PDBsum entry 2owo

Ligase/DNA

PDB id: 2owo

Contents

Protein chain

586 a.a. *

DNA/RNA

Ligands

AMP

SO4 ×4

Metals

_ZN

Waters ×320

* Residue conservation analysis

PDB id:

2owo

Name:

Ligase/DNA

Title:

Last stop on the road to repair: structure of e.Coli DNA ligase bound to nicked DNA-adenylate

Structure:

26-mer. Chain: b. Engineered: yes. 5'-d( Ap Cp Ap Ap Tp Tp Gp Cp Gp Ap Cp (Omc)p C)-3'. Chain: c. Engineered: yes. 5'-d( Cp Ap Cp Tp Ap Tp Cp Gp Gp Ap Ap Tp G)-3'. Chain: d. Engineered: yes.

Source:

Synthetic: yes. Other_details: chemically synthesized. Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: liga. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.30Å R-factor: 0.217 R-free: 0.254

Authors:

S.Shuman,J.Nandakumar,P.A.Nair

Key ref:

J.Nandakumar et al. (2007). Last Stop on the Road to Repair: Structure of E. coli DNA Ligase Bound to Nicked DNA-Adenylate. Mol Cell, 26, 257-271. PubMed id: 17466627 DOI: 10.1016/j.molcel.2007.02.026

Date:

16-Feb-07 Release date: 15-May-07

Protein chain

P15042  (DNLJ_ECOLI) -  DNA ligase from Escherichia coli (strain K12)

Seq: 671 a.a.

Struc: 586 a.a.

DNA/RNA chains

C-A-T-T-C-C-G-A-T-A-G-T-G-G-G-G-T-C-G-C-A-A-T-T-G-T 26 bases

A-C-A-A-T-T-G-C-G-A-C-OMC-C 13 bases

C-A-C-T-A-T-C-G-G-A-A-T-G 13 bases

Enzyme reactions

• Enzyme class: E.C.6.5.1.2 - Dna ligase (NAD(+)).
• Reaction: NAD⁺ + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho- (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta- nicotinamide D-nucleotide

NAD(+) + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho- (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP (Bound ligand (Het Group name = AMP) corresponds exactly) + beta- nicotinamide D-nucleotide

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

reference

DOI no: 10.1016/j.molcel.2007.02.026

Mol Cell 26:257-271 (2007)

PubMed id: 17466627

Last Stop on the Road to Repair: Structure of E. coli DNA Ligase Bound to Nicked DNA-Adenylate.

J.Nandakumar, P.A.Nair, S.Shuman.

ABSTRACT

NAD(+)-dependent DNA ligases (LigA) are ubiquitous in bacteria and essential for growth. Their distinctive substrate specificity and domain organization vis-a-vis human ATP-dependent ligases make them outstanding targets for anti-infective drug discovery. We report here the 2.3 A crystal structure of Escherichia coli LigA bound to an adenylylated nick, which captures LigA in a state poised for strand closure and reveals the basis for nick recognition. LigA envelops the DNA within a protein clamp. Large protein domain movements and remodeling of the active site orchestrate progression through the three chemical steps of the ligation reaction. The structure inspires a strategy for inhibitor design.

Selected figure(s)

Figure 1.
Figure 1. Comparison of the EcoLigA and Human Lig1 DNA Clamps
(A) Ribbon diagrams are shown of the structures EcoLigA (left) and human Lig1 (right, PDB 1X9N). The proteins were superimposed with respect to their NTase domains (colored cyan), which concomitantly aligned their respective OB domains (colored magenta). DNA is omitted from the central cavity to highlight the intradomain contacts that “close” the clamp (indicated by red arrows). In EcoLigA, the NTase and HhH (beige) domains make kissing contacts. In contrast, LigI closes its clamp via contacts between the N-terminal DNA binding domain (DBD, in beige) and the C-terminal OB domain (magenta). The terminal domains are indicated by N and C, respectively.
(B) Space-filling models of the EcoLigA and human Lig1 protein are shown with DNA in the cavity. The view is looking down the helical axis, similar to the orientation in (A).
(C) Stereo view of the clamp-closing contacts between amino acids in the NTase (cyan) and HhH (beige) domains of EcoLigA. The interactions occur within the DNA major groove opposite the nick, which has undergone step 2 catalysis to form the AppDNA intermediate.

Figure 4.
Figure 4. The Nucleotidyltransferase Domain
Stereo views of the NTase domain (shown as a cyan ribbon trace) bound to the nick, which is rendered as a transparent surface over a stick model.
(A) This view highlights the cage of β strand surrounding the nick 5′ adenylate (at top right) and the numerous interactions of the helix that inserts into the minor groove.
(B) This view illustrates the penetration of the Arg208 into the minor groove and the contacts of motif Ia (^135TRG^137) to the phosphates of the 3′-OH strand.

The above figures are reprinted by permission from Cell Press: Mol Cell (2007, 26, 257-271) copyright 2007.

Figures were selected by an automated process.