3SM8 | pdb_00003sm8

Crystal Structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase in Complex with an (N5) Flavin Adduct

• PDB DOI: https://doi.org/10.2210/pdb3SM8/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-06-27 Released: 2011-07-20 
• Deposition Author(s): Fu, G., Weber, I.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.07 Å
• R-Value Free: 
  0.165 (Depositor), 0.151 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.133 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Starting Model: experimental

Literature

Atomic-resolution structure of an N5 flavin adduct in D-arginine dehydrogenase.

Fu, G., Yuan, H., Wang, S., Gadda, G., Weber, I.T.

(2011) Biochemistry 50: 6292-6294

• PubMed: 21707047 
• DOI: https://doi.org/10.1021/bi200831a
• Primary Citation Related Structures: 
  3SM8


• PubMed Abstract: 
  

  D-Arginine dehydrogenase (DADH) catalyzes the flavin-dependent oxidative deamination of D-arginine and other D-amino acids to the corresponding imino acids. The 1.07 Å atomic-resolution structure of DADH crystallized with D-leucine unexpectedly revealed a covalent N(5) flavin adduct, instead of the expected iminoleucine product in the active site. This acyl adduct has been successfully reproduced by photoreduction of DADH in the presence of 4-methyl-2-oxopentanoic acid (ketoleucine). The iminoleucine may be released readily because of weak interactions in the binding site, in contrast to iminoarginine, converted to ketoleucine, which reacts with activated FAD to form the covalently linked acyl adduct.

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Organizational Affiliation: 
• Department of Biology, Georgia State University, Atlanta, Georgia 30303, USA.

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: 42.55 kDa 
• Atom Count: 3,439 
• Modeled Residue Count: 381 
• Deposited Residue Count: 381 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FAD-dependent catabolic D-arginine dehydrogenase, DauA	A	381	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: dauA, PA3863, PAO1 EC: 1.4.1 (PDB Primary Data), 1.4.99.6 (UniProt)
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FNK	E [auth A]	[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[7,8-dimethyl-5-(3-methylbutanoyl)-2,4-dioxo-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate C32 H43 N9 O16 P2 CXENQOVRLDMZEP-KQGUAMSLSA-N
GOL	B [auth A], C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.07 Å
• R-Value Free:  0.165 (Depositor), 0.151 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.133 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.072	α = 90
b = 77.933	β = 90
c = 89.31	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-20 
Deposition Author(s): Fu, G., Weber, I.T.

Revision History  

• Version 1.0: 2011-07-20
  Type: Initial release
  
• Version 1.1: 2012-01-11
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-04-03
  Changes: Refinement description