PDBsum entry 1klr

Transcription

PDB id: 1klr

Contents

Protein chain

30 a.a. *

Metals

_ZN

* Residue conservation analysis

PDB id:

1klr

Name:

Transcription

Title:

Nmr structure of the zfy-6t[y10f] zinc finger

Structure:

Zinc finger y-chromosomal protein. Chain: a. Engineered: yes. Mutation: yes

Source:

Synthetic: yes. Other_details: this peptide was synthesized by solid-phase synthesis. The sequence of the peptide is naturally found in homo sapiens (human).

NMR struc:

25 models

Authors:

M.J.Lachenmann,J.E.Ladbury,N.B.Phillips,N.Narayana,X.Qian,M.A.Weiss

Key ref:

M.J.Lachenmann et al. (2002). The hidden thermodynamics of a zinc finger. J Mol Biol, 316, 969-989. PubMed id: 11884136 DOI: 10.1006/jmbi.2001.5335

Date:

12-Dec-01 Release date: 13-Mar-02

Protein chain

P08048  (ZFY_HUMAN) -  Zinc finger Y-chromosomal protein from Homo sapiens

Seq: 801 a.a.

Struc: 30 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1006/jmbi.2001.5335

J Mol Biol 316:969-989 (2002)

PubMed id: 11884136

The hidden thermodynamics of a zinc finger.

M.J.Lachenmann, J.E.Ladbury, N.B.Phillips, N.Narayana, X.Qian, M.A.Weiss.

ABSTRACT

The Zn finger provides a model for studies of protein structure and stability. Its core contains a conserved phenylalanine residue adjoining three architectural elements: a beta-hairpin, an alpha-helix and a tetrahedral Zn(2+)-binding site. Here, we demonstrate that the consensus Phe is not required for high-affinity Zn(2+) binding but contributes to the specification of a precise DNA-binding surface. Substitution of Phe by leucine in a ZFY peptide permits Zn(2+)-dependent folding. Although a native-like structure is retained, structural fluctuations lead to attenuation of selected nuclear Overhauser enhancements and accelerated amide proton exchange. Surprisingly, wild-type Zn affinity is maintained by entropy-enthalpy compensation (EEC): a hidden entropy penalty (TDeltaDeltaS 7kcal/mol) is balanced by enhanced enthalpy of association (DeltaDeltaH -7kcal/mol) at 25 degrees C. Because the variant is less well ordered than the Phe-anchored domain, the net change in entropy is opposite to the apparent change in configurational entropy. By analogy to the thermodynamics of organometallic complexation, we propose that EEC arises from differences in solvent reorganization. Exclusion of Leu among biological sequences suggests an evolutionary constraint on the dynamics of a Zn finger.

Selected figure(s)

Figure 1.
Figure 1. (a) A ribbon model of the parent Zn finger showing Zn 2+ (blue sphere), ligands (two cysteine and two histidine side-chains; light blue), conserved leucine (L, light blue), and central aromatic side- chain (F10; red and asterisk). The C terminus of the peptide is indi- cated. (b) A CPK model of the parent Zn finger showing the edge of F10 in the potential crevice (dark blue); the remainder of the surface is shown in aquamarine. (c) A rep- resentation of parent (F10) and variant (L10) fingers. The side- chains shown in (a) are shaded. The numbering scheme refers to the synthetic peptide (30 residues 19 ). (d) CD spectra of Zn 2+ - free peptides (F10, continuous line; and L10 dashed line) and Zn 2+ - bound peptides: wild-type (Phe; filled circles) and variant (Leu; open circles). CD spectra were obtained at 25 ° C at a peptide con- centration of 100 mM.

Figure 3.
Figure 3. The 1D 1 H-NMR spec- tra of the (a) parent Zn finger and (b) variant Zn finger at 500 MHz and 25 °C. Asterisks in (b) indicate upfield methyl resonances of L10. The upfield region of the wild-type spectrum is remarkable for the b-methylene protons of K25 (labeled in (a)). Arrow indicates down-field amide resonance of Y7, a characteristic feature of Zn fingers. 17

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 316, 969-989) copyright 2002.

Figures were selected by an automated process.