5FJN

Structure of L-Amino acid deaminase from Proteus myxofaciens in complex with anthranilate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-Function Relationships in L-Amino Acid Deaminase, a Flavoprotein Belonging to a Novel Class of Biotechnologically Relevant Enzymes

Motta, P.Molla, G.Pollegioni, L.Nardini, M.

(2016) J.Biol.Chem. 291: 10457

  • DOI: 10.1074/jbc.M115.703819
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • l-Amino acid deaminase from Proteus myxofaciens (PmaLAAD) is a membrane flavoenzyme that catalyzes the deamination of neutral and aromatic l-amino acids into α-keto acids and ammonia. PmaLAAD does not use dioxygen to re-oxidize reduced FADH2 and thus ...

    l-Amino acid deaminase from Proteus myxofaciens (PmaLAAD) is a membrane flavoenzyme that catalyzes the deamination of neutral and aromatic l-amino acids into α-keto acids and ammonia. PmaLAAD does not use dioxygen to re-oxidize reduced FADH2 and thus does not produce hydrogen peroxide; instead, it uses a cytochrome b-like protein as an electron acceptor. Although the overall fold of this enzyme resembles that of known amine or amino acid oxidases, it shows the following specific structural features: an additional novel α+β subdomain placed close to the putative transmembrane α-helix and to the active-site entrance; an FAD isoalloxazine ring exposed to solvent; and a large and accessible active site suitable to bind large hydrophobic substrates. In addition, PmaLAAD requires substrate-induced conformational changes of part of the active site, particularly in Arg-316 and Phe-318, to achieve the correct geometry for catalysis. These studies are expected to pave the way for rationally improving the versatility of this flavoenzyme, which is critical for biocatalysis of enantiomerically pure amino acids.


    Organizational Affiliation

    From the Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi deII'Insubria, via J. H. Dunant 3, 21100 Varese, The Protein Factory, Politecnico di Milano and Università degli Studi deII'Insubria, 21100 Varese, and.,From the Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi deII'Insubria, via J. H. Dunant 3, 21100 Varese.,From the Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi deII'Insubria, via J. H. Dunant 3, 21100 Varese, The Protein Factory, Politecnico di Milano and Università degli Studi deII'Insubria, 21100 Varese, and gianluca.molla@uninsubria.it.,the Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy marco.nardini@unimi.it.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-AMINO ACID DEAMINASE
A, B
456Cosenzaea myxofaciensMutation(s): 0 
Find proteins for A0A158RFS7 (Cosenzaea myxofaciens)
Go to UniProtKB:  A0A158RFS7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
BE2
Query on BE2

Download SDF File 
Download CCD File 
A, B
2-AMINOBENZOIC ACID
C7 H7 N O2
RWZYAGGXGHYGMB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BE2Kd: 18400000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.156 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 72.810α = 90.00
b = 93.320β = 103.22
c = 75.070γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2016-06-15
    Type: Database references