5HUE | pdb_00005hue

DAHP synthase from Corynebacterium glutamicum in complex with tryptophan


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 
    0.285 (Depositor), 0.282 (DCC) 
  • R-Value Work: 
    0.247 (Depositor), 0.251 (DCC) 
  • R-Value Observed: 
    0.249 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Inter-Enzyme Allosteric Regulation of Chorismate Mutase in Corynebacterium glutamicum: Structural Basis of Feedback Activation by Trp.

Burschowsky, D.Thorbjornsrud, H.V.Heim, J.B.Fahrig-Kamarauskaite, J.R.Wurth-Roderer, K.Kast, P.Krengel, U.

(2018) Biochemistry 57: 557-573

  • DOI: https://doi.org/10.1021/acs.biochem.7b01018
  • Primary Citation Related Structures: 
    5HUB, 5HUC, 5HUD, 5HUE

  • PubMed Abstract: 

    Corynebacterium glutamicum is widely used for the industrial production of amino acids, nucleotides, and vitamins. The shikimate pathway enzymes DAHP synthase (CgDS, Cg2391) and chorismate mutase (CgCM, Cgl0853) play a key role in the biosynthesis of aromatic compounds. Here we show that CgCM requires the formation of a complex with CgDS to achieve full activity, and that both CgCM and CgDS are feedback regulated by aromatic amino acids binding to CgDS. Kinetic analysis showed that Phe and Tyr inhibit CgCM activity by inter-enzyme allostery, whereas binding of Trp to CgDS strongly activates CgCM. Mechanistic insights were gained from crystal structures of the CgCM homodimer, tetrameric CgDS, and the heterooctameric CgCM-CgDS complex, refined to 1.1, 2.5, and 2.2 Å resolution, respectively. Structural details from the allosteric binding sites reveal that DAHP synthase is recruited as the dominant regulatory platform to control the shikimate pathway, similar to the corresponding enzyme complex from Mycobacterium tuberculosis.


  • Organizational Affiliation
    • Department of Chemistry, University of Oslo , NO-0315 Oslo, Norway.

Macromolecule Content 

  • Total Structure Weight: 53.63 kDa 
  • Atom Count: 3,571 
  • Modeled Residue Count: 447 
  • Deposited Residue Count: 472 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
3-Deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase472Corynebacterium glutamicumMutation(s): 0 
Gene Names: Cgl2178
EC: 2.5.1.54
UniProt
Find proteins for Q8NNL5 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534))
Explore Q8NNL5 
Go to UniProtKB:  Q8NNL5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NNL5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRP

Query on TRP



Download:Ideal Coordinates CCD File
D [auth A]TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
PEP

Query on PEP



Download:Ideal Coordinates CCD File
C [auth A]PHOSPHOENOLPYRUVATE
C3 H5 O6 P
DTBNBXWJWCWCIK-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
J [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
M [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
MPD

Query on MPD



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
K [auth A],
L [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MN

Query on MN



Download:Ideal Coordinates CCD File
B [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free:  0.285 (Depositor), 0.282 (DCC) 
  • R-Value Work:  0.247 (Depositor), 0.251 (DCC) 
  • R-Value Observed: 0.249 (Depositor) 
Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.189α = 90
b = 109.189β = 90
c = 279.897γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Research Council of NorwayNorway214037

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Database references
  • Version 1.2: 2018-07-11
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description