PDBsum entry 3w2y

Hydrolase

PDB id: 3w2y

Contents

Protein chains

256 a.a.

Ligands

FMT ×12

PEG ×3

Metals

_MG ×2

Waters ×381

PDB id:

3w2y

Name:

Hydrolase

Title:

Crystal structure of DNA uridine endonuclease mth212 mutant w205s

Structure:

Exodeoxyribonuclease. Chain: a, d. Engineered: yes. Mutation: yes

Source:

Methanothermobacter thermautotrophicus. Organism_taxid: 187420. Strain: atcc 29096 / dsm 1053 / jcm 10044 / nbrc 100330 / delta h. Gene: mth212, mth_212. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.173 R-free: 0.192

Authors:

N.Tabata,T.Shida,R.Arai

Key ref:

N.Tabata et al. Crystal structure of DNA uridine endonuclease mth212. To be published, .

Date:

06-Dec-12 Release date: 11-Dec-13

Protein chains

O26314  (O26314_METTH) -  DNA uridine endonuclease from Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)

Seq: 257 a.a.

Struc: 256 a.a.*

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

Enzyme reactions

• Enzyme class 2: E.C.3.1.11.2 - exodeoxyribonuclease Iii.
• Reaction: Degradation of double-stranded DNA. It acts progressively in a 3'- to 5'-direction, releasing nucleoside 5'-phosphates.
• Enzyme class 3: E.C.4.2.99.18 - DNA-(apurinic or apyrimidinic site) lyase.
• Reaction: 2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)- 2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3- dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-phospho- 2'-deoxyribonucleoside-DNA + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.