PDBsum entry 3g0r

Hydrolase/DNA

PDB id: 3g0r

Contents

Protein chains

255 a.a. *

DNA/RNA

Ligands

GOL ×12

PG4 ×3

Metals

_NA ×2

Waters ×305

* Residue conservation analysis

PDB id:

3g0r

Name:

Hydrolase/DNA

Title:

Complex of mth0212 and an 8bp dsdna with distorted ends

Structure:

Exodeoxyribonuclease. Chain: a, b. Synonym: mth0212. Engineered: yes. Mutation: yes. 5'-d( Gp Cp Tp Gp Cp Gp Cp Ap Gp Gp Gp Cp G)-3'. Chain: g. Engineered: yes. 5'-d( Cp Cp Cp Tp Gp Up Gp Cp Ap Gp C)-3'.

Source:

Methanothermobacter thermautotrophicus. Organism_taxid: 187420. Strain: delta h (dsm 1053). Gene: mth0212, mth212, mth_212. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes

Resolution:

2.40Å R-factor: 0.181 R-free: 0.243

Authors:

K.Lakomek,A.Dickmanns,R.Ficner

Key ref:

K.Lakomek et al. (2010). Crystal structure analysis of DNA uridine endonuclease Mth212 bound to DNA. J Mol Biol, 399, 604-617. PubMed id: 20434457

Date:

28-Jan-09 Release date: 09-Mar-10

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: 255 a.a.*

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

DNA/RNA chains

G-C-T-G-C-G-C-A-G-G 10 bases

C-C-C-T-G-U-G-C-A-G-C 11 bases

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.

J Mol Biol 399:604-617 (2010)

PubMed id: 20434457

Crystal structure analysis of DNA uridine endonuclease Mth212 bound to DNA.

K.Lakomek, A.Dickmanns, E.Ciirdaeva, L.Schomacher, R.Ficner.

ABSTRACT

The reliable repair of pre-mutagenic U/G mismatches originated from hydrolytic cytosine deamination is crucial for the maintenance of the correct genomic information. In most organisms any uracil base in DNA is attacked by uracil DNA glycosylases (UDGs), but at least in Methanothermobacter thermautotrophicus DeltaH an alternative strategy has evolved. The exonuclease III homologue Mth212 from the thermophilic archaeon M. thermautotrophicus DeltaH exhibits a DNA uridine endonuclease activity in addition to the apyrimidinic / apurinic site (AP) endonuclease and 3'-->5'exonuclease functions. Mth212 alone compensates for the lack of a UDG in a single step reaction thus substituting the two step pathway that requires the consecutive action of UDG and AP endonuclease. In order to gain deeper insight into the structural basis required for the specific uridine recognition by Mth212, we have characterized the enzyme by means of X-ray crystallography. Structures of Mth212 wild-type or mutant proteins either alone or in complex with DNA substrates and products have been determined to a resolution of up to 1.2 A suggesting key residues for the uridine endonuclease activity. The insertion of the side chain of Arg209 into the DNA helical base stack resembles interactions observed in human UDG and seems to be crucial for the uridine recognition. In addition, Ser171, Asn153 and Lys125 in the substrate binding pocket appear to have important functions in the discrimination of aberrant uridine against naturally occuring thymidine and cytosine residues in double-stranded DNA.