5G4I | pdb_00005g4i

PLP-dependent phospholyase A1RDF1 from Arthrobacter aurescens TC1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.175 (Depositor), 0.186 (DCC) 
  • R-Value Work: 
    0.153 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 
    0.154 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for Phospholyase Activity of a Class III Transaminase Homologue.

Cuetos, A.Steffen-Munsberg, F.Mangas Sanchez, J.Frese, A.Bornscheuer, U.T.Hohne, M.Grogan, G.

(2016) Chembiochem 17: 2308-2311

  • DOI: https://doi.org/10.1002/cbic.201600482
  • Primary Citation Related Structures: 
    5G4I, 5G4J

  • PubMed Abstract: 

    Pyridoxal-phosphate (PLP)-dependent enzymes catalyse a remarkable diversity of chemical reactions in nature. A1RDF1 from Arthrobacter aurescens TC1 is a fold type I, PLP-dependent enzyme in the class III transaminase (TA) subgroup. Despite sharing 28 % sequence identity with its closest structural homologues, including β-alanine:pyruvate and γ-aminobutyrate:α-ketoglutarate TAs, A1RDF1 displayed no TA activity. Activity screening revealed that the enzyme possesses phospholyase (E.C. 4.2.3.2) activity towards O-phosphoethanolamine (PEtN), an activity described previously for vertebrate enzymes such as human AGXT2L1, enzymes for which no structure has yet been reported. In order to shed light on the distinctive features of PLP-dependent phospholyases, structures of A1RDF1 in complex with PLP (internal aldimine) and PLP⋅PEtN (external aldimine) were determined, revealing the basis of substrate binding and the structural factors that distinguish the enzyme from class III homologues that display TA activity.


  • Organizational Affiliation
    • York Structural Biology Laboratory, University of York, Heslington, York, YO10 5DD, UK.

Macromolecule Content 

  • Total Structure Weight: 97.61 kDa 
  • Atom Count: 7,107 
  • Modeled Residue Count: 845 
  • Deposited Residue Count: 892 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOSPHOLYASE
A, B
446Paenarthrobacter aurescens TC1Mutation(s): 0 
EC: 4.2.3.2
UniProt
Find proteins for A1RDF1 (Paenarthrobacter aurescens (strain TC1))
Explore A1RDF1 
Go to UniProtKB:  A1RDF1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1RDF1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B3P

Query on B3P



Download:Ideal Coordinates CCD File
G [auth A]2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
PLP

Query on PLP



Download:Ideal Coordinates CCD File
C [auth A],
H [auth B]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
D [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ACT

Query on ACT



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
M [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.175 (Depositor), 0.186 (DCC) 
  • R-Value Work:  0.153 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 0.154 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.937α = 90
b = 97.176β = 90
c = 124.261γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
BALBESphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2017-03-01
    Changes: Database references
  • Version 1.2: 2025-04-09
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary