2RJR

Substrate mimic bound to SgTAM

• PDB DOI: https://doi.org/10.2210/pdb2RJR/pdb

• Classification: ISOMERASE
• Organism(s): Streptomyces globisporus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-10-15 Released: 2008-01-15 
• Deposition Author(s): Montavon, T.J., Christianson, C.V., Bruner, S.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.212 
• R-Value Work: 0.173 
• R-Value Observed: 0.176 

Literature

Design and characterization of mechanism-based inhibitors for the tyrosine aminomutase SgTAM.

Montavon, T.J., Christianson, C.V., Festin, G.M., Shen, B., Bruner, S.D.

(2008) Bioorg Med Chem Lett 18: 3099-3102

• PubMed: 18078753 
• DOI: https://doi.org/10.1016/j.bmcl.2007.11.046
• Primary Citation of Related Structures:  
  2QVE, 2RJR, 2RJS


• PubMed Abstract: 
  

  The synthesis and evaluation of two classes of inhibitors for SgTAM, a 4-methylideneimidazole-5-one (MIO) containing tyrosine aminomutase, are described. A mechanism-based strategy was used to design analogs that mimic the substrate or product of the reaction and form covalent interactions with the enzyme through the MIO prosthetic group. The analogs were characterized by measuring inhibition constants and X-ray crystallographic structural analysis of the co-complexes bound to the aminomutase, SgTAM.

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Organizational Affiliation: 

Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 116.54 kDa 
• Atom Count: 8,501 
• Modelled Residue Count: 1,052 
• Deposited Residue Count: 1,074 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine aminomutase	A, B	537	Streptomyces globisporus	Mutation(s): 0  Gene Names: SgcC4 EC: 5.4.3.6
UniProt
Find proteins for Q8GMG0 (Streptomyces globisporus) Explore Q8GMG0  Go to UniProtKB:  Q8GMG0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
295	C [auth A]	(2S,3S)-3-(4-fluorophenyl)-2,3-dihydroxypropanoic acid C9 H9 F O4 DWYLYIVEFVSGCP-YUMQZZPRSA-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

Binding Affinity Annotations
ID	Source	Binding Affinity
295	PDBBind:  2RJR	IC50: 1.16e+7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.212 
• R-Value Work: 0.173 
• R-Value Observed: 0.176 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.245	α = 90
b = 145.648	β = 90
c = 75.114	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-15 
Deposition Author(s): Montavon, T.J., Christianson, C.V., Bruner, S.D.

Revision History  

• Version 1.0: 2008-01-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-11-16
  Changes: Atomic model
• Version 1.3: 2017-10-25
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations