PDBsum entry: 1w0h

Hydrolase

PDB id: 1w0h

Contents

Protein chain

200 a.a. *

Ligands

AMP

Metals

_MG ×2

Waters ×371

* Residue conservation analysis

PDB id:

1w0h

Name:

Hydrolase

Title:

Crystallographic structure of the nuclease domain of 3'hexo, a deddh family member, bound to ramp

Structure:

3'-5' exonuclease eri1. Chain: a. Fragment: nuclease domain, residues 122-321. Synonym: eri-1 homolog, protein 3'hexo. Engineered: yes. Other_details: ramp

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 469008. Other_details: synthetic gene

Resolution:

1.59Å R-factor: 0.170 R-free: 0.202

Authors:

Y.Cheng,D.Patel

Key ref:

Y.Cheng and D.J.Patel (2004). Crystallographic structure of the nuclease domain of 3'hExo, a DEDDh family member, bound to rAMP. J Mol Biol, 343, 305-312. PubMed id: 15451662 DOI: 10.1016/j.jmb.2004.08.055

Date:

04-Jun-04 Release date: 30-Sep-04

Protein chain

Q8IV48  (ERI1_HUMAN) -  3'-5' exoribonuclease 1

Seq: 349 a.a.

Struc: 200 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: intracellular (1 term)
• Biochemical function: nucleic acid binding (2 terms)

DOI no: 10.1016/j.jmb.2004.08.055

J Mol Biol 343:305-312 (2004)

PubMed id: 15451662

Crystallographic structure of the nuclease domain of 3'hExo, a DEDDh family member, bound to rAMP.

Y.Cheng, D.J.Patel.

ABSTRACT

A human 3'-5'-exoribonuclease (3'hExo) has recently been identified and shown to be responsible for histone mRNA degradation. Functionally, 3'hExo and a stem-loop binding protein (SLBP) target opposite faces of a unique highly conserved stem-loop RNA scaffold towards the 3' end of histone mRNA, which is composed of a 6 bp stem and a 4 nt loop, followed by an ACCCA sequence. Its Caenorhabditis elegans homologue, ERI-1, has been shown to degrade small interfering RNA in vitro and to function as a negative regulator of RNA interference in neuronal cells. We have determined the structure of the nuclease domain (Nuc) of 3'hExo complexed with rAMP in the presence of Mg2+ at 1.6 A resolution. The Nuc domain adopts an alpha/beta globular fold, with four acidic residues coordinating a binuclear metal cluster within the active site, whose topology is related to DEDDh exonuclease family members, despite a very low level of primary sequence identity. The two magnesium cations in the Nuc active site are coordinated to D134, E136, D234 and D298, and together with H293, which can potentially act as a general base, provide a platform for hydrolytic cleavage of bound RNA in the 3' --> 5' direction. The bound rAMP is positioned within a deep active-site pocket, with its purine ring close-packed with the hydrophobic F185 and L189 side-chains and its sugar 2'-OH and 3'-OH groups hydrogen bonded to backbone atoms of Nuc. There are striking similarities between the active sites of Nuc and epsilon186, an Escherichia coli DNA polymerase III proofreading domain, providing a common hydrolytic cleavage mechanism for RNA degradation and DNA editing, respectively.

Selected figure(s)

Figure 3.
Figure 3. Stereo views looking into the binding cavity of rAMP-bound Nuc. Overview (A) and close-up view (B) of the rAMP binding pocket within Nuc, with hydrogen bonds defining the divalent cation coordination sites (in A) and defining intermolecular contacts (in B) indicated by broken lines. The 2F[o] -F[c] map contoured at 1.0 is shown in B.

Figure 4.
Figure 4. Active sites and proposed hydrolysis mechanism. The active sites of (A) Nuc and (B) e186. Two conformations of dTMP bound to e186 are indicated by different occupancy (in B). (C) The proposed hydrolysis mechanism of Nuc. The coordination between DEDDh residues, rAMP and divalent ions is indicated by broken lines. The remaining residues are omitted for clarity.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 343, 305-312) copyright 2004.

Figures were selected by an automated process.