4KKV

Crystal structure of candida glabrata FMN adenylyltransferase D181A Mutant

• PDB DOI: https://doi.org/10.2210/pdb4KKV/pdb

• Classification: TRANSFERASE
• Organism(s): Nakaseomyces glabratus CBS 138
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-05-06 Released: 2013-05-29 
• Deposition Author(s): Huerta, C., Zhang, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.201 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 

Literature

The "Super Mutant" of Yeast FMN Adenylyltransferase Enhances the Enzyme Turnover Rate by Attenuating Product Inhibition.

Huerta, C., Grishin, N.V., Zhang, H.

(2013) Biochemistry 52: 3615-3617

• PubMed: 23663086 
• DOI: https://doi.org/10.1021/bi400454w
• Primary Citation of Related Structures:  
  4KKV


• PubMed Abstract: 
  

  FMN adenylyltransferase (FMNAT) is an essential enzyme catalyzing the last step of a two-step pathway converting riboflavin (vitamin B2) to FAD, the ubiquitous flavocoenzyme. A structure-based mutagenesis and steady-state kinetic analysis of yeast FMNAT unexpectedly revealed that mutant D181A had a much faster turnover rate than the wild-type enzyme. Product inhibition analysis showed that wild-type FMNAT is strongly inhibited by FAD, whereas the D181A mutant has an attenuated product inhibition. These results provide a structural basis for the product inhibition of the enzyme and suggest that product release may be the rate-limiting step of the reaction.

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Organizational Affiliation: 

Department of Biophysics and Department of Biochemistry and ‡Howard Hughes Medical Institute, University of Texas Southwestern Medical Center , 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.16 kDa 
• Atom Count: 2,958 
• Modelled Residue Count: 295 
• Deposited Residue Count: 308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Similar to uniprot|P38913 Saccharomyces cerevisiae YDL045c FAD synthetase	A	308	Nakaseomyces glabratus CBS 138	Mutation(s): 1  Gene Names: CAGL0K01397g, FAD1 EC: 2.7.7.2
UniProt
Find proteins for Q6FNA9 (Candida glabrata (strain ATCC 2001 / BCRC 20586 / JCM 3761 / NBRC 0622 / NRRL Y-65 / CBS 138)) Explore Q6FNA9  Go to UniProtKB:  Q6FNA9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	B [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.201 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.257	α = 90
b = 80.257	β = 90
c = 78.169	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-29 
Deposition Author(s): Huerta, C., Zhang, H.

Revision History  

• Version 1.0: 2013-05-29
  Type: Initial release
  
• Version 1.1: 2013-12-25
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary