PDBsum entry 1iym

DNA binding protein

PDB id: 1iym

Contents

Protein chain

55 a.a. *

Metals

_ZN ×2

* Residue conservation analysis

PDB id:

1iym

Name:

DNA binding protein

Title:

Ring-h2 finger domain of el5

Structure:

El5. Chain: a. Fragment: ring-h2 finger domain. Engineered: yes

Source:

Oryza sativa. Rice. Organism_taxid: 4530. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

NMR struc:

15 models

Authors:

E.Katoh,S.Katoh,E.Minami,T.Yamazaki

Key ref:

S.Katoh et al. (2003). High precision NMR structure and function of the RING-H2 finger domain of EL5, a rice protein whose expression is increased upon exposure to pathogen-derived oligosaccharides. J Biol Chem, 278, 15341-15348. PubMed id: 12588869 DOI: 10.1074/jbc.M210531200

Date:

30-Aug-02 Release date: 22-Jul-03

Protein chain

Q9LRB7  (EL5_ORYSJ) -  E3 ubiquitin-protein ligase EL5 from Oryza sativa subsp. japonica

Seq: 325 a.a.

Struc: 55 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

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.M210531200

J Biol Chem 278:15341-15348 (2003)

PubMed id: 12588869

High precision NMR structure and function of the RING-H2 finger domain of EL5, a rice protein whose expression is increased upon exposure to pathogen-derived oligosaccharides.

S.Katoh, C.Hong, Y.Tsunoda, K.Murata, R.Takai, E.Minami, T.Yamazaki, E.Katoh.

ABSTRACT

EL5, a RING-H2 finger protein, is rapidly induced by N-acetylchitooligosaccharides in rice cell. We expressed the EL5 RING-H2 finger domain in Escherichia coli and determined its structure in solution by NMR spectroscopy. The EL5 RING-H2 finger domain consists of two-stranded beta-sheets (beta1, Ala(147)-Phe(149); beta2, Gly(156)-His(158)), one alpha-helix (Cys(161)-Leu(166)), and two large N- and C-terminal loops. It is stabilized by two tetrahedrally coordinated zinc ions. This structure is similar to that of other RING finger domains of proteins of known function. From structural analogies, we inferred that the EL5 RING-H2 finger is a binding domain for ubiquitin-conjugating enzyme (E2). The binding site is probably formed by solvent-exposed hydrophobic residues of the N- and C-terminal loops and the alpha-helix. We demonstrated that the fusion protein with EL5-(96-181) and maltose-binding protein (MBP) was polyubiquitinated by incubation with ubiquitin, ubiquitin-activating enzyme (E1), and a rice E2 protein, OsUBC5b. This supported the idea that the EL5 RING finger domain is essential for ubiquitin-ligase activity of EL5. By NMR titration experiments, we identified residues that are critical for the interaction between the EL5 RING-H2 finger and OsUBC5b. We conclude that the RING-H2 finger domain of EL5 is the E2 binding site of EL5.

Selected figure(s)

Figure 2.
Fig. 2. a, best-fit superposition of the backbone (N, C , and C') atoms of the final 15 structures of the RING-H2 finger domain of EL5. The structures are superimposed on the energy-minimized average structure using the backbone coordinates of residues 132-178. b, ribbon diagram of the energy-minimized average structure of the RING-H2 finger domain of EL5.

Figure 3.
Fig. 3. a, comparison of the free RING finger domain of EL5 with the E2-bound form of c-Cbl and the dimerization domain of RAG1. The additional -helices at the N and C termini of RAG1 are shown in yellow. b, surface potential representations of these domains. Positively charged areas are blue, and negatively charged areas are red. The hydrophobic grooves in c-Cbl and EL5 are indicated by arrows. The atomic coordinates for c-Cbl and RAG1 were downloaded from the Protein Data Bank at Brookhaven National Laboratory (accession numbers: 1FBV and 1RMD, respectively).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 15341-15348) copyright 2003.

Figures were selected by an automated process.