PROSITE documentation PDOC00651

{PDOC00651}
{PS00829; GREAB_1}
{PS00830; GREAB_2}
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* Prokaryotic transcription elongation factors signatures *
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Bacterial proteins   greA and  greB [1,2]  are  necessary  for  efficient  RNA
polymerase transcription elongation  past  template-encoded  arresting  sites.
Arresting sites  in  DNA  have  the property of trapping a certain fraction of
elongating RNA polymerases  that  pass  through, resulting in  locked DNA/RNA/
polymerase ternary  complexes.  Cleavage of the nascent transcript by cleavage
factors, such  as  greA or greB, allows  the resumption of elongation from the
new 3'terminus.  GreA  induces cleavage 2 or 3 nucleotides behind the terminus
while greB releases longer sequences up to 9 nucleotides in length.

GreA and greB are related proteins  of about 160 amino-acid residues.  We have
developed two   signature   patterns   for  this  protein  family.  The  first
corresponds to  a  conserved region in the N-terminal section, the second to a
region in the C-terminal section.

-Consensus pattern: [EKH]-[LHVI]-x(9,10)-[IVNLR]-x(3)-[LIV]-x(6)-G-D-x(2)-E-N-
                    [GSA]-x-Y
-Sequences known to belong to this class detected by the pattern: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Consensus pattern: S-x(2)-S-[PK]-[LIVMF]-[AG]-x-[SAGNE]-[LIVM]-[LIVY]-x(4)-
                    [DNG]-[DE]
-Sequences known to belong to this class detected by the pattern: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Last update: December 2004 / Pattern and text revised.

[ 1] Borukhov S., Sagitov V., Goldfarb A.
     "Transcript cleavage factors from E. coli."
     Cell 72:459-466(1993).
     PubMed=8431948
[ 2] Stebbins C.E., Borukhov S., Orlova M., Polyakov A., Goldfarb A.,
     Darst S.A.
     "Crystal structure of the GreA transcript cleavage factor from
     Escherichia coli."
     Nature 373:636-640(1995).
     PubMed=7854424; DOI=10.1038/373636a0

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