1GPJ

Glutamyl-tRNA Reductase from Methanopyrus kandleri


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

V-Shaped Structure of Glutamyl-tRNA Reductase, the First Enzyme of tRNA-Dependent Tetrapyrrole Biosynthesis.

Moser, J.Schubert, W.-D.Beier, V.Bringemeier, I.Jahn, D.Heinz, D.W.

(2001) Embo J. 20: 6583

  • DOI: 10.1093/emboj/20.23.6583

  • PubMed Abstract: 
  • Processes vital to life such as respiration and photosynthesis critically depend on the availability of tetrapyrroles including hemes and chlorophylls. tRNA-dependent catalysis generally is associated with protein biosynthesis. An exception is the re ...

    Processes vital to life such as respiration and photosynthesis critically depend on the availability of tetrapyrroles including hemes and chlorophylls. tRNA-dependent catalysis generally is associated with protein biosynthesis. An exception is the reduction of glutamyl-tRNA to glutamate-1-semialdehyde by the enzyme glutamyl-tRNA reductase. This reaction is the indispensable initiating step of tetrapyrrole biosynthesis in plants and most prokaryotes. The crystal structure of glutamyl-tRNA reductase from the archaeon Methanopyrus kandleri in complex with the substrate-like inhibitor glutamycin at 1.9 A resolution reveals an extended yet planar V-shaped dimer. The well defined interactions of the inhibitor with the active site support a thioester-mediated reduction process. Modeling the glutamyl-tRNA onto each monomer reveals an extensive protein-tRNA interface. We furthermore propose a model whereby the large void of glutamyl-tRNA reductase is occupied by glutamate-1-semialdehyde-1,2-mutase, the subsequent enzyme of this pathway, allowing for the efficient synthesis of 5-aminolevulinic acid, the common precursor of all tetrapyrroles.


    Organizational Affiliation

    Institute of Microbiology, Technical University Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUTAMYL-TRNA REDUCTASE
A
404Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)Gene Names: hemA
EC: 1.2.1.70
Find proteins for Q9UXR8 (Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938))
Go to UniProtKB:  Q9UXR8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
GLU
Query on GLU

Download SDF File 
Download CCD File 
A
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
GMC
Query on GMC

Download SDF File 
Download CCD File 
A
(2R,3R,4S,5S)-4-AMINO-2-[6-(DIMETHYLAMINO)-9H-PURIN-9-YL]-5-(HYDROXYMETHYL)TETRAHYDRO-3-FURANOL
6N-DIMETHYL-3'-DEOXY-AMINO-ADENOSINE
C12 H18 N6 O3
RYSMHWILUNYBFW-GRIPGOBMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.267α = 90.00
b = 98.650β = 90.00
c = 68.606γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SOLOMONphasing
DENZOdata reduction
SHARPphasing
SOLVEphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-01-04
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance