PDBsum entry: 2f96

Structural genomics, hydrolase

PDB-id: 2f96

Biological unit* = asymmetric unit, as shown
(*as deduced by PQS)

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References

PROCHECK

Protein chains

202 a.a. *

Metal ions

_MG ×2

Waters ×230

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

2f96

Name:

Structural genomics, hydrolase

Title:

2.1 a crystal structure of pseudomonas aeruginosa rnase t (ribonuclease t)

Structure:

Ribonuclease t. Chain: a, b. Synonym: exoribonuclease t, rnase t. Engineered: yes

Source:

Pseudomonas aeruginosa pao1. Organism_taxid: 208964. Strain: pao1. Atcc: 15692. Gene: rnt, pa3528. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biological unit:

Dimer (from PQS)

UniProt:

Chains A, B: Q9HY82 (RNT_PSEAE)

Seq:

224 a.a.

Struc:

202 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Resolution:

2.09Å

R-factor:

0.160

R-free:

0.204

Authors:

H.Zheng,M.Chruszcz,M.Cymborowski,Y.Wang, E.Gorodichtchenskaia,T.Skarina,J.Guthrie,A.Savchenko, A.Edwards,W.Minor,Midwest Center For Structural Genomics (Mcsg)

Key ref:

Y.Zuo et al. (2007). Crystal Structure of RNase T, an Exoribonuclease Involved in tRNA Maturation and End Turnover.. Structure, 15, 417-428. [PubMed id: 17437714] [DOI: 10.1016/j.str.2007.02.004]

Date:

05-Dec-05

Release date:

14-Feb-06

Related entries:

Apc5754 related db: targetdb

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Clefts

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ProFunc

Key reference

DOI no: 10.1016/j.str.2007.02.004

Structure 15:417-428 (2007)

PubMed id: 17437714

Crystal Structure of RNase T, an Exoribonuclease Involved in tRNA Maturation and End Turnover.

Y.Zuo, H.Zheng, Y.Wang, M.Chruszcz, M.Cymborowski, T.Skarina, A.Savchenko, A.Malhotra, W.Minor.

ABSTRACT

The 3' processing of most bacterial precursor tRNAs involves exonucleolytic trimming to yield a mature CCA end. This step is carried out by RNase T, a member of the large DEDD family of exonucleases. We report the crystal structures of RNase T from Escherichia coli and Pseudomonas aeruginosa, which show that this enzyme adopts an opposing dimeric arrangement, with the catalytic DEDD residues from one monomer closely juxtaposed with a large basic patch on the other monomer. This arrangement suggests that RNase T has to be dimeric for substrate specificity, and agrees very well with prior site-directed mutagenesis studies. The dimeric architecture of RNase T is very similar to the arrangement seen in oligoribonuclease, another bacterial DEDD family exoribonuclease. The catalytic residues in these two enzymes are organized very similarly to the catalytic domain of the third DEDD family exoribonuclease in E. coli, RNase D, which is monomeric.

Selected figure(s)

Figure 1.
Figure 1. Structure-Based Multiple Alignment of E. coli and P. aeruginosa RNase T and Related Nucleases
Structures included here are: E. coli RNase T (PDB ID code 2IS3); P. aeruginosa putative RNase T (PDB ID code 2F96); E. coli DNA polymerase III epsilon subunit (PDB ID code 1J53); E. coli oligoribonuclease (PDB ID code 1YTA); E. coli exonuclease I (PDB ID code 1FXX); three human 3′–5′ exoribonucleases, PARN (PDB ID code 2A1R), 3′hExo (PDB ID code 1W0H), and ISG20 (PDB ID code 1WLJ); yeast POP2 protein exonuclease domain (PDB ID code 1UOC); E. coli RNase D (PDB ID code 1YT3); E. coli DNA polymerase I Klenow fragment (PDB ID code 2KZZ); and T. gorgonarius DNA polymerase (PDB ID code 1TGO). The last three belong to the DEDDy subgroup, while the others have DEDDh folds. Sequence alignments were initially generated using T-Coffee (http://www.tcoffee.org) (Notredame et al., 2000), followed by some manual adjustment. The three conserved Exo motifs are labeled at the bottom with the DEDD residues marked by red triangles. The NBS basic residues conserved in RNase T orthologs are highlighted using blue rectangles. The numbering at the top is based on the E. coli RNase T sequence, with the secondary structure of P. aeruginosa RNase T.

Figure 4.
Figure 4. Close-Up of the DEDDh Active Site in P. aeruginosa RNase T: Monomer B in Stereo View
The conserved DEDDh residues are shown as sticks (red and yellow). The Mg ion located at the B site is shown as a green sphere. Also shown are a few water molecules (small red spheres) at the active center. The experimental electron-density map after solvent flattening is shown contoured at 2σ.

The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2007, 15, 417-428) copyright 2007.

Figures were selected by an automated process.