PDBsum entry 2dfh

Hydrolase

PDB id: 2dfh

Contents

Protein chain

221 a.a. *

Waters ×158

* Residue conservation analysis

PDB id:

2dfh

Name:

Hydrolase

Title:

Crystal structure of tk-rnase hii(1-212)-c

Structure:

Ribonuclease hii. Chain: a. Synonym: rnase hii. Engineered: yes. Mutation: yes

Source:

Thermococcus kodakarensis. Organism_taxid: 69014. Strain: kod1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.27Å R-factor: 0.197 R-free: 0.245

Authors:

Y.Katagiri,K.Takano,H.Chon,H.Matsumura,Y.Koga,S.Kanaya

Key ref:

K.Takano et al. (2007). Conformational contagion in a protein: structural properties of a chameleon sequence. Proteins, 68, 617-625. PubMed id: 17510955 DOI: 10.1002/prot.21451

Date:

01-Mar-06 Release date: 06-Mar-07

Protein chain

O74035  (RNH2_THEKO) -  Ribonuclease HII from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)

Seq: 228 a.a.

Struc: 221 a.a.*

* PDB and UniProt seqs differ at 9 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.1.26.4 - ribonuclease H.
• Reaction: Endonucleolytic cleavage to 5'-phosphomonoester.

DOI no: 10.1002/prot.21451

Proteins 68:617-625 (2007)

PubMed id: 17510955

Conformational contagion in a protein: structural properties of a chameleon sequence.

K.Takano, Y.Katagiri, A.Mukaiyama, H.Chon, H.Matsumura, Y.Koga, S.Kanaya.

ABSTRACT

Certain sequences, known as chameleon sequences, take both alpha- and beta-conformations in natural proteins. We demonstrate that a wild chameleon sequence fused to the C-terminal alpha-helix or beta-sheet in foreign stable proteins from hyperthermophiles forms the same conformation as the host secondary structure. However, no secondary structural formation is observed when the sequence is attached to the outside of the secondary structure. These results indicate that this sequence inherently possesses an ability to make either alpha- or beta-conformation, depending on the sequentially neighboring secondary structure if little other nonlocal interaction occurs. Thus, chameleon sequences take on a satellite state through contagion by the power of a secondary structure. We propose this "conformational contagion" as a new nonlocal determinant factor in protein structure and misfolding related to protein conformational diseases.

Selected figure(s)

Figure 1.
Figure 1. Structure of Pf-PCP[1-208] and Pf-PCP[1-204]-C. (a) Crystal structure of Pf-PCP[1-208] (wild-type) (PDB: 1IOF).[14] Blue, C-terminal -helix (residues 190-206); green, others. (b) Schematic diagram of Pf-PCP[1-208] (wild-type) and designed variant, Pf-PCP[1-204]-C. Blue, -helix; purple, chameleon sequence; green, others. (c) Crystal structure of Pf-PCP[1-204]-C. Blue, C-terminal -helix; purple, chameleon sequence; green, others. (d) The structure of the chameleon sequence of Pf-PCP[1-204]-C. The hydrogen bonds are represented by dotted lines.

Figure 2.
Figure 2. Structure of Pf-MAP[1-295] and Pf-MAP[1-292]-C. (a) Crystal structure of Pf-MAP[1-295] (wild-type) (PDB: 1XGS).[15] Blue, C-terminal -sheet (residues 276-292); green, others. (b) Schematic diagram of Pf-MAP[1-295] (wild-type) and designed variant, Pf-MAP[1-292]-C. Blue, -strands; purple, chameleon sequence; green, others. (c) Crystal structure of Pf-MAP[1-292]-C. Blue, C-terminal -sheet; purple, chameleon sequence; green, others. (d) The structure of the chameleon sequence of Pf-MAP[1-292]-C. The hydrogen bonds are represented by dotted lines.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2007, 68, 617-625) copyright 2007.

Figures were selected by an automated process.