Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 88.03 kDa 
• Atom Count: 6,279 
• Modelled Residue Count: 758 
• Deposited Residue Count: 776 
• Unique protein chains: 1

 2SFP

ALANINE RACEMASE WITH BOUND PROPIONATE INHIBITOR

• PDB DOI:  https://doi.org/10.2210/pdb2SFP/pdb

• Classification: RACEMASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli str. K-12 substr. W3110
• Mutation(s): No 


• Deposited: 1999-02-16 Released: 1999-02-24 
• Deposition Author(s): Morollo, A.A., Petsko, G.A., Ringe, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.259 
• R-Value Work: 0.205 

Literature

Structure of a Michaelis complex analogue: propionate binds in the substrate carboxylate site of alanine racemase.

Morollo, A.A., Petsko, G.A., Ringe, D.

(1999) Biochemistry 38: 3293-3301

• PubMed: 10079072 
• DOI: https://doi.org/10.1021/bi9822729
• Primary Citation of Related Structures:  
  2SFP


• PubMed Abstract: 
  

The structure of alanine racemase from Bacillus stearothermophilus with the inhibitor propionate bound in the active site was determined by X-ray crystallography to a resolution of 1.9 A. The enzyme is a homodimer in solution and crystallizes with a dimer in the asymmetric unit. Both active sites contain a pyridoxal 5'-phosphate (PLP) molecule in aldimine linkage to Lys39 as a protonated Schiff base, and the pH-independence of UV-visible absorption spectra suggests that the protonated PLP-Lys39 Schiff base is the reactive form of the enzyme. The carboxylate group of propionate bound in the active site makes numerous interactions with active-site residues, defining the substrate binding site of the enzyme. The propionate-bound structure therefore approximates features of the Michaelis complex formed between alanine racemase and its amino acid substrate. The structure also provides evidence for the existence of a carbamate formed on the side-chain amino group of Lys129, stabilized by interactions with one of the residues interacting with the carboxylate group of propionate, Arg136. We propose that this novel interaction influences both substrate binding and catalysis by precisely positioning Arg136 and modulating its charge.

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Related Citations: 

• Reaction of alanine racemase with 1-aminoethylphosphonic acid forms a stable external aldimine.
  Stamper, G.F., Morollo, A.A., Ringe, D., Stamper, C.G.
  (1998) Biochemistry 37: 10438

• Determination of the structure of alanine racemase from Bacillus stearothermophilus at 1.9-A resolution.
  Shaw, J.P., Petsko, G.A., Ringe, D.
  (1997) Biochemistry 36: 1329

• X-ray crystallographic studies of the alanine-specific racemase from Bacillus stearothermophilus. Overproduction, crystallization, and preliminary characterization.
  Neidhart, D.J., Distefano, M.D., Tanizawa, K., Soda, K., Walsh, C.T., Petsko, G.A.
  (1987) J Biol Chem 262: 15323

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Organizational Affiliation: 

Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02254, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (ALANINE RACEMASE)	A, B	388	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: alr, dal EC: 5.1.1.1
UniProt
Find proteins for P10724 (Geobacillus stearothermophilus) Explore P10724  Go to UniProtKB:  P10724

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth A], F [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
PPI	D [auth A], E [auth B]	PROPANOIC ACID C3 H6 O2 XBDQKXXYIPTUBI-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A, B	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Binding Affinity Annotations
ID	Source	Binding Affinity
PPI	PDBBind:  2SFP	Ki: 2.00e+7 (nM) from 1 assay(s)
	Binding MOAD:  2SFP	Ki: 2.00e+7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.259 
• R-Value Work: 0.205 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.7	α = 90
b = 90	β = 90
c = 85.2	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-02-24 
Deposition Author(s): Morollo, A.A., Petsko, G.A., Ringe, D.

Revision History  

• Version 1.0: 1999-02-24
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2019-11-06
  Changes: Data collection, Database references, Derived calculations