Glutamate 5-kinase from Escherichia coli complexed with glutamate

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

Starting Model: experimental
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A Novel Two-Domain Architecture within the Amino Acid Kinase Enzyme Family Revealed by the Crystal Structure of Escherichia Coli Glutamate 5-Kinase.

Marco-Marin, C.Gil-Ortiz, F.Perez-Arellano, I.Cervera, J.Fita, I.Rubio, V.

(2007) J Mol Biol 367: 1431

  • DOI: https://doi.org/10.1016/j.jmb.2007.01.073
  • Primary Citation of Related Structures:  
    2J5T, 2J5V

  • PubMed Abstract: 

    Glutamate 5-kinase (G5K) makes the highly unstable product glutamyl 5-phosphate (G5P) in the initial, controlling step of proline/ornithine synthesis, being feedback-inhibited by proline or ornithine, and causing, when defective, clinical hyperammonaemia. We determined two crystal structures of G5K from Escherichia coli, at 2.9 A and 2.5 A resolution, complexed with glutamate and sulphate, or with G5P, sulphate and the proline analogue 5-oxoproline. E. coli G5K presents a novel tetrameric (dimer of dimers) architecture. Each subunit contains a 257 residue AAK domain, typical of acylphosphate-forming enzymes, with characteristic alpha(3)beta(8)alpha(4) sandwich topology. This domain is responsible for catalysis and proline inhibition, and has a crater on the beta sheet C-edge that hosts the active centre and bound 5-oxoproline. Each subunit contains a 93 residue C-terminal PUA domain, typical of RNA-modifying enzymes, which presents the characteristic beta(5)beta(4) sandwich fold and three alpha helices. The AAK and PUA domains of one subunit associate non-canonically in the dimer with the same domains of the other subunit, leaving a negatively charged hole between them that hosts two Mg ions in one crystal, in line with the G5K requirement for free Mg. The tetramer, formed by two dimers interacting exclusively through their AAK domains, is flat and elongated, and has in each face, pericentrically, two exposed active centres in alternate subunits. This would permit the close apposition of two active centres of bacterial glutamate-5-phosphate reductase (the next enzyme in the proline/ornithine-synthesising route), supporting the postulated channelling of G5P. The structures clarify substrate binding and catalysis, justify the high glutamate specificity, explain the effects of known point mutations, and support the binding of proline near glutamate. Proline binding may trigger the movement of a loop that encircles glutamate, and which participates in a hydrogen bond network connecting active centres, which is possibly involved in the cooperativity for glutamate.

  • Organizational Affiliation

    Instituto de Biomedicina de Valencia (IBV-CSIC) and Center for Biomedical Research on Rare Diseases (CIBERER-ISCIII), Jaume Roig 11, Valencia-46010, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F, G, H
367Escherichia coliMutation(s): 1 
Find proteins for P0A7B5 (Escherichia coli (strain K12))
Explore P0A7B5 
Go to UniProtKB:  P0A7B5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7B5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GLU

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
GA [auth E]
HA [auth E]
I [auth A]
AA [auth D],
BA [auth D],
GA [auth E],
HA [auth E],
I [auth A],
J [auth A],
OA [auth F],
P [auth B],
PA [auth F],
UA [auth G],
V [auth C],
VA [auth G]
C5 H9 N O4
Query on SO4

Download Ideal Coordinates CCD File 
BB [auth H]
DA [auth D]
JA [auth E]
K [auth A]
Q [auth B]
BB [auth H],
DA [auth D],
JA [auth E],
K [auth A],
Q [auth B],
QA [auth F],
W [auth C],
WA [auth G]
O4 S
Query on CL

Download Ideal Coordinates CCD File 
CB [auth H]
EA [auth D]
FA [auth D]
KA [auth E]
L [auth A]
CB [auth H],
EA [auth D],
FA [auth D],
KA [auth E],
L [auth A],
LA [auth E],
M [auth A],
MA [auth E],
N [auth A],
R [auth B],
RA [auth F],
S [auth B],
SA [auth F],
T [auth B],
X [auth C],
XA [auth G],
Y [auth C],
YA [auth G],
Z [auth C],
ZA [auth G]
Query on MG

Download Ideal Coordinates CCD File 
AB [auth G]
CA [auth D]
DB [auth H]
IA [auth E]
NA [auth E]
AB [auth G],
CA [auth D],
DB [auth H],
IA [auth E],
NA [auth E],
O [auth A],
TA [auth F],
U [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.302α = 90
b = 124.108β = 93.96
c = 144.927γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description