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1q2s

Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Queuine tRNA-ribosyltransferase

Zymomonas mobilis

UniProt P28720

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Monomer Protein 1 RNA 1 5'-R(*AP*GP*CP*AP*CP*GP*GP*CP*UP*(PQ1)P*UP*AP*AP*AP*CP*CP*GP*UP*GP*C)-3' × 1 ZINC ION × 1 water × 2 Consistent with all polymers
2 Protein monomer Monomer Protein 1 ZINC ION × 1 water × 1 Consistent with protein count
3 Protein–RNA Monomer Protein 1 RNA 1 ;RNA (5'-R(*AP*GP*CP*AP*CP*GP*GP*CP*UP*(N)P*UP*AP*AP*AP*CP*CP*GP*UP*GP*C)-3') ; × 1 ZINC ION × 1 9-DEAZAGUANINE × 1 water × 2 Consistent with all polymers
4 Protein monomer Monomer Protein 1 ZINC ION × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1pud 1q2r 1q2r 1q2s 1q2s 1wkd 1wke 1wkf

8 assemblies

Homodimer
1efz 1enu 1f3e 1k4g 1k4h 1n2v 1ozm 1ozq 1p0b 1p0d 1p0e 1pud

172 assemblies; showing the first 12

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1q2r 1q2r 1q2s 1q2s

4 assemblies

View Construct and Data Evidence
UniProt name TGT_ZYMMO
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 2–386； UniProt 1–385 Author chain B； PDBConstruct 2–386； UniProt 1–385 Author chain C； PDBConstruct 2–386； UniProt 1–385 Author chain D； PDBConstruct 2–386； UniProt 1–385

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id1q2s
Deposition date deposition_date2003-07-25
Structure title titleChemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate
Keywords keywordsTIM barrel, Protein-RNA complex, Covalent intermediat, Transferase-RNA COMPLEX; Transferase/RNA
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1q2s__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1q2s__assembly_3__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1q2s__assembly_3__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）22.30 Å
Rg (electron density)21.12 Å
Total Rg21.86 Å
Atom count3359
Residues396
Excluded volume57811 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1q2s__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1q2s__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 1q2s__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 1q2s__assembly_4__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1q2sa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.20 — tRNA-guanine transglycosylase
Family Family familyc.1.20.1 — tRNA-guanine transglycosylase
Domain ID domain_idd1q2sb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.20 — tRNA-guanine transglycosylase
Family Family familyc.1.20.1 — tRNA-guanine transglycosylase
Domain ID domain_idd1q2sc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.20 — tRNA-guanine transglycosylase
Family Family familyc.1.20.1 — tRNA-guanine transglycosylase
Domain ID domain_idd1q2sd_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.20 — tRNA-guanine transglycosylase
Family Family familyc.1.20.1 — tRNA-guanine transglycosylase

CATH v4.4 (4 domains)

Domain ID domain_id1q2sA00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily105 — Queuine tRNA-ribosyltransferase-like
Domain ID domain_id1q2sB00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily105 — Queuine tRNA-ribosyltransferase-like
Domain ID domain_id1q2sC00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily105 — Queuine tRNA-ribosyltransferase-like
Domain ID domain_id1q2sD00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily105 — Queuine tRNA-ribosyltransferase-like
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7. Citations (1)