PDBsum entry 5ftd

Hydrolase

PDB id: 5ftd

Contents

Protein chain

429 a.a.

Ligands

PO4

Waters ×442

PDB id:

5ftd

Name:

Hydrolase

Title:

Crystal structure of pif1 helicase from bacteroides apo form

Structure:

Tpr domain protein. Chain: a. Synonym: helicase. Engineered: yes

Source:

Bacteroides. Organism_taxid: 457390. Strain: sp. 3_1_23. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.70Å R-factor: 0.170 R-free: 0.194

Authors:

W.-F.Chen,Y.-X.Dai,X.-L.Duan,N.-N.Liu,W.Shi,M.Li,S.-X.Dou,N.Li,Y.- H.Dong,S.Rety,X.-G.Xi

Key ref:

W.F.Chen et al. (2016). Crystal structures of the BsPif1 helicase reveal that a major movement of the 2B SH3 domain is required for DNA unwinding. Nucleic Acids Res, 44, 2949-2961. PubMed id: 26809678 DOI: 10.1093/nar/gkw033

Date:

12-Jan-16 Release date: 03-Feb-16

Protein chain

D7K0H3  (D7K0H3_9BACE) -  TPR domain protein from Bacteroides sp. 3_1_23

Seq: 433 a.a.

Struc: 429 a.a.

Enzyme reactions

• Enzyme class: E.C.3.6.4.12 - Dna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

ATP + H2O = ADP + phosphate + H(+) (Bound ligand (Het Group name = PO4) corresponds exactly)

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

reference

DOI no: 10.1093/nar/gkw033

Nucleic Acids Res 44:2949-2961 (2016)

PubMed id: 26809678

Crystal structures of the BsPif1 helicase reveal that a major movement of the 2B SH3 domain is required for DNA unwinding.

W.F.Chen, Y.X.Dai, X.L.Duan, N.N.Liu, W.Shi, N.Li, M.Li, S.X.Dou, Y.H.Dong, S.Rety, X.G.Xi.

ABSTRACT

Pif1 helicases are ubiquitous members of the SF1B family and are essential for maintaining genome stability. It was speculated that Pif1-specific motifs may fold in specific structures, conferring distinct activities upon it. Here, we report the crystal structures of the Pif1 helicase fromBacteroides sppwith and without adenosine triphosphate (ATP) analog/ssDNA. BsPif1 shares structural similarities with RecD2 and Dda helicases but has specific features in the 1B and 2B domains. The highly conserved Pif1 family specific sequence motif interacts with and constraints a putative pin-loop in domain 1B in a precise conformation. More importantly, we found that the 2B domain which contains a specific extended hairpin undergoes a significant rotation and/or movement upon ATP and DNA binding, which is absolutely required for DNA unwinding. We therefore propose a mechanism for DNA unwinding in which the 2B domain plays a predominant role. The fact that the conformational change regulates Pif1 activity may provide insight into the puzzling observation that Pif1 becomes highly processive during break-induced replication in association with Polδ, while the isolated Pif1 has low processivity.