PDBsum entry 1r11

Translation, hydrolase

PDB id: 1r11

Contents

Protein chains

303 a.a. *

* Residue conservation analysis

PDB id:

1r11

Name:

Translation, hydrolase

Title:

Structure determination of the dimeric endonuclease in a pseudo-face- centerd p21 space group

Structure:

tRNA-intron endonuclease. Chain: a, b. Synonym: splicing endonuclease. Intron endonuclease. Enda. Engineered: yes

Source:

Archaeoglobus fulgidus. Organism_taxid: 224325. Strain: dsm 4304. Gene: enda. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.70Å R-factor: 0.231 R-free: 0.293

Authors:

H.Li,Y.Zhang

Key ref:

Y.Zhang and H.Li (2004). Structure determination of a truncated dimeric splicing endonuclease in pseudo-face-centered space group P2(1)2(1)2. Acta Crystallogr D Biol Crystallogr, 60, 447-452. PubMed id: 14993668 DOI: 10.1107/S0907444903029482

Date:

23-Sep-03 Release date: 09-Mar-04

Protein chains

O29362  (ENDA_ARCFU) -  tRNA-splicing endonuclease from Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)

Seq: 305 a.a.

Struc: 303 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.4.6.1.16 - tRNA-intron lyase.
• Reaction: pretRNA = a 3'-half-tRNA molecule with a 5'-OH end + a 5'-half-tRNA molecule with a 2',3'-cyclic phosphate end + an intron with a 2',3'-cyclic phosphate and a 5'-hydroxyl terminus

DOI no: 10.1107/S0907444903029482

Acta Crystallogr D Biol Crystallogr 60:447-452 (2004)

PubMed id: 14993668

Structure determination of a truncated dimeric splicing endonuclease in pseudo-face-centered space group P2(1)2(1)2.

Y.Zhang, H.Li.

ABSTRACT

RNA-splicing endonuclease is responsible for the excision of introns in transfer RNA and archaeal ribosomal RNAs. The archaeal form of the enzyme recognizes a unique RNA motif that consists of two three-nucleotide bulges separated by a four base-paired helix, known as the bulge-helix-bulge (BHB) motif. A crystal structure of the RNA-splicing endonuclease from Archaeoglobus fulgidus (AF) has been reported previously at 2.8 A. A truncated but fully active form of AF endonuclease that lacks the N-terminal domain was expressed and crystallized in an orthorhombic space group with two dimers in the asymmetric unit. The calculated native Patterson map suggests strong pseudo-face-centering characteristics, which lead to incorrect space-group assignment by the autoindexing program. The correct space group was determined to be P2(1)2(1)2 after reindexing. The structure was solved using molecular replacement and was refined to 2.0 A. The truncated AF endonuclease structure is essentially identical to the corresponding portion of the wild-type AF endonuclease structure in space group P4(3)2(1)2 as reported previously, with the exception of loop L9, which differs owing to different crystallographic packing. These results confirm the previously described structural features of dimeric splicing endonuclease.

Selected figure(s)

Figure 1.
Figure 1 The pseudo-face-centering feature of the AFN crystal. AFN dimers (cyan and brown) within one asymmetric unit are compared with the position of an AFN dimer placed at the C-center of the original cell (green). The brown and green copies of the dimer have nearly identical translations from the cyan copy. However, the brown copy is rotated [78]~ 4° from the green copy.

The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2004, 60, 447-452) copyright 2004.

Figure was selected by the author.