 |
PDBsum entry 2e4l
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
PDB id:
|
|
|
|
| Name: |
|
Hydrolase
|
|
|
Title:
|
|
Thermodynamic and structural analysis of thermolabile rnase hi from shewanella oneidensis mr-1
|
|
Structure:
|
|
Ribonuclease hi. Chain: a. Synonym: rnase hi. Engineered: yes
|
|
Source:
|
|
Shewanella oneidensis. Organism_taxid: 211586. Strain: mr-1. Gene: rnha. Expressed in: escherichia coli. Expression_system_taxid: 562.
|
|
Resolution:
|
|
|
2.00Å
|
R-factor:
|
0.190
|
R-free:
|
0.219
|
|
|
Authors:
|
|
T.Tadokoro,D.J.You,H.Chon,H.Matsumura,Y.Koga,K.Takano,S.Kanaya
|
|
Key ref:
|
|
T.Tadokoro
et al.
(2007).
Structural, thermodynamic, and mutational analyses of a psychrotrophic RNase HI.
Biochemistry,
46,
7460-7468.
PubMed id:
|
|
|
Date:
|
|
|
13-Dec-06
|
Release date:
|
01-May-07
|
|
|
|
|
|
|
PROCHECK
|
|
|
|
|
|
Headers
|
|
|
|
References
|
|
|
|
|
|
|
|
Q8EE30
(RNH_SHEON) -
Ribonuclease HI from Shewanella oneidensis (strain MR-1)
|
|
|
|
Seq:
Struc:
|
|
|
|
158 a.a.
155 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Key: |
 |
PfamA domain |
|
|
 |
Secondary structure |
|
 |
CATH domain |
|
|
|
|
|
|
|
|
|
|
|
|
|
Enzyme class:
|
|
E.C.3.1.26.4
- ribonuclease H.
|
|
|
|
|
|
|
Reaction:
|
|
Endonucleolytic cleavage to 5'-phosphomonoester.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
|
Biochemistry
46:7460-7468
(2007)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Structural, thermodynamic, and mutational analyses of a psychrotrophic RNase HI.
|
|
T.Tadokoro,
D.J.You,
Y.Abe,
H.Chon,
H.Matsumura,
Y.Koga,
K.Takano,
S.Kanaya.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
Ribonuclease (RNase) HI from the psychrotrophic bacterium Shewanella oneidensis
MR-1 was overproduced in Escherichia coli, purified, and structurally and
biochemically characterized. The amino acid sequence of MR-1 RNase HI is 67%
identical to that of E. coli RNase HI. The crystal structure of MR-1 RNase HI
determined at 2.0 A resolution was highly similar to that of E. coli RNase HI,
except that the number of intramolecular ion pairs and the fraction of polar
surface area of MR-1 RNase HI were reduced compared to those of E. coli RNase
HI. The enzymatic properties of MR-1 RNase HI were similar to those of E. coli
RNase HI. However, MR-1 RNase HI was much less stable than E. coli RNase HI. The
stability of MR-1 RNase HI against heat inactivation was lower than that of E.
coli RNase HI by 19 degrees C. The conformational stability of MR-1 RNase HI was
thermodynamically analyzed by monitoring the CD values at 220 nm. MR-1 RNase HI
was less stable than E. coli RNase HI by 22.4 degrees C in Tm and 12.5 kJ/mol in
DeltaG(H2O). The thermodynamic stability curve of MR-1 RNase HI was
characterized by a downward shift and increased curvature, which results in an
increased DeltaCp value, compared to that of E. coli RNase HI. Site-directed
mutagenesis studies suggest that the difference in the number of intramolecular
ion pairs partly accounts for the difference in stability between MR-1 and E.
coli RNases HI.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
K.Takano,
T.Okamoto,
J.Okada,
S.Tanaka,
C.Angkawidjaja,
Y.Koga,
and
S.Kanaya
(2011).
Stabilization by Fusion to the C-terminus of Hyperthermophile Sulfolobus tokodaii RNase HI: A Possibility of Protein Stabilization Tag.
|
| |
PLoS One,
6,
e16226.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.Okada,
T.Okamoto,
A.Mukaiyama,
T.Tadokoro,
D.J.You,
H.Chon,
Y.Koga,
K.Takano,
and
S.Kanaya
(2010).
Evolution and thermodynamics of the slow unfolding of hyperstable monomeric proteins.
|
| |
BMC Evol Biol,
10,
207.
|
|
|
|
|
|
|
J.Gu,
and
V.J.Hilser
(2009).
Sequence-based analysis of protein energy landscapes reveals nonuniform thermal adaptation within the proteome.
|
| |
Mol Biol Evol,
26,
2217-2227.
|
|
|
|
|
|
|
M.S.Rohman,
T.Tadokoro,
C.Angkawidjaja,
Y.Abe,
H.Matsumura,
Y.Koga,
K.Takano,
and
S.Kanaya
(2009).
Destabilization of psychrotrophic RNase HI in a localized fashion as revealed by mutational and X-ray crystallographic analyses.
|
| |
FEBS J,
276,
603-613.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
T.Tadokoro,
and
S.Kanaya
(2009).
Ribonuclease H: molecular diversities, substrate binding domains, and catalytic mechanism of the prokaryotic enzymes.
|
| |
FEBS J,
276,
1482-1493.
|
|
|
|
|
|
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
code is
shown on the right.
|
|
Links
