 |
PDBsum entry 1e3h
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Polyribonucleotide transferase
|
PDB id
|
|
|
|
1e3h
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, Processivity, And regulation.
|
|
|
Authors
|
|
M.F.Symmons,
G.H.Jones,
B.F.Luisi.
|
|
|
Ref.
|
|
Structure, 2000,
8,
1215-1226.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
BACKGROUND: Polynucleotide phosphorylase (PNPase) is a polyribonucleotide
nucleotidyl transferase (E.C.2.7.7.8) that degrades mRNA in prokaryotes.
Streptomyces antibioticus PNPase also assays as a guanosine 3'-diphosphate
5'-triphosphate (pppGpp) synthetase (E.C.2.7.6.5). It may function to coordinate
changes in mRNA lifetimes with pppGpp levels during the Streptomyces lifecycle.
RESULTS: The structure of S. antibioticus PNPase without bound RNA but with the
phosphate analog tungstate bound at the PNPase catalytic sites was determined by
X-ray crystallography and shows a trimeric multidomain protein with a central
channel. The structural core has a novel duplicated architecture formed by
association of two homologous domains. The tungstate derivative structure
reveals the PNPase active site in the second of these core domains.
Structure-based sequence analysis suggests that the pppGpp synthetase active
site is located in the first core domain. CONCLUSIONS: This is the first
structure of a PNPase and shows the structural basis for the trimer assembly,
the arrangement of accessory RNA binding domains, and the likely catalytic
residues of the PNPase active site. A possible function of the trimer channel is
as a contribution to both the processivity of degradation and the regulation of
PNPase action by RNA structural elements.
|
|
|
|
|
|
Figure 6.
Figure 6. View Into Putative PNPase Active Site(a)
Difference density at tungstate binding site with contours at 5
s (colored green). Overlaid is 2F[O]-F[C] sigmaa-weighted map
[45] and final refined model for tungstate derivative with
contours at 1.00 s (the model is colored red on outer and purple
on inner surfaces).(b) Secondary structure and key conserved
residues around the tungstate binding site. Sidechain atoms of
residues in tungstate binding loop and other key conserved
residues are shown. Residues of two additional conserved loops
are shown as colored Ca positions and numbered in corresponding
color. Residues 458-460 are shown with serine, asparagine, and
glycine colored pink, green, and black, respectively; residues
369-371 are shown with arginine, glycine, glutamic acid, and
threonine colored blue, black, orange, and pink, respectively;
and residues 412-413 are shown with glycine and glutamic acid as
black and orange, respectively
|
|
|
|
|
|
The above figure is
reprinted
by permission from Cell Press:
Structure
(2000,
8,
1215-1226)
copyright 2000.
|
|
|
|
|
|
|
