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Structure paper

TitleCrystal Structure Analysis of DNA Uridine Endonuclease Mth212 Bound to DNA
Journal, issue, pagesJ. Mol. Biol., Vol. 399, Page 604-617, Year 2010
Publish dateJan 26, 2009 (structure data deposition date)
AuthorsLakomek, K. / Dickmanns, A. / Ciirdaeva, E. / Schomacher, L. / Ficner, R.
External linksJ. Mol. Biol. / PubMed:20434457
MethodsX-ray diffraction
Resolution1.23 - 3.1 Å
Structure data

PDB-3fzi:
1.9 Angstrom structure of the thermophilic exonuclease III homologue Mth0212
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-3g00:
Mth0212 in complex with a 9bp blunt end dsDNA at 1.7 Angstrom
Method: X-RAY DIFFRACTION / Resolution: 1.74 Å

PDB-3g0a:
Mth0212 with two bound manganese ions
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-3g0r:
Complex of Mth0212 and an 8bp dsDNA with distorted ends
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

PDB-3g1k:
Mth0212 (WT) crystallized in a monoclinic space group
Method: X-RAY DIFFRACTION / Resolution: 3.1 Å

PDB-3g2c:
Mth0212 in complex with a short ssDNA (CGTA)
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-3g2d:
Complex of Mth0212 and a 4 bp dsDNA with 3'-overhang
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-3g38:
The catalytically inactive mutant Mth0212 (D151N) in complex with an 8 bp dsDNA
Method: X-RAY DIFFRACTION / Resolution: 3.04 Å

PDB-3g3c:
Mth0212 (WT) in complex with a 6bp dsDNA containing a single one nucleotide long 3'-overhang
Method: X-RAY DIFFRACTION / Resolution: 3.04 Å

PDB-3g3y:
Mth0212 in complex with ssDNA in space group P32
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-3g4t:
Mth0212 (WT) in complex with a 7bp dsDNA
Method: X-RAY DIFFRACTION / Resolution: 2.64 Å

PDB-3g8v:
The rationally designed catalytically inactive mutant Mth0212(D151N)
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

PDB-3g91:
1.2 Angstrom structure of the exonuclease III homologue Mth0212
Method: X-RAY DIFFRACTION / Resolution: 1.23 Å

PDB-3ga6:
Mth0212 in complex with two DNA helices
Method: X-RAY DIFFRACTION / Resolution: 1.898 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-HOH:
WATER / Water

ChemComp-PO4:
PHOSPHATE ION / Phosphate

ChemComp-GOL:
GLYCEROL / Glycerol

ChemComp-MPD:
(4S)-2-METHYL-2,4-PENTANEDIOL / precipitant*YM / 2-Methyl-2,4-pentanediol

ChemComp-MN:
Unknown entry

ChemComp-PG4:
TETRAETHYLENE GLYCOL / precipitant*YM / Polyethylene glycol

ChemComp-NA:
Unknown entry

ChemComp-MRD:
(4R)-2-METHYLPENTANE-2,4-DIOL / precipitant*YM / 2-Methyl-2,4-pentanediol

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER / Diethylene glycol

Source
  • methanothermobacter thermautotrophicus (archaea)
KeywordsHYDROLASE / alpha/beta-sandwich / double-strand specific 3'-5' exonuclease / AP endonuclease / 2'-deoxyuridine endonuclease / HYDROLASE/DNA / protein-DNA complex / HYDROLASE-DNA COMPLEX / coordination of two manganese ions / magnesium-dependent double-strand specific 3'-5' exonuclease / single-stranded DNA / flipped nucleotide / PO4 / Mg2+ / dsDNA with 3'-overhang / 3'- phosphate moiety bound / double-stranded DNA / inorganic phosphate / 2'-desoxyuridine endonuclease / rationally designed catalytically inactive mutant / twin / disorder of DNA / 3'-5' exonuclease

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