8X41

Crystal structure of DIMT1 in complex with 5'-methylthioadenosine and adenosine from Pyrococcus horikoshii

PDB DOI: https://doi.org/10.2210/pdb8X41/pdb

Classification: TRANSFERASE
Organism(s): Pyrococcus horikoshii OT3
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-11-14 Released: 2024-08-28
Deposition Author(s): Saha, S., Mandal, S.K., Dutta, A., Kanaujia, S.P.
Funding Organization(s): Science and Engineering Research Board (SERB)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.205
R-Value Work: 0.165
R-Value Observed: 0.167

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structural and functional characterization of archaeal DIMT1 unveils distinct protein dynamics essential for efficient catalysis.

Saha, S., Kanaujia, S.P.

(2024) Structure

PubMed: 39146930 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2024.07.013
Primary Citation of Related Structures:
8X3W, 8X41, 8X44, 8X45, 8X46, 8X47, 8X4G, 8X4I, 8X4L, 8X4O, 8X4P

PubMed Abstract:
Dimethyladenosine transferase 1 (DIMT1), an ortholog of bacterial KsgA is a conserved protein that assists in ribosome biogenesis by modifying two successive adenosine bases near the 3' end of small subunit (SSU) rRNA. Although KsgA/DIMT1 proteins have been characterized in bacteria and eukaryotes, they are yet unexplored in archaea. Also, their dynamics are not well understood. Here, we structurally and functionally characterized the apo and holo forms of archaeal DIMT1 from Pyrococcus horikoshii. Wild-type protein and mutants were analyzed to capture different transition states, including open, closed, and intermediate states. This study reports a unique inter-domain movement that is needed for substrate (RNA) positioning in the catalytic pocket, and is only observed in the presence of the cognate cofactors S-adenosyl-L-methionine (SAM) or S-adenosyl-L-homocysteine (SAH). The binding of the inhibitor sinefungine, an analog of SAM or SAH, to archaeal DIMT1 blocks the catalytic pocket and renders the enzyme inactive.

Organizational Affiliation

Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.

Macromolecule Content

Total Structure Weight: 70.54 kDa
Atom Count: 4,970
Modelled Residue Count: 538
Deposited Residue Count: 580
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable ribosomal RNA small subunit methyltransferase A	A, B	290	Pyrococcus horikoshii OT3	Mutation(s): 0 Gene Names: DIMT1 EC: 2.1.1.182
UniProt
Find proteins for O59487 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59487 Go to UniProtKB: O59487
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O59487
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MTA (Subject of Investigation/LOI) Query on MTA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain CA [auth B] MOL2 format, chain C [auth A] MOL2 format, chain CA [auth B]	C [auth A], CA [auth B]	5'-DEOXY-5'-METHYLTHIOADENOSINE C₁₁ H₁₅ N₅ O₃ S WUUGFSXJNOTRMR-IOSLPCCCSA-N		Interactions Focus chain C [auth A] Focus chain CA [auth B] Interactions & Density Focus chain C [auth A] Focus chain CA [auth B]
ADN (Subject of Investigation/LOI) Query on ADN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain DA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain DA [auth B]	D [auth A], DA [auth B]	ADENOSINE C₁₀ H₁₃ N₅ O₄ OIRDTQYFTABQOQ-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain DA [auth B] Interactions & Density Focus chain D [auth A] Focus chain DA [auth B]
ARG Query on ARG Download Ideal Coordinates CCD File SDF format, chain BA [auth A] MOL2 format, chain BA [auth A]	BA [auth A]	ARGININE C₆ H₁₅ N₄ O₂ ODKSFYDXXFIFQN-BYPYZUCNSA-O		Interactions Focus chain BA [auth A] Interactions & Density Focus chain BA [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain OA [auth B] MOL2 format, chain OA [auth B]	OA [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain OA [auth B] Interactions & Density Focus chain OA [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain KA [auth B] SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A]	KA [auth B] LA [auth B] MA [auth B] NA [auth B] Q [auth A] KA [auth B], LA [auth B], MA [auth B], NA [auth B], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A]
SO3 Query on SO3 Download Ideal Coordinates CCD File SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A]	IA [auth B], JA [auth B], O [auth A], P [auth A]	SULFITE ION O₃ S LSNNMFCWUKXFEE-UHFFFAOYSA-L		Interactions Focus chain IA [auth B] Focus chain JA [auth B] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain IA [auth B] Focus chain JA [auth B] Focus chain O [auth A] Focus chain P [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain EA [auth B] SDF format, chain F [auth A] SDF format, chain FA [auth B] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A]	E [auth A] EA [auth B] F [auth A] FA [auth B] G [auth A] E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], I [auth A], J [auth A], K [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A]	W [auth A], X [auth A], Y [auth A], Z [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain PA [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain PA [auth B]	AA [auth A], PA [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth A] Focus chain PA [auth B] Interactions & Density Focus chain AA [auth A] Focus chain PA [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A]	HA [auth B], L [auth A], M [auth A], N [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain HA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain HA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]