PDBsum entry 3vnc

DNA binding protein

PDB id: 3vnc

Contents

Protein chains

148 a.a.

Waters ×55

PDB id:

3vnc

Name:

DNA binding protein

Title:

Crystal structure of tip-alpha n25 from helicobacter pylori in its natural dimeric form

Structure:

Tip-alpha. Chain: a, b. Fragment: residues 25-192. Synonym: putative uncharacterized protein. Engineered: yes

Source:

Helicobacter pylori. Organism_taxid: 85962. Strain: 26695. Gene: hp_0596. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.60Å R-factor: 0.231 R-free: 0.264

Authors:

M.Gao,D.Li,Y.Hu,Q.Zou,D.-C.Wang

Key ref:

M.Gao et al. (2012). Crystal structure of TNF-α-inducing protein from Helicobacter pylori in active form reveals the intrinsic molecular flexibility for unique DNA-binding. Plos One, 7, e41871. PubMed id: 22860022

Date:

11-Jan-12 Release date: 03-Oct-12

Protein chains

O25318  (O25318_HELPY) -  Tumor necrosis factor alpha-inducing protein from Helicobacter pylori (strain ATCC 700392 / 26695)

Seq: 192 a.a.

Struc: 148 a.a.

Enzyme reactions

• Enzyme class: E.C.?

Plos One 7:e41871 (2012)

PubMed id: 22860022

Crystal structure of TNF-α-inducing protein from Helicobacter pylori in active form reveals the intrinsic molecular flexibility for unique DNA-binding.

M.Gao, D.Li, Y.Hu, Y.Zhang, Q.Zou, D.C.Wang.

ABSTRACT

Tipα (TNF-α-inducing protein) from Helicobacter pylori is a carcinogenic effector. Studies on this protein revealed that a homodimer linked by a pair of intermolecular disulfide bridges (Cys25-Cys25 and Cys27-Cys27) was absolutely necessary for its biological functions. The activities of Tipα would be abolished when both disulfide bridges were disrupted. The crystal structures of Tipα reported to date, however, were based on inactive, monomeric mutants with their N-terminal, including residues Cys25 and Cys27, truncated. Here we report the crystal structure of H. pylori Tipα protein, TipαN(25), at 2.2Å resolution, in which Cys25 and Cys27 form a pair of inter-chain disulfide bridges linking an active dimer. The disulfide bridges exhibit structural flexibility in the present structure. A series of structure-based mutagenesis, biochemical assays and molecular dynamic simulations on DNA-Tipα interactions reveal that Tipα utilizes the dimeric interface as the DNA-binding site and that residues His60, Arg77 and Arg81 located at the interface are crucial for DNA binding. Tipα could bind to one ssDNA, two ssDNA or one dsDNA in experiments, respectively, in the native or mutant states. The unique DNA-binding activities of Tipα indicate that the intrinsic flexible nature of disulfide bridges could endow certain elasticity to the Tipα dimer for its unique bioactivities. The results shed light on the possible structural mechanism for the functional performances of Tipα.