PDBsum entry 1mm2

DNA binding protein

PDB id: 1mm2

Contents

Protein chain

61 a.a. *

Metals

_ZN ×2

* Residue conservation analysis

PDB id:

1mm2

Name:

DNA binding protein

Title:

Solution structure of the 2nd phd domain from mi2b

Structure:

Mi2-beta. Chain: a. Fragment: mi2-beta (residues 446-501). Synonym: chromodomain helicase-DNA-binding protein 4. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: chd4. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

NMR struc:

20 models

Authors:

A.H.Y.Kwan,D.A.Gell,A.Verger,M.Crossley,J.M.Matthews,J.P.Mackay

Key ref:

A.H.Kwan et al. (2003). Engineering a protein scaffold from a PHD finger. Structure, 11, 803-813. PubMed id: 12842043 DOI: 10.1016/S0969-2126(03)00122-9

Date:

02-Sep-02 Release date: 22-Jul-03

Protein chain

Q14839  (CHD4_HUMAN) -  Chromodomain-helicase-DNA-binding protein 4 from Homo sapiens

Seq: 1912 a.a.

Struc: 61 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

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

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

reference

DOI no: 10.1016/S0969-2126(03)00122-9

Structure 11:803-813 (2003)

PubMed id: 12842043

Engineering a protein scaffold from a PHD finger.

A.H.Kwan, D.A.Gell, A.Verger, M.Crossley, J.M.Matthews, J.P.Mackay.

ABSTRACT

The design of proteins with tailored functions remains a relatively elusive goal. Small size, a well-defined structure, and the ability to maintain structural integrity despite multiple mutations are all desirable properties for such designer proteins. Many zinc binding domains fit this description. We determined the structure of a PHD finger from the transcriptional cofactor Mi2beta and investigated the suitability of this domain as a scaffold for presenting selected binding functions. The two flexible loops in the structure were mutated extensively by either substitution or expansion, without affecting the overall fold of the domain. A binding site for the corepressor CtBP2 was also grafted onto the domain, creating a new PHD domain that can specifically bind CtBP2 both in vitro and in the context of a eukaryotic cell nucleus. These results represent a step toward designing new regulatory proteins for modulating aberrant gene expression in vivo.

Selected figure(s)

Figure 2.
Figure 2. Solution Structures of Mi2b-P2 and Structure Comparisons with PHDs from WSTF and KAP-1(A) Ensemble of the best 20 structures of Mi2b-P2. Structures are superimposed over the backbone atoms (C^a, C', N) of residues 9-43 and 48-53 (residues 1-7 and 55-61, which are unstructured, are omitted for clarity). The zinc-chelating side chains are shown in yellow and green, and the zinc atom is shown in magenta. The L1 and L3 loops are shown in blue and red, respectively.(B) Ribbon diagram of the lowest energy structure of Mi2b-P2, showing elements of secondary structure as recognized in the program MOLMOL (Koradi et al., 1996). Structures in (A) and (B) are shown as wall-eyed stereo images.(C and D) Overlay of ribbon diagrams of the lowest energy structures of Mi2b-P2 and the solution structure of the PHDs from (C) WSTF and (D) KAP-1. Structures are superimposed over the backbone atoms (C^a, C', N) of residues 9-43 and 48-53 in Mi2b-P2 and the corresponding residues in WSTF-PHD and KAP-1-PHD, respectively. End terminal unstructured residues are omitted for clarity.

The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 803-813) copyright 2003.

Figure was selected by the author.