4ESV | pdb_00004esv

A New Twist on the Translocation Mechanism of Helicases from the Structure of DnaB with its Substrates

PDB DOI: https://doi.org/10.2210/pdb4ESV/pdb
NAKB: 4ESV

Classification: HYDROLASE/DNA
Organism(s): synthetic construct, Geobacillus stearothermophilus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-04-23 Released: 2012-10-24
Deposition Author(s): Itsathitphaisarn, O., Wing, R.A., Eliason, W.K., Wang, J., Steitz, T.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.289 (Depositor), 0.281 (DCC)
R-Value Work:
0.242 (Depositor), 0.239 (DCC)
R-Value Observed:
0.245 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The Hexameric Helicase DnaB Adopts a Nonplanar Conformation during Translocation.

Itsathitphaisarn, O., Wing, R.A., Eliason, W.K., Wang, J., Steitz, T.A.

(2012) Cell 151: 267-277

PubMed: 23022319 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.cell.2012.09.014
Primary Citation Related Structures:
4ESV

PubMed 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.

Organizational Affiliation

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

Macromolecule Content

Total Structure Weight: 623.32 kDa
Atom Count: 40,296
Modeled Residue Count: 5,099
Deposited Residue Count: 5,475
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicative helicase	C [auth A] D [auth B] E [auth C] F [auth D] G [auth E] C [auth A], D [auth B], E [auth C], F [auth D], G [auth E], H [auth F], I [auth G], J [auth H], K [auth I], L [auth J], M [auth K], N [auth L]	454	Geobacillus stearothermophilus	Mutation(s): 0 Gene Names: dnaB EC: 3.6.4.12 (PDB Primary Data), 5.6.2.3 (UniProt)
UniProt
Find proteins for Q9X4C9 (Geobacillus stearothermophilus) Explore Q9X4C9 Go to UniProtKB: Q9X4C9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X4C9
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 1
5'-D(PTPTPTPTPTPTPTPTPTPTPTPTPTPT)-3'	A [auth V]	14	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
5'-D(PTPTPTPTPTPTPTPTPTPTPTPTP*T)-3'	B [auth W]	13	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain GA [auth E] SDF format, chain KA [auth F] SDF format, chain MA [auth G] SDF format, chain PA [auth I] SDF format, chain Q [auth A] SDF format, chain VA [auth K] SDF format, chain X [auth C] SDF format, chain XA [auth L] SDF format, chain TA [auth J] SDF format, chain CA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain KA [auth F] MOL2 format, chain MA [auth G] MOL2 format, chain PA [auth I] MOL2 format, chain Q [auth A] MOL2 format, chain VA [auth K] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth L] MOL2 format, chain TA [auth J] MOL2 format, chain CA [auth D] mmCIF format, chain GA [auth E] mmCIF format, chain KA [auth F] mmCIF format, chain MA [auth G] mmCIF format, chain PA [auth I] mmCIF format, chain Q [auth A] mmCIF format, chain VA [auth K] mmCIF format, chain X [auth C] mmCIF format, chain XA [auth L] mmCIF format, chain TA [auth J] mmCIF format, chain CA [auth D]	CA [auth D] GA [auth E] KA [auth F] MA [auth G] PA [auth I] CA [auth D], GA [auth E], KA [auth F], MA [auth G], PA [auth I], Q [auth A], TA [auth J], VA [auth K], X [auth C], XA [auth L]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain CA [auth D] Focus chain GA [auth E] Focus chain KA [auth F] Focus chain MA [auth G] Focus chain PA [auth I] Focus chain Q [auth A] Focus chain TA [auth J] Focus chain VA [auth K] Focus chain X [auth C] Focus chain XA [auth L] Interactions & Density Focus chain CA [auth D] Focus chain GA [auth E] Focus chain KA [auth F] Focus chain MA [auth G] Focus chain PA [auth I] Focus chain Q [auth A] Focus chain TA [auth J] Focus chain VA [auth K] Focus chain X [auth C] Focus chain XA [auth L]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain JA [auth E] SDF format, chain O [auth W] SDF format, chain SA [auth I] SDF format, chain BA [auth C] MOL2 format, chain JA [auth E] MOL2 format, chain O [auth W] MOL2 format, chain SA [auth I] MOL2 format, chain BA [auth C] mmCIF format, chain JA [auth E] mmCIF format, chain O [auth W] mmCIF format, chain SA [auth I] mmCIF format, chain BA [auth C]	BA [auth C], JA [auth E], O [auth W], SA [auth I]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain JA [auth E] Focus chain O [auth W] Focus chain SA [auth I] Interactions & Density Focus chain BA [auth C] Focus chain JA [auth E] Focus chain O [auth W] Focus chain SA [auth I]
ALF Query on ALF Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain IA [auth E] SDF format, chain NA [auth G] SDF format, chain S [auth A] SDF format, chain UA [auth J] SDF format, chain WA [auth K] SDF format, chain YA [auth L] SDF format, chain Z [auth C] SDF format, chain RA [auth I] SDF format, chain AA [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain IA [auth E] MOL2 format, chain NA [auth G] MOL2 format, chain S [auth A] MOL2 format, chain UA [auth J] MOL2 format, chain WA [auth K] MOL2 format, chain YA [auth L] MOL2 format, chain Z [auth C] MOL2 format, chain RA [auth I] MOL2 format, chain AA [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain IA [auth E] mmCIF format, chain NA [auth G] mmCIF format, chain S [auth A] mmCIF format, chain UA [auth J] mmCIF format, chain WA [auth K] mmCIF format, chain YA [auth L] mmCIF format, chain Z [auth C] mmCIF format, chain RA [auth I] mmCIF format, chain AA [auth C]	AA [auth C] EA [auth D] IA [auth E] NA [auth G] RA [auth I] AA [auth C], EA [auth D], IA [auth E], NA [auth G], RA [auth I], S [auth A], UA [auth J], WA [auth K], YA [auth L], Z [auth C]	TETRAFLUOROALUMINATE ION Al F₄ UYOMQIYKOOHAMK-UHFFFAOYSA-J		Interactions Focus chain AA [auth C] Focus chain EA [auth D] Focus chain IA [auth E] Focus chain NA [auth G] Focus chain RA [auth I] Focus chain S [auth A] Focus chain UA [auth J] Focus chain WA [auth K] Focus chain YA [auth L] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain EA [auth D] Focus chain IA [auth E] Focus chain NA [auth G] Focus chain RA [auth I] Focus chain S [auth A] Focus chain UA [auth J] Focus chain WA [auth K] Focus chain YA [auth L] Focus chain Z [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain FA [auth D] SDF format, chain HA [auth E] SDF format, chain LA [auth F] SDF format, chain P [auth A] SDF format, chain QA [auth I] SDF format, chain T [auth A] SDF format, chain V [auth A] SDF format, chain W [auth B] SDF format, chain Y [auth C] SDF format, chain ZA [auth L] SDF format, chain U [auth A] SDF format, chain R [auth A] SDF format, chain OA [auth G] MOL2 format, chain DA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain LA [auth F] MOL2 format, chain P [auth A] MOL2 format, chain QA [auth I] MOL2 format, chain T [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain ZA [auth L] MOL2 format, chain U [auth A] MOL2 format, chain R [auth A] MOL2 format, chain OA [auth G] mmCIF format, chain DA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain HA [auth E] mmCIF format, chain LA [auth F] mmCIF format, chain P [auth A] mmCIF format, chain QA [auth I] mmCIF format, chain T [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain ZA [auth L] mmCIF format, chain U [auth A] mmCIF format, chain R [auth A] mmCIF format, chain OA [auth G]	DA [auth D] FA [auth D] HA [auth E] LA [auth F] OA [auth G] DA [auth D], FA [auth D], HA [auth E], LA [auth F], OA [auth G], P [auth A], QA [auth I], R [auth A], T [auth A], U [auth A], V [auth A], W [auth B], Y [auth C], ZA [auth L]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain FA [auth D] Focus chain HA [auth E] Focus chain LA [auth F] Focus chain OA [auth G] Focus chain P [auth A] Focus chain QA [auth I] Focus chain R [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth B] Focus chain Y [auth C] Focus chain ZA [auth L] Interactions & Density Focus chain DA [auth D] Focus chain FA [auth D] Focus chain HA [auth E] Focus chain LA [auth F] Focus chain OA [auth G] Focus chain P [auth A] Focus chain QA [auth I] Focus chain R [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth B] Focus chain Y [auth C] Focus chain ZA [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.289 (Depositor), 0.281 (DCC)
R-Value Work: 0.242 (Depositor), 0.239 (DCC)
R-Value Observed: 0.245 (Depositor)

Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.124	α = 90
b = 180.321	β = 90
c = 279.128	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
SHELX	model building
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-10-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-10-24
Type: Initial release
Version 1.1: 2017-11-15
Changes: Advisory, Refinement description
Version 1.2: 2018-06-06
Changes: Data collection, Refinement description, Source and taxonomy
Version 1.3: 2024-02-28
Changes: Advisory, Data collection, Database references, Derived calculations