAICEDLEKE
FLFCEKKLAVWETQRLLSGEADKNSCFLTINAGAGGTESCDWVEMLFRMY
SRWATKHQWALEVVDRLDGEVVGIKHVTVKFSGMYAYGYAKAERGVHRLV
RISPFDSNGKRHTSFASVDVFPEIDDQIKIEIRPNDLRIDTFRSSGAGGQ
HVNVTESAVRITHLPSGVVVSCQNERSQIQNRESCMKMLQAKLYQQVLQE
RLEKQSLDRKDKKEIAWGSQIRNYVFQPYTLVKDVRTGHETGNVQAMLDG
ELLDEFIKAYLAEFGEVS$

Gene Nucleotide Sequence:  Sequence Viewer
ATGCAGGAAAATTTAGACAAGCGTTTGGAAGCACTTCGCACGGAAATATC
TTTAGCTGCGAGGTCTCTTTGACCTCGATAAAAAACAAAAAGAACTTCAA
GTTTTAGAAGAAGAAAGTTCCGAAGAAAATTTTTGGCAAGACAGTGTTCA
TGCTGGAAAAATTTCTGAACAGATTGTAAGTCTGAGACGACAAATCCAAG
AGTATCAGGAATTAAAAAGCAAAATAGATGCTATAGAGTTTTTCCTCGAG
GATGCCGATGCTCTTGAAGACCCTGCGATTTGTGAAGACTTAGAGAAAGA
ATTTCTCTTTTGTGAGAAGAAACTTGCTGTTTGGGAGACGCAACGGTTGC
TTTCCGGAGAGGCAGACAAGAACTCTTGTTTCCTTACGATCAATGCTGGG
GCAGGTGGGACGGAGTCGTGTGATTGGGTAGAGATGCTGTTTCGTATGTA
TTCCCGATGGGCGACGAAACATCAATGGGCCTTAGAGGTTGTCGATCGCT
TAGATGGTGAAGTTGTTGGAATTAAGCATGTTACTGTAAAGTTTTCAGGA
ATGTATGCTTATGGGTATGCCAAGGCAGAGCGAGGAGTACATCGTTTGGT
GCGTATCTCACCTTTCGATAGTAATGGGAAACGTCACACTAGCTTTGCTT
CTGTAGACGTCTTCCCTGAGATTGATGATCAGATTAAGATTGAGATACGA
CCTAATGATTTACGTATAGATACGTTTCGTTCTTCGGGAGCAGGAGGACA
ACACGTCAACGTTACGGAATCCGCAGTCAGGATCACGCACCTACCTTCTG
GAGTCGTTGTTTCATGTCAAAATGAACGTAGTCAGATACAGAATCGTGAG
AGCTGTATGAAAATGCTACAAGCAAAGTTGTATCAGCAGGTTTTACAAGA
ACGTTTAGAGAAGCAATCTCTTGATCGCAAAGATAAAAAGGAAATTGCTT
GGGGATCTCAAATTCGCAACTACGTATTTCAGCCCTATACTCTTGTTAAA
GATGTACGTACGGGACATGAAACAGGAAATGTCCAAGCGATGCTCGACGG
CGAGCTATTGGATGAATTTATTAAAGCATATTTGGCAGAGTTTGGAGAAG
TTTCATGA


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