6HQF

Structure of Phenylalanine ammonia-lyase from Petroselinum crispum in complex with (R)-APEP

• PDB DOI: https://doi.org/10.2210/pdb6HQF/pdb

• Classification: LYASE
• Organism(s): Petroselinum crispum
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-09-24 Released: 2019-10-09 
• Deposition Author(s): Bata, Z., Molnar, B., Leveles, I., Poppe, L., Vertessy, G.B.
• Funding Organization(s): National Research Development and Innovation Office (NKFIH), Ministry of Human Capacities, Hungarian Academy of Sciences, Romania, National Authority for Scientific Research and Innovation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.205 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 

Literature

Substrate Tunnel Engineering Aided by X-ray Crystallography and Functional Dynamics Swaps the Function of MIO-Enzymes

Bata, Z., Molnar, Z., Madaras, E., Molnar, B., Santa-Bell, E., Varga, A., Leveles, I., Qian, R., Hammerschmidt, F., Paizs, C., Vertessy, B.G., Poppe, L.

(2021) ACS Catal : 4538-4549

• DOI: https://doi.org/10.1021/acscatal.1c00266

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 156.1 kDa 
• Atom Count: 10,955 
• Modelled Residue Count: 1,346 
• Deposited Residue Count: 1,428 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylalanine ammonia-lyase 1	A, B	714	Petroselinum crispum	Mutation(s): 3  Gene Names: PAL1 EC: 4.3.1.24
UniProt
Find proteins for P24481 (Petroselinum crispum) Explore P24481  Go to UniProtKB:  P24481

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PPH	C [auth A], D [auth B]	[(1R)-1-amino-2-phenylethyl]phosphonic acid C8 H12 N O3 P FQCNOURLMNHAQN-MRVPVSSYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MDO	A, B	L-PEPTIDE LINKING	C8 H11 N3 O3		ALA, SER, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.205 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.878	α = 90
b = 160.951	β = 90
c = 141.58	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-10-09 
Deposition Author(s): Bata, Z., Molnar, B., Leveles, I., Poppe, L., Vertessy, G.B.

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Funding Organization	Location	Grant Number
National Research Development and Innovation Office (NKFIH)	Hungary	K119493
National Research Development and Innovation Office (NKFIH)	Hungary	NVKP_16-1-2016-0020
National Research Development and Innovation Office (NKFIH)	Hungary	2017-1.3.1-VKE-2017-00002
National Research Development and Innovation Office (NKFIH)	Hungary	2017-1.3.1-VKE-2017-00013
National Research Development and Innovation Office (NKFIH)	Hungary	VEKOP-2.3.2-16-2017-00013
National Research Development and Innovation Office (NKFIH)	Hungary	NKP-2018-1.2.1-NKP-2018-00005
Ministry of Human Capacities	Hungary	BME FIKP-BIO
Hungarian Academy of Sciences	Hungary	MedinProt grant
Ministry of Human Capacities	Hungary	UNKP-2017-3-III
Romania, National Authority for Scientific Research and Innovation	Romania	ID P_37_273, Cod MySMIS 103413
National Research Development and Innovation Office (NKFIH)	Hungary	SNN-125637

Revision History  

• Version 1.0: 2019-10-09
  Type: Initial release
  
• Version 2.0: 2021-04-07
  Changes: Atomic model, Author supporting evidence, Database references, Derived calculations, Structure summary
• Version 2.1: 2021-04-14
  Changes: Database references
• Version 3.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 3.1: 2024-01-24
  Changes: Refinement description