2YII

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

Structural Biology Knowledgebase: 2YII SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.214
  • R-Value Work: 0.179

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2YII

Classification: LYASE

Total Structure Weight: 311118.42

Macromolecule Entities
Molecule Chains Length Organism Details
PHENYLALANINE AMMONIA-LYASE A, B, C, D 707 Taxus wallichiana EC#: 5.4.3.10 IUBMB
Mutation: A175X, S175X, G175X
Details: THIOESTER BOND BETWEEN THE MDO PROSTHETIC GROUP AND A MOLECULE OF BETA-MERCAPTOETHANOL, DISULFIDE BRIDGE BETWEEN RESIDUE C89 AND A BETA-MERCAPTOETHANOL MOLECULE, COVALENT BOND BETWEEN MDO 175 AND RESIDUE D178
Gene Name(s): pam

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GOL
Query on GOL

B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BME
Query on BME

A, B, C, D BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FMT
Query on FMT

A, B, C, D FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
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
  • R-Value Work: 0.179
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 99.45 α = 90.00
b = 146.00 β = 99.51
c = 99.68 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-05-13
  • Released Date: 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.

Revision History

  • 2013-01-30
    Type: Citation | Details: JRNL
  • 2012-01-25
    Type: Other | Details: Other, Citation