7RDF | pdb_00007rdf

Crystal structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase Y249F co-crystallized in the presence of D-arginine

• PDB DOI: https://doi.org/10.2210/pdb7RDF/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-07-09 Released: 2021-12-22 
• Deposition Author(s): Reis, R.A.G., Iyer, A., Agniswamy, A., Weber, I.T., Gadda, G.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 
  0.157 (Depositor), 0.157 (DCC) 
• R-Value Work: 
  0.126 (Depositor), 0.128 (DCC) 
• R-Value Observed: 
  0.128 (Depositor) 

Starting Model: experimental

Literature

Discovery of a new flavin N5-adduct in a tyrosine to phenylalanine variant of d-Arginine dehydrogenase.

Iyer, A., Reis, R.A.G., Agniswamy, J., Weber, I.T., Gadda, G.

(2021) Arch Biochem Biophys 715: 109100-109100

• PubMed: 34864048 
• DOI: https://doi.org/10.1016/j.abb.2021.109100
• Primary Citation Related Structures: 
  7RDF


• PubMed Abstract: 
  

  d-Arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH) catalyzes the flavin-dependent oxidation of d-arginine and other d-amino acids. Here, we report the crystal structure at 1.29 Å resolution for PaDADH-Y249F expressed and co-crystallized with d-arginine. The overall structure of PaDADH-Y249F resembled PaDADH-WT, but the electron density for the flavin cofactor was ambiguous, suggesting the presence of modified flavins. Electron density maps and mass spectrometric analysis confirmed the presence of both N5-(4-guanidino-oxobutyl)-FAD and 6-OH-FAD in a single crystal of PaDADH-Y249F and helped with the further refinement of the X-ray crystal structure. The versatility of the reduced flavin is apparent in the PaDADH-Y249F structure and is evidenced by the multiple functions it can perform in the same active site.

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Organizational Affiliation: 
• Department of Chemistry, Georgia State University, Atlanta, GA, 30302, USA.
Department of Biology, Georgia State University, Atlanta, GA, 30302, USA.
Department of Chemistry, Georgia State University, Atlanta, GA, 30302, USA; Department of Biology, Georgia State University, Atlanta, GA, 30302, USA.
Department of Chemistry, Georgia State University, Atlanta, GA, 30302, USA; Department of Biology, Georgia State University, Atlanta, GA, 30302, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30302, USA. Electronic address: [e-mail].

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: 42.69 kDa 
• Atom Count: 3,816 
• Modeled Residue Count: 375 
• Deposited Residue Count: 375 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FAD-dependent catabolic D-arginine dehydrogenase DauA	A	375	Pseudomonas aeruginosa PAO1	Mutation(s): 1  Gene Names: dauA, PA3863 EC: 1.4.99.6
UniProt
Find proteins for Q9HXE3 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HXE3  Go to UniProtKB:  Q9HXE3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4R2 (Subject of Investigation/LOI)	B [auth A]	[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-5-[5-[(~{E})-4-carbamimidamidobut-2-enoyl]-7,8-dimethyl-2,4-bis(oxidanylidene)-1~{H}-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate C32 H42 N12 O16 P2 UNPAMCKSCHHHHK-IGVXTPOKSA-N
6FA (Subject of Investigation/LOI)	C [auth A]	6-HYDROXY-FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O16 P2 BJSUUWFQAMLNKU-OKXKTURISA-N
PEG	G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free:  0.157 (Depositor), 0.157 (DCC) 
• R-Value Work:  0.126 (Depositor), 0.128 (DCC) 
• R-Value Observed: 0.128 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.01	α = 90
b = 76.33	β = 90
c = 76.76	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-12-22 
Deposition Author(s): Reis, R.A.G., Iyer, A., Agniswamy, A., Weber, I.T., Gadda, G.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE1506518

Revision History  

• Version 1.0: 2021-12-22
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description