 |
PDBsum entry 4esv
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Hydrolase/DNA
|
PDB id
|
|
|
|
4esv
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
PDB id:
|
|
|
|
| Name: |
|
Hydrolase/DNA
|
|
|
Title:
|
|
A new twist on the translocation mechanism of helicases from the structure of dnab with its substrates
|
|
Structure:
|
|
5'-d(p Tp Tp Tp Tp Tp Tp Tp Tp Tp Tp Tp Tp Tp T)-3'. Chain: v. Engineered: yes. 5'-d(p Tp Tp Tp Tp Tp Tp Tp Tp Tp Tp Tp Tp T)-3'. Chain: w. Engineered: yes. Replicative helicase. Chain: a, b, c, d, e, f, g, h, i, j, k, l. Synonym: dnab.
|
|
Source:
|
|
Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Geobacillus stearothermophilus. Organism_taxid: 1422. Gene: dnab. Expressed in: escherichia coli. Expression_system_taxid: 562
|
|
Resolution:
|
|
|
3.20Å
|
R-factor:
|
0.245
|
R-free:
|
0.289
|
|
|
Authors:
|
|
O.Itsathitphaisarn,R.A.Wing,W.K.Eliason,J.Wang,T.A.Steitz
|
|
Key ref:
|
|
O.Itsathitphaisarn
et al.
(2012).
The hexameric helicase DnaB adopts a nonplanar conformation during translocation.
Cell,
151,
267-277.
PubMed id:
|
|
|
Date:
|
|
|
23-Apr-12
|
Release date:
|
24-Oct-12
|
|
|
|
|
|
|
PROCHECK
|
|
|
|
|
|
Headers
|
|
|
|
References
|
|
|
|
|
|
|
|
Q9X4C9
(Q9X4C9_GEOSE) -
Replicative DNA helicase from Geobacillus stearothermophilus
|
|
|
|
Seq:
Struc:
|
|
|
|
454 a.a.
418 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Key: |
 |
PfamA domain |
|
|
 |
Secondary structure |
|
 |
CATH domain |
|
|
|
|
|
|
|
|
|
|
|
|
T-T-T-T-T-T-T-T-T-T-T-T-T-T
14 bases
|
|
|
|
T-T-T-T-T-T-T-T-T-T-T-T-T
13 bases
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Enzyme class:
|
|
E.C.3.6.4.12
- Dna helicase.
|
|
|
|
|
|
|
Reaction:
|
|
ATP + H2O = ADP + phosphate + H+
|
|
|
|
|
|
ATP
|
+
|
H2O
|
=
|
ADP
Bound ligand (Het Group name = )
matches with 96.43% similarity
|
+
|
phosphate
|
+
|
H(+)
|
|
|
|
|
|
|
|
|
|
|
|
|
Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
|
| |
|
|
Cell
151:267-277
(2012)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
The hexameric helicase DnaB adopts a nonplanar conformation during translocation.
|
|
O.Itsathitphaisarn,
R.A.Wing,
W.K.Eliason,
J.Wang,
T.A.Steitz.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
DNA polymerases can only synthesize nascent DNA from single-stranded DNA (ssDNA)
templates. In bacteria, the unwinding of parental duplex DNA is carried out by
the replicative DNA helicase (DnaB) that couples NTP hydrolysis to 5' to 3'
translocation. The crystal structure of the DnaB hexamer in complex with
GDP-AlF(4) and ssDNA reported here reveals that DnaB adopts a closed spiral
staircase quaternary structure around an A-form ssDNA with each C-terminal
domain coordinating two nucleotides of ssDNA. The structure not only provides
structural insights into the translocation mechanism of superfamily IV helicases
but also suggests that members of this superfamily employ a translocation
mechanism that is distinct from other helicase superfamilies. We propose a
hand-over-hand mechanism in which sequential hydrolysis of NTP causes a
sequential 5' to 3' movement of the subunits along the helical axis of the
staircase, resulting in the unwinding of two nucleotides per subunit.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Links
