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Structure paper

TitleStructural and functional characterization of archaeal DIMT1 unveils distinct protein dynamics essential for efficient catalysis.
Journal, issue, pagesStructure, Vol. 32, Page 1760-1775.e7, Year 2024
Publish dateNov 14, 2023 (structure data deposition date)
AuthorsSaha, S. / Kanaujia, S.P.
External linksStructure / PubMed:39146930
MethodsX-ray diffraction
Resolution2.01 - 3.3 Å
Structure data

PDB-8x3w:
Crystal structure of DIMT1 from the thermophilic archaeon, Pyrococcus horikoshii
Method: X-RAY DIFFRACTION / Resolution: 2.01 Å

PDB-8x41:
Crystal structure of DIMT1 in complex with 5'-methylthioadenosine and adenosine from Pyrococcus horikoshii
Method: X-RAY DIFFRACTION / Resolution: 2.35 Å

PDB-8x44:
Crystal structure of DIMT1 in complex with 5'-methylthioadenosine from Pyrococcus horikoshii (FormI)
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-8x45:
Crystal structure of DIMT1 in complex with 5'-methylthioadenosine from Pyrococcus horikoshii (FormII)
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-8x46:
Crystal structure of DIMT1 in complex with adenosylornithine (SFG) from Pyrococcus horikoshii
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

PDB-8x47:
Crystal structure of DIMT1 in complex with S-adenosyl-L-homocysteine (SAH) from Pyrococcus horikoshii
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-8x4g:
Crystal structure of the D117A mutant of DIMT1 from Pyrococcus horikoshii
Method: X-RAY DIFFRACTION / Resolution: 3.3 Å

PDB-8x4i:
Crystal structure of the D117A mutant of DIMT1 in complex with 5'-methylthioadenosine from Pyrococcus horikoshii
Method: X-RAY DIFFRACTION / Resolution: 3.3 Å

PDB-8x4l:
Crystal structure of the N132A mutant of DIMT1 from Pyrococcus horikoshii
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-8x4o:
Crystal structure of the Y135A mutant of DIMT1 in complex with 5'-methylthioadenosine from Pyrococcus horikoshii
Method: X-RAY DIFFRACTION / Resolution: 3 Å

PDB-8x4p:
Crystal structure of the Y135A mutant of DIMT1 in complex with adenosylornithine (SFG) from Pyrococcus horikoshii
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-SO3:
SULFITE ION

ChemComp-GOL:
GLYCEROL

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-ACT:
ACETATE ION

ChemComp-ARG:
ARGININE

ChemComp-EPE:
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / pH buffer*YM

ChemComp-HOH:
WATER

ChemComp-MTA:
5'-DEOXY-5'-METHYLTHIOADENOSINE

ChemComp-ADN:
ADENOSINE

ChemComp-CL:
Unknown entry

ChemComp-PGE:
TRIETHYLENE GLYCOL

ChemComp-SFG:
SINEFUNGIN

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE

Source
  • pyrococcus horikoshii ot3 (archaea)
KeywordsTRANSFERASE / Archaea / KsgA/DIMT1 / rRNA methyltransferase / SAM / SAH / SFG

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