 |
PDBsum entry 3qkf
|
|
|
|
Obsolete entry |
|
|
PDB id:
|
|
|
|
| Name: |
|
Isomerase
|
|
|
Title:
|
|
Crystal structure of the mutant p317a of d-mannonate dehydratase from chromohalobacter salexigens complexed with mg and d-gluconate
|
|
Structure:
|
|
Mandelate racemase/muconate lactonizing enzyme. Chain: a, b, c, d, e, f, g, h. Engineered: yes. Mutation: yes
|
|
Source:
|
|
Chromohalobacter salexigens. Organism_taxid: 158080. Gene: csal_2974. Expressed in: escherichia coli. Expression_system_taxid: 562
|
|
Resolution:
|
|
|
1.45Å
|
R-factor:
|
0.201
|
R-free:
|
0.229
|
|
|
Authors:
|
|
A.A.Fedorov,E.V.Fedorov,D.Wichelecki,J.A.Gerlt,S.C.Almo
|
|
Key ref:
|
|
S.R.Connell
et al.
(2008).
A new tRNA intermediate revealed on the ribosome during EF4-mediated back-translocation.
Nat Struct Biol,
15,
910-915.
PubMed id:
|
|
|
Date:
|
|
|
01-Feb-11
|
Release date:
|
01-Feb-12
|
|
|
|
|
|
|
PROCHECK
|
|
|
|
|
|
Headers
|
|
|
|
References
|
|
|
|
|
|
|
|
Q1QT89
(DMGD_CHRSD) -
D-galactonate dehydratase family member ManD from Chromohalobacter salexigens (strain ATCC BAA-138 / DSM 3043 / CIP 106854 / NCIMB 13768 / 1H11)
|
|
|
|
Seq:
Struc:
|
|
|
|
403 a.a.
393 a.a.*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Key: |
 |
PfamA domain |
|
|
 |
Secondary structure |
|
 |
CATH domain |
|
|
*
PDB and UniProt seqs differ
at 2 residue positions (black
crosses)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
|
Nat Struct Biol
15:910-915
(2008)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
A new tRNA intermediate revealed on the ribosome during EF4-mediated back-translocation.
|
|
S.R.Connell,
M.Topf,
Y.Qin,
D.N.Wilson,
T.Mielke,
P.Fucini,
K.H.Nierhaus,
C.M.Spahn.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
EF4 (LepA) is an almost universally conserved translational GTPase in
eubacteria. It seems to be essential under environmental stress conditions and
has previously been shown to back-translocate the tRNAs on the ribosome, thereby
reverting the canonical translocation reaction. In the current work, EF4 was
directly visualized in the process of back-translocating tRNAs by
single-particle cryo-EM. Using flexible fitting methods, we built a model of
ribosome-bound EF4 based on the cryo-EM map and a recently published unbound EF4
X-ray structure. The cryo-EM map establishes EF4 as a noncanonical elongation
factor that interacts not only with the elongating ribosome, but also with the
back-translocated tRNA in the A-site region, which is present in a previously
unseen, intermediate state and deviates markedly from the position of a
canonical A-tRNA. Our results, therefore, provide insight into the underlying
structural principles governing back-translocation.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
L.Wang,
F.Yang,
D.Zhang,
Z.Chen,
R.M.Xu,
K.H.Nierhaus,
W.Gong,
and
Y.Qin
(2012).
A conserved proline switch on the ribosome facilitates the recruitment and binding of trGTPases.
|
| |
Nat Struct Mol Biol,
19,
403-410.
|
|
|
|
|
|
|
G.Blaha,
R.E.Stanley,
and
T.A.Steitz
(2009).
Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome.
|
| |
Science,
325,
966-970.
|
|
|
PDB codes:
|
|
|
|
|
|
|
The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
|
|
Links
