6C5C

Crystal structure of the 3-dehydroquinate synthase (DHQS) domain of Aro1 from Candida albicans SC5314 in complex with NADH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Molecular analysis and essentiality of Aro1 shikimate biosynthesis multi-enzyme in Candida albicans.

Stogios, P.J.Liston, S.D.Semper, C.Quade, B.Michalska, K.Evdokimova, E.Ram, S.Otwinowski, Z.Borek, D.Cowen, L.E.Savchenko, A.

(2022) Life Sci Alliance 5

  • DOI: https://doi.org/10.26508/lsa.202101358
  • Primary Citation of Related Structures:  
    6C5C, 7TBU, 7TBV, 7U5S, 7U5T, 7U5U

  • PubMed Abstract: 

    In the human fungal pathogen Candida albicans , ARO1 encodes an essential multi-enzyme that catalyses consecutive steps in the shikimate pathway for biosynthesis of chorismate, a precursor to folate and the aromatic amino acids. We obtained the first molecular image of C. albicans Aro1 that reveals the architecture of all five enzymatic domains and their arrangement in the context of the full-length protein. Aro1 forms a flexible dimer allowing relative autonomy of enzymatic function of the individual domains. Our activity and in cellulo data suggest that only four of Aro1's enzymatic domains are functional and essential for viability of C. albicans , whereas the 3-dehydroquinate dehydratase (DHQase) domain is inactive because of active site substitutions. We further demonstrate that in C. albicans , the type II DHQase Dqd1 can compensate for the inactive DHQase domain of Aro1, suggesting an unrecognized essential role for this enzyme in shikimate biosynthesis. In contrast, in Candida glabrata and Candida parapsilosis , which do not encode a Dqd1 homolog, Aro1 DHQase domains are enzymatically active, highlighting diversity across Candida species.


  • Organizational Affiliation

    Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-dehydroquinate synthase
A, B
390Candida albicans SC5314Mutation(s): 0 
Gene Names: ARO1CAALFM_C400890WACaO19.12175CaO19.4704
EC: 4.2.3.4 (PDB Primary Data), 4.2.1.10 (UniProt), 1.1.1.25 (UniProt), 2.7.1.71 (UniProt), 2.5.1.19 (UniProt)
UniProt
Find proteins for Q5AME2 (Candida albicans (strain SC5314 / ATCC MYA-2876))
Explore Q5AME2 
Go to UniProtKB:  Q5AME2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5AME2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
C [auth A],
N [auth B]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
M [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.678α = 90
b = 92.06β = 97.57
c = 88.915γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
SBC-Collectdata collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201700060C

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-24
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2021-04-14
    Changes: Structure summary
  • Version 1.4: 2022-11-23
    Changes: Database references
  • Version 1.5: 2023-10-25
    Changes: Data collection, Refinement description