Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 176.11 kDa 
• Atom Count: 13125 
• Residue Count: 1488 
• Unique protein chains: 1

2ZZE

Crystal structure of alanyl-tRNA synthetase without oligomerization domain in lysine-methylated form

• DOI: 10.2210/pdb2ZZE/pdb

• Classification: LIGASE
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-10 Released: 2009-07-21 
• Deposition Author(s): Sokabe, M., Ose, T., Tokunaga, K., Nakamura, A., Nureki, O., Yao, M., Tanaka, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 0.227 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Literature

The structure of alanyl-tRNA synthetase with editing domain.

Sokabe, M., Ose, T., Nakamura, A., Tokunaga, K., Nureki, O., Yao, M., Tanaka, I.

(2009) Proc Natl Acad Sci U S A 106: 11028-11033

• PubMed: 19549823 
• DOI: 10.1073/pnas.0904645106
• Primary Citation of Related Structures:  
  2ZZE, 2ZZF, 2ZZG


• PubMed Abstract: 
  

Alanyl-tRNA synthetase (AlaRS) catalyzes synthesis of Ala-tRNA(Ala) and hydrolysis of mis-acylated Ser- and Gly-tRNA(Ala) at 2 different catalytic sites. Here, we describe the monomer structures of C-terminal truncated archaeal AlaRS, with both activation and editing domains in the apo form, in complex with an Ala-AMP analog, and in a high-resolution lysine-methylated form. The structures show docking of the editing domain to the activation domain opposite from the predicted tRNA-binding surface. Thus, the editing site is positioned >35 A from the activation site, prompting us to model 2 different tRNA complexes: one binding tRNA at the activation site, and the other binding tRNA at the editing site. Interestingly, a gel-shift assay also implies the presence of 2 types of tRNA complex with different mobility. These results suggest that tRNA translocation via a canonical CCA flipping is unlikely to occur in AlaRS. The structure also demonstrated the binding of zinc in the editing site, in which the specific coordination of zinc would be facilitated by a conserved GGQ motif, implying that the editing mechanism may not be the same as in ThrRS. As Asn-194 in eubacterial AlaRS important for Ser misactivation is replaced by Thr-213 in archaeal AlaRS, a different Ser accommodation mechanism is proposed.

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Organizational Affiliation: 

Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0810, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alanyl-tRNA synthetase	A, B	752	Pyrococcus horikoshii	Mutation(s): 0  Gene Names: alaS, PH0297 EC: 6.1.1.7
Find proteins for O58035 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58035  Go to UniProtKB:  O58035

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	A,B	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS
OCS	A,B	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 0.227 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.063	α = 90
b = 130.151	β = 117.46
c = 94.855	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-02-10 
• Released Date: 2009-07-21 
Deposition Author(s): Sokabe, M., Ose, T., Tokunaga, K., Nakamura, A., Nureki, O., Yao, M., Tanaka, I.

Revision History 

• Version 1.0: 2009-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-11
  Changes: Refinement description