Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 58709.43 
• Atom Count: 3813 
• Residue Count: 501 
• Unique protein chains: 1

1NJ1

Crystal structure of Prolyl-tRNA Synthetase from Methanothermobacter thermautotrophicus bound to cysteine sulfamoyl adenylate

• DOI: 10.2210/pdb1NJ1/pdb

• Classification: LIGASE
• Organism(s): Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
• Expression System: Escherichia coli


• Deposited: 2002-12-30 Released: 2003-03-04 
• Deposition Author(s): Kamtekar, S., Kennedy, W.D., Wang, J., Stathopoulos, C., Soll, D., Steitz, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.257 
• R-Value Work: 0.225 

Literature

The structural basis of cysteine aminoacylation of tRNAPro by prolyl-tRNA synthetases

Kamtekar, S., Kennedy, W.D., Wang, J., Stathopoulos, C., Soll, D., Steitz, T.A.

(2003) Proc.Natl.Acad.Sci.USA 100: 1673-1678

• PubMed: 12578991 
• DOI: 10.1073/pnas.0437911100
• Primary Citation of Related Structures:  
  1NJ8, 1NJ6, 1NJ5, 1NJ2


• PubMed Abstract: 
  

Cysteinyl-tRNA synthetase is an essential enzyme required for protein synthesis. Genes encoding this protein have not been identified in Methanocaldococcus jannaschii, Methanothermobacter thermautotrophicus, or Methanopyrus kandleri. It has previously been proposed that the prolyl-tRNA synthetase (ProRS) enzymes in these organisms recognize either proline or cysteine and can aminoacylate their cognate tRNAs through a dual-specificity mechanism. We report five crystal structures at resolutions between 2.6 and 3.2 A: apo M. jannaschii ProRS, and M. thermautotrophicus ProRS in apo form and in complex with cysteinyl-sulfamoyl-, prolyl-sulfamoyl-, and alanyl-sulfamoyl-adenylates. These aminoacyl-adenylate analogues bind to a single active-site pocket and induce an identical set of conformational changes in loops around the active site when compared with the ligand-free conformation of ProRS. The cysteinyl- and prolyl-adenylate analogues have similar, nanomolar affinities for M. thermautotrophicus ProRS. Homology modeling of tRNA onto these adenylate complexes places the 3'-OH of A76 in an appropriate position for the transfer of any of the three amino acids to tRNA. Thus, these structures explain recent biochemical experiments showing that M. jannaschii ProRS misacylates tRNA(Pro) with cysteine, and argue against the proposal that these archaeal ProRS enzymes possess the dual capacity to aminoacylate both tRNA(Pro) and tRNA(Cys) with their cognate amino acids.

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Organizational Affiliation: 

Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520-8114, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Proline-tRNA Synthetase	A	501	Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)	Mutation(s): 0  Gene Names: proS EC: 6.1.1.15
Find proteins for O26708 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Go to UniProtKB:  O26708

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
5CA	A	5'-O-(N-(L-CYSTEINYL)-SULFAMOYL)ADENOSINE C13 H19 N7 O7 S2 FTSDEWPMACCNGN-YTMOPEAISA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
5CA	Ki: 25 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.257 
• R-Value Work: 0.225 
• Space Group: P 6₅ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 143.750	α = 90.00
b = 143.750	β = 90.00
c = 163.890	γ = 120.00

Software Package:

Software Name	Purpose
AMoRE	phasing
HKL-2000	data reduction
CNS	refinement
SCALEPACK	data scaling
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-12-30 
• Released Date: 2003-03-04 
• Deposition Author(s): Kamtekar, S., Kennedy, W.D., Wang, J., Stathopoulos, C., Soll, D., Steitz, T.A.

Revision History 

• Version 1.0: 2003-03-04
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Derived calculations, Version format compliance