PDBsum entry 1wp9

Hydrolase

PDB id: 1wp9

Contents

Protein chains

(+ 0 more) 479 a.a. *

Ligands

PO4 ×6

Waters ×49

* Residue conservation analysis

PDB id:

1wp9

Name:

Hydrolase

Title:

Crystal structure of pyrococcus furiosus hef helicase domain

Structure:

Atp-dependent RNA helicase, putative. Chain: a, b, c, d, e, f. Fragment: residues 2-495. Synonym: hef helicase, nuclease. Engineered: yes

Source:

Pyrococcus furiosus. Organism_taxid: 186497. Strain: dsm 3638. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Hexamer (from PQS)

Resolution:

2.90Å R-factor: 0.257 R-free: 0.286

Authors:

T.Nishino,K.Komori,D.Tsuchiya,Y.Ishino,K.Morikawa

Key ref:

T.Nishino et al. (2005). Crystal structure and functional implications of Pyrococcus furiosus hef helicase domain involved in branched DNA processing. Structure, 13, 143-153. PubMed id: 15642269 DOI: 10.1016/j.str.2004.11.008

Date:

31-Aug-04 Release date: 01-Feb-05

Protein chains

Q8TZH8  (Q8TZH8_PYRFU) -  ATP-dependent RNA helicase, putative from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 764 a.a.

Struc: 479 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.6.1.3 - Deleted entry.
• Reaction: ATP + H₂O = ADP + phosphate

ATP + H(2)O = ADP + phosphate (Bound ligand (Het Group name = PO4) corresponds exactly)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.str.2004.11.008

Structure 13:143-153 (2005)

PubMed id: 15642269

Crystal structure and functional implications of Pyrococcus furiosus hef helicase domain involved in branched DNA processing.

T.Nishino, K.Komori, D.Tsuchiya, Y.Ishino, K.Morikawa.

ABSTRACT

DNA and RNA frequently form various branched intermediates that are important for the transmission of genetic information. Helicases play pivotal roles in the processing of these transient intermediates during nucleic acid metabolism. The archaeal Hef helicase/ nuclease is a representative protein that processes flap- or fork-DNA structures, and, intriguingly, its C-terminal half belongs to the XPF/Mus81 nuclease family. Here, we report the crystal structure of the helicase domain of the Hef protein from Pyrococcus furiosus. The structure reveals a novel helical insertion between the two conserved helicase core domains. This positively charged extra region, structurally similar to the "thumb" domain of DNA polymerase, plays critical roles in fork recognition. The Hef helicase/nuclease exhibits sequence similarity to the Mph1 helicase from Saccharomyces cerevisiae; XPF/Rad1, involved in DNA repair; and a putative Hef homolog identified in mammals. Hence, our findings provide a structural basis for the functional mechanisms of this helicase/nuclease family.

Selected figure(s)

Figure 6.
Figure 6. Models of Hef in Complex with Branched Structure DNA
Hef is shown as the surface representation whose orientation is the same as in Figure 1B. The surface was colored according to its electrostatic surface potential at + or - 10 kB T/e for positive (blue) or negative (red) charge potential by using the program GRASP (Nicholls, 1993). DNA is shown as schematic double helices.
(A) Model 1. Domain 2 interacts with the double-stranded region of the branched structure, and the fork-structured DNA is recognized by the coordinated action of all three domains.
(B) Model 2. Domain 2 directly interacts with a moiety near the junction, and the helicase core domains support double- or single-stranded DNA binding in a mode similar to the case of RecG.

The above figure is reprinted by permission from Cell Press: Structure (2005, 13, 143-153) copyright 2005.

Figure was selected by an automated process.