2P6R | pdb_00002p6r

Crystal structure of superfamily 2 helicase Hel308 in complex with unwound DNA

• PDB DOI: https://doi.org/10.2210/pdb2P6R/pdb
• NAKB: 2P6R

• Classification: DNA binding protein/DNA
• Organism(s): Archaeoglobus fulgidus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-03-19 Released: 2007-06-12 
• Deposition Author(s): Buettner, K., Nehring, S., Hopfner, K.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.275 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.234 (DCC) 

Literature

Structural basis for DNA duplex separation by a superfamily-2 helicase.

Buttner, K., Nehring, S., Hopfner, K.P.

(2007) Nat Struct Mol Biol 14: 647-652

• PubMed: 17558417 
• DOI: https://doi.org/10.1038/nsmb1246
• Primary Citation Related Structures: 
  2P6R, 2P6U


• PubMed Abstract: 
  

  To reveal the mechanism of processive strand separation by superfamily-2 (SF2) 3'-->5' helicases, we determined apo and DNA-bound crystal structures of archaeal Hel308, a helicase that unwinds lagging strands and is related to human DNA polymerase theta. Our structure captures the duplex-unwinding reaction, shows that initial strand separation does not require ATP and identifies a prominent beta-hairpin loop as the unwinding element. Similar loops in hepatitis C virus NS3 helicase and RNA-decay factors support the idea that this duplex-unwinding mechanism is applicable to a broad subset of SF2 helicases. Comparison with ATP-bound SF2 enzymes suggests that ATP promotes processive unwinding of 1 base pair by ratchet-like transport of the 3' product strand. Our results provide a first structural framework for strand separation by processive SF2 3'-->5' helicases and reveal important mechanistic differences from SF1 helicases.

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Organizational Affiliation: 
• Center for Integrated Protein Science, Gene Center and Department of Chemistry and Biochemistry, Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 91.37 kDa 
• Atom Count: 6,219 
• Modeled Residue Count: 723 
• Deposited Residue Count: 742 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
afUHEL308 HELICASE	C [auth A]	702	Archaeoglobus fulgidus	Mutation(s): 0  EC: 5.6.2.4
UniProt
Find proteins for P0DMI1 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore P0DMI1  Go to UniProtKB:  P0DMI1

Entity ID: 1
Molecule	Chains	Length	Organism	Image
25-MER	A [auth X]	25	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*CP*TP*AP*GP*AP*GP*AP*CP*TP*AP*TP*CP*GP*AP*T)-3'	B [auth Y]	15	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.275 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.234 (DCC) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.379	α = 90
b = 138.379	β = 90
c = 252.973	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-12 
Deposition Author(s): Buettner, K., Nehring, S., Hopfner, K.P.

Revision History  

• Version 1.0: 2007-06-12
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references