PDBsum entry 1e4u

Gene regulation

PDB id: 1e4u

Contents

Protein chain

78 a.a. *

Metals

_ZN ×2

* Residue conservation analysis

PDB id:

1e4u

Name:

Gene regulation

Title:

N-terminal ring finger domain of human not-4

Structure:

Transcriptional repressor not4. Chain: a. Fragment: ring finger domain. Engineered: yes

Source:

Homo sapiens. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562

NMR struc:

30 models

Authors:

H.Hanzawa,M.J.De Ruwe,T.K.Albert,P.C.Van Der Vliet,H.T.Timmers, R.Boelens

Key ref:

H.Hanzawa et al. (2001). The structure of the C4C4 ring finger of human NOT4 reveals features distinct from those of C3HC4 RING fingers. J Biol Chem, 276, 10185-10190. PubMed id: 11087754 DOI: 10.1074/jbc.M009298200

Date:

12-Jul-00 Release date: 31-Mar-01

Protein chain

O95628  (CNOT4_HUMAN) -  CCR4-NOT transcription complex subunit 4 from Homo sapiens

Seq: 575 a.a.

Struc: 78 a.a.

Enzyme reactions

• Enzyme class: E.C.2.3.2.27 - RING-type E3 ubiquitin transferase.
• Reaction: S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N₆- ubiquitinyl-[acceptor protein]-L-lysine

DOI no: 10.1074/jbc.M009298200

J Biol Chem 276:10185-10190 (2001)

PubMed id: 11087754

The structure of the C4C4 ring finger of human NOT4 reveals features distinct from those of C3HC4 RING fingers.

H.Hanzawa, M.J.de Ruwe, T.K.Albert, P.C.van Der Vliet, H.T.Timmers, R.Boelens.

ABSTRACT

The NOT4 protein is a component of the CCR4.NOT complex, a global regulator of RNA polymerase II transcription. Human NOT4 (hNOT4) contains a RING finger motif of the C(4)C(4) type. We expressed and purified the N-terminal region of hNOT4 (residues 1-78) encompassing the RING finger motif and determined the solution structure by heteronuclear NMR. NMR experiments using a (113)Cd-substituted hNOT4 RING finger showed that two metal ions are bound through cysteine residues in a cross-brace manner. The three-dimensional structure of the hNOT4 RING finger was refined with root mean square deviation values of 0.58 +/- 0.13 A for the backbone atoms and 1.08 +/- 0.12 A for heavy atoms. The hNOT4 RING finger consists of an alpha-helix and three long loops that are stabilized by zinc coordination. The overall folding of the hNOT4 RING finger is similar to that of the C(3)HC(4) RING fingers. The relative orientation of the two zinc-chelating loops and the alpha-helix is well conserved. However, for the other regions, the secondary structural elements are distinct.

Selected figure(s)

Figure 3.
Fig. 3. A, superposition of the backbone atoms of 30 simulated annealing structures of hNOT4-N78. The three loop regions (residues 12-22, 27-38, and 49-61) are colored green; the region containing the -helix (residues 39-48) is in red; residues 23-26 containing the helical turn are in orange; and the remaining unstructured region is in white. Zinc atoms are indicated as magenta balls. B-D, overview of the structural parameters of residues 10-65 of hNOT4-N78. B, number of distance restraints per residue; C and D, root mean square deviation (RMSD) for backbone atoms and all heavy atoms versus the residue number, respectively.

Figure 5.
Fig. 5. Schematic view of the RING finger structures of NOT4, IEEHV, RAG1, and c-Cbl. Please note that in RAG1, the first zinc-binding site of the RING finger is part of the binuclear zinc cluster. The conserved -helix is colored red, and the remaining helices and helical turns are in yellow. The -sheet is colored green. Zinc ions are indicated as balls and colored magenta for conserved zinc and gray for the remaining zinc in RAG1. Residues that coordinate zinc ions are shown and colored yellow for cysteine and blue for histidine.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 10185-10190) copyright 2001.

Figures were selected by the author.

Author's comment

Note that only residues 12-61 represent the structured part of the protein.
R.Boelens.