PDBsum entry 4d05

Ligase

PDB id: 4d05

Contents

Protein chains

258 a.a.

Ligands

SO4 ×9

AMP ×2

Metals

_MG

Waters ×652

PDB id:

4d05

Name:

Ligase

Title:

Structure and activity of a minimal-type atp-dependent DNA ligase from a psychrotolerant bacterium

Structure:

Atp-dependent DNA ligase. Chain: a, b. Engineered: yes. Other_details: link between amp and lys173

Source:

Psychromonas sp. Sp041. Organism_taxid: 1365007. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: plyss. Other_details: psychromonas sp. Strain sp041 (genbank accession no. Erp003516)

Resolution:

1.65Å R-factor: 0.147 R-free: 0.192

Authors:

A.Williamson,U.Rothweiler,H.-K.S.Leiros

Key ref:

A.Williamson et al. (2014). Enzyme-adenylate structure of a bacterial ATP-dependent DNA ligase with a minimized DNA-binding surface. Acta Crystallogr D Biol Crystallogr, 70, 3043-3056. PubMed id: 25372693 DOI: 10.1107/S1399004714021099

Date:

24-Apr-14 Release date: 12-Nov-14

Protein chains

A0A0A6YVN6  (A0A0A6YVN6_9GAMM) -  Atp-dependent dna ligase from Psychromonas sp. SP041

Seq: 258 a.a.

Struc: 258 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 + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho- (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP (Bound ligand (Het Group name = AMP) matches with 95.65% similarity) + diphosphate

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

reference

DOI no: 10.1107/S1399004714021099

Acta Crystallogr D Biol Crystallogr 70:3043-3056 (2014)

PubMed id: 25372693

Enzyme-adenylate structure of a bacterial ATP-dependent DNA ligase with a minimized DNA-binding surface.

A.Williamson, U.Rothweiler, H.K.Leiros.

ABSTRACT

DNA ligases are a structurally diverse class of enzymes which share a common catalytic core and seal breaks in the phosphodiester backbone of double-stranded DNA via an adenylated intermediate. Here, the structure and activity of a recombinantly produced ATP-dependent DNA ligase from the bacterium Psychromonas sp. strain SP041 is described. This minimal-type ligase, like its close homologues, is able to ligate singly nicked double-stranded DNA with high efficiency and to join cohesive-ended and blunt-ended substrates to a more limited extent. The 1.65 Å resolution crystal structure of the enzyme-adenylate complex reveals no unstructured loops or segments, and suggests that this enzyme binds the DNA without requiring full encirclement of the DNA duplex. This is in contrast to previously characterized minimal DNA ligases from viruses, which use flexible loop regions for DNA interaction. The Psychromonas sp. enzyme is the first structure available for the minimal type of bacterial DNA ligases and is the smallest DNA ligase to be crystallized to date.