5HUD | pdb_00005hud

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 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.250 (Depositor), 0.253 (DCC) 
  • R-Value Observed: 
    0.252 (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: 262.23 kDa 
  • Atom Count: 18,279 
  • Modeled Residue Count: 2,134 
  • Deposited Residue Count: 2,248 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  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
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
Find similar proteins by:|  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 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.250 (Depositor), 0.253 (DCC) 
  • R-Value Observed: 0.252 (Depositor) 
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