PDBsum entry 2hvq

Ligase

PDB id: 2hvq

Contents

Protein chain

317 a.a. *

Metals

_MG ×2

Waters ×116

* Residue conservation analysis

PDB id:

2hvq

Name:

Ligase

Title:

Structure of adenylated full-length t4 RNA ligase 2

Structure:

Hypothetical 37.6 kda protein in gp24-hoc intergenic region. Chain: a. Synonym: orf1. Engineered: yes

Source:

Enterobacteria phage t4. Organism_taxid: 10665. Gene: y10a, 24.1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.40Å R-factor: 0.211 R-free: 0.274

Authors:

J.Nandakumar,C.D.Lima

Key ref:

J.Nandakumar et al. (2006). RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward. Cell, 127, 71-84. PubMed id: 17018278 DOI: 10.1016/j.cell.2006.08.038

Date:

30-Jul-06 Release date: 17-Oct-06

Protein chain

P32277  (RLIG2_BPT4) -  RNA ligase 2 from Enterobacteria phage T4

Seq: 334 a.a.

Struc: 317 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.6.5.1.3 - Rna ligase (ATP).
• Reaction: ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho-(ribonucleotide)m = (ribonucleotide)n+m + AMP + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.cell.2006.08.038

Cell 127:71-84 (2006)

PubMed id: 17018278

RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward.

J.Nandakumar, S.Shuman, C.D.Lima.

ABSTRACT

T4 RNA ligase 2 (Rnl2) and kinetoplastid RNA editing ligases exemplify a family of RNA repair enzymes that seal 3'OH/5'PO(4) nicks in duplex RNAs via ligase adenylylation (step 1), AMP transfer to the nick 5'PO(4) (step 2), and attack by the nick 3'OH on the 5'-adenylylated strand to form a phosphodiester (step 3). Crystal structures are reported for Rnl2 at discrete steps along this pathway: the covalent Rnl2-AMP intermediate; Rnl2 bound to an adenylylated nicked duplex, captured immediately following step 2; and Rnl2 at an adenylylated nick in a state poised for step 3. These structures illuminate the stereochemistry of nucleotidyl transfer and reveal how remodeling of active-site contacts and conformational changes propel the ligation reaction forward. Mutational analysis and comparison of nick-bound structures of Rnl2 and human DNA ligase I highlight common and divergent themes of substrate recognition that can explain their specialization for RNA versus DNA repair.

Selected figure(s)

Figure 1.
Figure 1. Three-Step Pathway of Nick Sealing by ATP-Dependent Polynucleotide Ligases

Figure 3.
Figure 3. Serial Remodeling of Contacts in the Rnl2 Active Site in Synch with the Chemical Steps of Ligation

The above figures are reprinted by permission from Cell Press: Cell (2006, 127, 71-84) copyright 2006.

Figures were selected by an automated process.