PDBsum entry 2faq

Hydrolase/transferase

PDB id: 2faq

Contents

Protein chains

295 a.a. *

Ligands

SO4 ×3

ATP ×2

Metals

_MN ×4

Waters ×462

* Residue conservation analysis

PDB id:

2faq

Name:

Hydrolase/transferase

Title:

Crystal structure of pseudomonas aeruginosa ligd polymerase domain with atp and manganese

Structure:

Probable atp-dependent DNA ligase. Chain: a, b. Fragment: polymerase domain, residues 533-840. Engineered: yes

Source:

Pseudomonas aeruginosa. Organism_taxid: 287. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.198 R-free: 0.226

Authors:

H.Zhu,J.Nandakumar,J.Aniukwu,L.K.Wang,M.S.Glickman,C.D.Lima,S.Shuman

Key ref:

H.Zhu et al. (2006). Atomic structure and nonhomologous end-joining function of the polymerase component of bacterial DNA ligase D. Proc Natl Acad Sci U S A, 103, 1711-1716. PubMed id: 16446439 DOI: 10.1073/pnas.0509083103

Date:

07-Dec-05 Release date: 23-May-06

Protein chains

Q9I1X7  (LIGD_PSEAE) -  Multifunctional non-homologous end joining protein LigD from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

Seq: 840 a.a.

Struc: 295 a.a.

Enzyme reactions

• Enzyme class: E.C.6.5.1.1 - Dna ligase (ATP).
• Reaction: ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho- (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + diphosphate

ATP (Bound ligand (Het Group name = ATP) corresponds exactly) + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho- (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + diphosphate

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

reference

DOI no: 10.1073/pnas.0509083103

Proc Natl Acad Sci U S A 103:1711-1716 (2006)

PubMed id: 16446439

Atomic structure and nonhomologous end-joining function of the polymerase component of bacterial DNA ligase D.

H.Zhu, J.Nandakumar, J.Aniukwu, L.K.Wang, M.S.Glickman, C.D.Lima, S.Shuman.

ABSTRACT

DNA ligase D (LigD) is a large polyfunctional protein that participates in a recently discovered pathway of nonhomologous end-joining in bacteria. LigD consists of an ATP-dependent ligase domain fused to a polymerase domain (Pol) and a phosphoesterase module. The Pol activity is remarkable for its dependence on manganese, its ability to perform templated and nontemplated primer extension reactions, and its preference for adding ribonucleotides to blunt DNA ends. Here we report the 1.5-A crystal structure of the Pol domain of Pseudomonas LigD and its complexes with manganese and ATP/dATP substrates, which reveal a minimized polymerase with a two-metal mechanism and a fold similar to that of archaeal DNA primase. Mutational analysis highlights the functionally relevant atomic contacts in the active site. Although distinct nucleoside conformations and contacts for ATP versus dATP are observed in the cocrystals, the functional analysis suggests that the ATP-binding mode is the productive conformation for dNMP and rNMP incorporation. We find that a mutation of Mycobacterium LigD that uniquely ablates the polymerase activity results in increased fidelity of blunt-end double-strand break repair in vivo by virtue of eliminating nucleotide insertions at the recombination junctions. Thus, LigD Pol is a direct catalyst of mutagenic nonhomologous end-joining in vivo. Our studies underscore a previously uncharacterized role for the primase-like polymerase family in DNA repair.

Selected figure(s)

Figure 2.
Fig. 2. Structure of the LigD Pol domain. The overall fold of the Pol domain of Pseudomonas LigD is depicted as a ribbon diagram with -helices colored magenta and -strands colored green. The N and C termini are indicated. ATP is bound within a cleft formed by two central -sheets; the cleft is viewed from the side in A and from above in B.

Figure 4.
Fig. 4. Active site of LigD Pol. Stereo views are shown of the active site constituents of the apoenzyme (A), the Mn-ATP cocrystal (B), and the Mn-dATP cocrystal (C). Potential hydrogen-bonding interactions are denoted by dashed lines. Manganese ions and waters are rendered as blue and red spheres, respectively. Amino acids and sulfate (A), ATP (B), or dATP (C) ligands are labeled and shown in stick representation.

Figures were selected by an automated process.