5HUD

Non-covalent complex of and DAHP synthase and chorismate mutase from Corynebacterium glutamicum with bound transition state analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-Deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase
A, B, C, D
472Corynebacterium glutamicumMutation(s): 0 
Gene Names: Cgl2178
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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Chorismate mutase
E, F, G, H
90Corynebacterium glutamicumMutation(s): 0 
Gene Names: Cgl0853
EC: 5.4.99.5
UniProt
Find proteins for Q8NS29 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534))
Explore Q8NS29 
Go to UniProtKB:  Q8NS29
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NS29
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TSA
Query on TSA

Download Ideal Coordinates CCD File 
FD [auth F],
QD [auth G],
VC [auth E],
WD [auth H]
8-HYDROXY-2-OXA-BICYCLO[3.3.1]NON-6-ENE-3,5-DICARBOXYLIC ACID
C10 H12 O6
KRZHNRULRHECRF-JQCUSGDOSA-N
TRP
Query on TRP

Download Ideal Coordinates CCD File 
FA [auth B],
LB [auth C],
NC [auth D],
Q [auth A]
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
CA [auth B],
HC [auth D],
IB [auth C],
IC [auth D],
JC [auth D]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
DB [auth C]
DD [auth F]
EB [auth C]
ED [auth F]
FB [auth C]
DB [auth C],
DD [auth F],
EB [auth C],
ED [auth F],
FB [auth C],
FC [auth D],
GB [auth C],
GC [auth D],
HB [auth C],
M [auth A],
PD [auth G],
SC [auth E],
TC [auth E],
UC [auth E]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AB [auth C]
AC [auth D]
BA [auth B]
BB [auth C]
BC [auth D]
AB [auth C],
AC [auth D],
BA [auth B],
BB [auth C],
BC [auth D],
CB [auth C],
CC [auth D],
CD [auth F],
DC [auth D],
EC [auth D],
K [auth A],
L [auth A],
MD [auth G],
ND [auth G],
OD [auth G],
ZB [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
EA [auth B]
KB [auth C]
LC [auth D]
MC [auth D]
O [auth A]
EA [auth B],
KB [auth C],
LC [auth D],
MC [auth D],
O [auth A],
P [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth B]
AD [auth F]
BD [auth F]
GA [auth C]
GD [auth G]
AA [auth B],
AD [auth F],
BD [auth F],
GA [auth C],
GD [auth G],
HA [auth C],
HD [auth G],
I [auth A],
IA [auth C],
ID [auth G],
J [auth A],
JA [auth C],
JD [auth G],
KA [auth C],
KD [auth G],
LA [auth C],
LD [auth G],
MA [auth C],
MB [auth D],
NA [auth C],
NB [auth D],
OA [auth C],
OB [auth D],
OC [auth E],
PA [auth C],
PB [auth D],
PC [auth E],
QA [auth C],
QB [auth D],
QC [auth E],
R [auth B],
RA [auth C],
RB [auth D],
RC [auth E],
RD [auth H],
S [auth B],
SA [auth C],
SB [auth D],
SD [auth H],
T [auth B],
TA [auth C],
TB [auth D],
TD [auth H],
U [auth B],
UA [auth C],
UB [auth D],
UD [auth H],
V [auth B],
VA [auth C],
VB [auth D],
VD [auth H],
W [auth B],
WA [auth C],
WB [auth D],
WC [auth F],
X [auth B],
XA [auth C],
XB [auth D],
XC [auth F],
Y [auth B],
YA [auth C],
YB [auth D],
YC [auth F],
Z [auth B],
ZA [auth C],
ZC [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
DA [auth B],
JB [auth C],
KC [auth D],
N [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.622α = 90
b = 110.481β = 101.41
c = 134.652γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
Aimlessdata scaling
XDSdata scaling
XDSdata reduction

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, Derived calculations, Refinement description