1K9V | pdb_00001k9v

Structural evidence for ammonia tunelling across the (beta-alpha)8-barrel of the imidazole glycerol phosphate synthase bienzyme complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.278 (Depositor) 
  • R-Value Work: 
    0.224 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

Starting Model: other
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 1K9V

This is version 1.4 of the entry. See complete history

Literature

Structural evidence for ammonia tunneling across the (beta alpha)(8) barrel of the imidazole glycerol phosphate synthase bienzyme complex.

Douangamath, A.Walker, M.Beismann-Driemeyer, S.Vega-Fernandez, M.C.Sterner, R.Wilmanns, M.

(2002) Structure 10: 185-193

  • DOI: https://doi.org/10.1016/s0969-2126(02)00702-5
  • Primary Citation Related Structures: 
    1GPW, 1K9V

  • PubMed Abstract: 

    Since reactive ammonia is not available under physiological conditions, glutamine is used as a source for the incorporation of nitrogen in a number of metabolic pathway intermediates. The heterodimeric ImGP synthase that links histidine and purine biosynthesis belongs to the family of glutamine amidotransferases in which the glutaminase activity is coupled with a subsequent synthase activity specific for each member of the enzyme family. Its X-ray structure from the hyperthermophile Thermotoga maritima shows that the glutaminase subunit is associated with the N-terminal face of the (beta alpha)(8) barrel cyclase subunit. The complex reveals a putative tunnel for the transfer of ammonia over a distance of 25 A. Although ammonia tunneling has been reported for glutamine amidotransferases, the ImGP synthase has evolved a novel mechanism, which extends the known functional properties of the versatile (beta alpha)(8) barrel fold.


  • Organizational Affiliation
    • EMBL Hamburg Outstation c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 23.19 kDa 
  • Atom Count: 1,643 
  • Modeled Residue Count: 200 
  • Deposited Residue Count: 201 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Amidotransferase hisHA [auth F]201Thermotoga maritimaMutation(s): 0 
EC: 2.4.2 (PDB Primary Data), 4.3.2.10 (UniProt), 3.5.1.2 (UniProt)
UniProt
Find proteins for Q9X0C8 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X0C8 
Go to UniProtKB:  Q9X0C8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X0C8
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACY

Query on ACY



Download:Ideal Coordinates CCD File
B [auth F]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.278 (Depositor) 
  • R-Value Work:  0.224 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.008α = 90
b = 35.837β = 90
c = 42.507γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-02-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description