2YII | pdb_00002yii

Manipulating the regioselectivity of phenylalanine aminomutase: new insights into the reaction mechanism of MIO-dependent enzymes from structure-guided directed evolution

PDB DOI: https://doi.org/10.2210/pdb2YII/pdb

Classification: LYASE
Organism(s): Taxus chinensis
Expression System: Escherichia coli K-12
Mutation(s): Yes

Deposited: 2011-05-13 Released: 2011-11-09
Deposition Author(s): Wu, B., Szymanski, W., Wybenga, G.G., Heberling, M.M., Bartsch, S., Wildeman, S., Poelarends, G.J., Feringa, B.L., Dijkstra, B.W., Janssen, D.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free:
0.214 (Depositor), 0.213 (DCC)
R-Value Work:
0.179 (Depositor), 0.180 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Mechanism-Inspired Engineering of Phenylalanine Aminomutase for Enhanced Beta-Regioselective Asymmetric Amination of Cinnamates.

Wu, B., Szymanski, W., Wybenga, G.G., Heberling, M.M., Bartsch, S., De Wildeman, S., Poelarends, G.J., Feringa, B.L., Dijkstra, B.W., Janssen, D.B.

(2012) Angew Chem Int Ed Engl 51: 482

PubMed: 22113970 Search on PubMed
DOI: https://doi.org/10.1002/anie.201106372
Primary Citation Related Structures:
2YII

PubMed Abstract:
Turn to switch: A mutant of phenylalanine aminomutase was engineered that can catalyze the regioselective amination of cinnamate derivatives (see scheme, red) to, for example, β-amino acids. This regioselectivity, along with the X-ray crystal structures, suggests two distinct carboxylate binding modes differentiated by C(β)-C(ipso) bond rotation, which determines if β- (see scheme) or α-addition takes place.

Organizational Affiliation

Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.

Macromolecule Content

Total Structure Weight: 311.12 kDa
Atom Count: 20,965
Modeled Residue Count: 2,585
Deposited Residue Count: 2,820
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHENYLALANINE AMMONIA-LYASE	A, B, C, D	705	Taxus chinensis	Mutation(s): 1 EC: 5.4.3 (PDB Primary Data), 4.3.1.24 (PDB Primary Data), 5.4.3.10 (UniProt)
UniProt
Find proteins for Q68G84 (Taxus chinensis) Explore Q68G84 Go to UniProtKB: Q68G84
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q68G84
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
BME Query on BME Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] H [auth B] I [auth B] L [auth C] E [auth A], F [auth A], H [auth B], I [auth B], L [auth C], M [auth C], O [auth D], P [auth D]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain N [auth C] SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A], K [auth B], N [auth C], Q [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free: 0.214 (Depositor), 0.213 (DCC)
R-Value Work: 0.179 (Depositor), 0.180 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.454	α = 90
b = 145.999	β = 99.51
c = 99.68	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-11-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-11-09
Type: Initial release
Version 1.1: 2012-01-25
Changes: Other
Version 1.2: 2013-01-30
Changes: Database references
Version 1.3: 2019-10-23
Changes: Data collection, Database references, Derived calculations, Other
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations
Version 2.1: 2023-12-20
Changes: Refinement description
Version 2.2: 2025-10-01
Changes: Advisory, Derived calculations, Structure summary