5UQR

Crystal structure of 2-methylcitrate synthase from Aspergillus fumigatus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Comparative studies of Aspergillus fumigatus 2-methylcitrate synthase and human citrate synthase.

Schlachter, C.R.Klapper, V.Radford, T.Chruszcz, M.

(2019) Biol Chem 400: 1567-1581

  • DOI: https://doi.org/10.1515/hsz-2019-0106
  • Primary Citation of Related Structures:  
    5UQO, 5UQQ, 5UQR, 5UQS, 5UQU, 5UZP, 5UZQ, 5UZR, 6BOL, 6BOM, 6BON, 6BOO, 6BOP

  • PubMed Abstract: 

    Aspergillus fumigatus is a ubiquitous fungus that is not only a problem in agriculture, but also in healthcare. Aspergillus fumigatus drug resistance is becoming more prominent which is mainly attributed to the widespread use of fungicides in agriculture. The fungi-specific 2-methylcitrate cycle is responsible for detoxifying propionyl-CoA, a toxic metabolite produced as the fungus breaks down proteins and amino acids. The enzyme responsible for this detoxification is 2-methylcitrate synthase (mcsA) and is a potential candidate for the design of new anti-fungals. However, mcsA is very similar in structure to human citrate synthase (hCS) and catalyzes the same reaction. Therefore, both enzymes were studied in parallel to provide foundations for design of mcsA-specific inhibitors. The first crystal structures of citrate synthase from humans and 2-methylcitrate synthase from A. fumigatus are reported. The determined structures capture various conformational states of the enzymes and several inhibitors were identified and characterized. Despite a significant homology, mcsA and hCS display pronounced differences in substrate specificity and cooperativity. Considering that the active sites of the enzymes are almost identical, the differences in reactions catalyzed by enzymes are caused by residues that are in the vicinity of the active site and influence conformational changes of the enzymes.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-methylcitrate synthase, mitochondrial
A, B
441Aspergillus fumigatusMutation(s): 0 
Gene Names: mcsAcit1
EC: 2.3.3.5 (PDB Primary Data), 2.3.3.16 (PDB Primary Data)
UniProt
Find proteins for B0YD89 (Aspergillus fumigatus (strain CBS 144.89 / FGSC A1163 / CEA10))
Explore B0YD89 
Go to UniProtKB:  B0YD89
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0YD89
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8JD
Query on 8JD

Download Ideal Coordinates CCD File 
H [auth B][(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (3R)-4-[(3-{[2-(ethylsulfanyl)ethyl]amino}-3-oxopropyl)amino]-3-hydroxy-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate (non-preferred name)
C23 H39 N7 O13 P2 S
ZYQGAGMIMDQCKA-ZSJPKINUSA-N
OAA
Query on OAA

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
OXALOACETATE ION
C4 H3 O5
KHPXUQMNIQBQEV-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B],
G [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.724α = 90
b = 94.11β = 90
c = 124.404γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-3000phasing
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2020-06-17
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Derived calculations, Refinement description