2BTE | pdb_00002bte

Thermus thermophilus Leucyl-tRNA synthetase complexed with a tRNAleu transcript in the post-editing conformation and a post- transfer editing substrate analogue

PDB DOI: https://doi.org/10.2210/pdb2BTE/pdb
NAKB: 2BTE

Classification: LIGASE
Organism(s): Thermus thermophilus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2005-05-31 Released: 2005-09-15
Deposition Author(s): Cusack, S., Tukalo, M., Yaremchuk, A., Fukunaga, R., Yokoyama, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.253 (Depositor), 0.240 (DCC)
R-Value Work:
0.217 (Depositor), 0.220 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The Crystal Structure of Leucyl-tRNA Synthetase Complexed with tRNA(Leu) in the Post-Transfer- Editing Conformation.

Tukalo, M., Yaremchuk, A., Fukunaga, R., Yokoyama, S., Cusack, S.

(2005) Nat Struct Mol Biol 12: 923

PubMed: 16155583 Search on PubMed
DOI: https://doi.org/10.1038/nsmb986
Primary Citation of Related Structures:
2BTE, 2BYT

PubMed Abstract:
Leucyl-tRNA synthetase (LeuRS) has a specific post-transfer editing activity directed against mischarged isoleucine and similar noncognate amino acids. We describe the post-transfer-editing and product complexes of Thermus thermophilus LeuRS (LeuRSTT) with tRNA(Leu) at 2.9- to 3.3-A resolution. In the post-transfer-editing configuration, A76 binds in the editing active site exactly as previously found for the adenosine moiety of a small-molecule editing-substrate analog. The 60 C-terminal residues of LeuRSTT, unseen in previous structures, fold into a compact domain flexibly linked to the rest of the molecule and interacting with the G19-C56 tertiary base pair of tRNA(Leu). LeuRS recognition of tRNA(Leu) depends essentially on tRNA shape rather than base-specific interactions. The structures show that considerable domain rotations, notably of the editing domain, accompany the tRNA-3' end dynamics associated successively with aminoacylation, post-transfer editing and product release.

Organizational Affiliation

European Molecular Biology Laboratory, Grenoble Outstation, c/o Institut Laue-Langevin, 156X, F-38042 Grenoble Cedex 9, France.

Macromolecule Content

Total Structure Weight: 260.23 kDa
Atom Count: 17,815
Modelled Residue Count: 1,908
Deposited Residue Count: 1,922
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AMINOACYL-TRNA SYNTHETASE	A, C [auth D]	878	Thermus thermophilus	Mutation(s): 0 EC: 6.1.1.4
UniProt
Find proteins for Q7SIE4 (Thermus thermophilus) Explore Q7SIE4 Go to UniProtKB: Q7SIE4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7SIE4
Sequence Annotations Expand
Reference Sequence LOADING

Entity ID: 2
Molecule	Chains	Length	Organism	Image
TRNALEU TRANSCRIPT WITH ANTICODON CAG	B, D [auth E]	83	Thermus thermophilus
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2AD Query on 2AD Download Ideal Coordinates CCD File SDF format, chain OA [auth D] SDF format, chain U [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain U [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain U [auth A]	OA [auth D], U [auth A]	2'-AMINO-2'-DEOXYADENOSINE C₁₀ H₁₄ N₆ O₃ CQKMBZHLOYVGHW-QYYRPYCUSA-N		Interactions Focus chain OA [auth D] Focus chain U [auth A] Interactions & Density Focus chain OA [auth D] Focus chain U [auth A]
HG Query on HG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain Y [auth D] MOL2 format, chain G [auth A] MOL2 format, chain Y [auth D] mmCIF format, chain G [auth A] mmCIF format, chain Y [auth D]	G [auth A], Y [auth D]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain Y [auth D] Interactions & Density Focus chain G [auth A] Focus chain Y [auth D]
LEU Query on LEU Download Ideal Coordinates CCD File SDF format, chain MA [auth D] SDF format, chain V [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain V [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain V [auth A]	MA [auth D], V [auth A]	LEUCINE C₆ H₁₃ N O₂ ROHFNLRQFUQHCH-YFKPBYRVSA-N		Interactions Focus chain MA [auth D] Focus chain V [auth A] Interactions & Density Focus chain MA [auth D] Focus chain V [auth A]
NVA Query on NVA Download Ideal Coordinates CCD File SDF format, chain NA [auth D] SDF format, chain T [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain T [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain T [auth A]	NA [auth D], T [auth A]	NORVALINE C₅ H₁₁ N O₂ SNDPXSYFESPGGJ-BYPYZUCNSA-N		Interactions Focus chain NA [auth D] Focus chain T [auth A] Interactions & Density Focus chain NA [auth D] Focus chain T [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain S [auth A] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain R [auth A] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain S [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain R [auth A] mmCIF format, chain Z [auth D]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] EA [auth D] AA [auth D], BA [auth D], CA [auth D], DA [auth D], EA [auth D], FA [auth D], GA [auth D], H [auth A], HA [auth D], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain Z [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain F [auth A]	E [auth A], F [auth A], W [auth D], X [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain W [auth D] Focus chain X [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.253 (Depositor), 0.240 (DCC)
R-Value Work: 0.217 (Depositor), 0.220 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 204.121	α = 90
b = 125.705	β = 120.86
c = 175.432	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-09-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-09-15
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description