1NIU | pdb_00001niu

ALANINE RACEMASE WITH BOUND INHIBITOR DERIVED FROM L-CYCLOSERINE

• PDB DOI: https://doi.org/10.2210/pdb1NIU/pdb

• Classification: ISOMERASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-12-26 Released: 2003-09-16 
• Deposition Author(s): Fenn, T.D., Stamper, G.F., Morollo, A.A., Ringe, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.231 (Depositor) 
• R-Value Work: 
  0.194 (Depositor), 0.200 (DCC) 

Literature

A side reaction of alanine racemase: transamination of cycloserine.

Fenn, T.D., Stamper, G.F., Morollo, A.A., Ringe, D.

(2003) Biochemistry 42: 5775-5783

• PubMed: 12741835 
• DOI: https://doi.org/10.1021/bi027022d
• Primary Citation Related Structures: 
  1EPV, 1NIU


• PubMed Abstract: 
  

  Alanine racemase (EC 5.1.1.1) catalyzes the interconversion of alanine enantiomers, and thus represents the first committed step involved in bacterial cell wall biosynthesis. Cycloserine acts as a suicide inhibitor of alanine racemase and as such, serves as an antimicrobial agent. The chemical means by which cycloserine inhibits alanine racemase is unknown. Through spectroscopic assays, we show here evidence of a pyridoxal derivative (arising from either isomer of cycloserine) saturated at the C4' carbon position. We additionally report the L- and D-cycloserine inactivated crystal structures of Bacillus stearothermophilus alanine racemase, which corroborates the spectroscopy via evidence of a 3-hydroxyisoxazole pyridoxamine derivative. Upon the basis of the kinetic and structural properties of both the L- and D-isomers of the inhibitor, we propose a mechanism of alanine racemase inactivation by cycloserine. This pathway involves an initial transamination step followed by tautomerization to form a stable aromatic adduct, a scheme similar to that seen in cycloserine inactivation of aminotransferases.

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Organizational Affiliation: 
• Department of Biochemistry and Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454, USA.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 88.06 kDa 
• Atom Count: 6,387 
• Modeled Residue Count: 762 
• Deposited Residue Count: 776 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alanine Racemase	A, B	388	Geobacillus stearothermophilus	Mutation(s): 1  Gene Names: ALR OR DAL EC: 5.1.1.1
UniProt
Find proteins for P10724 (Geobacillus stearothermophilus) Explore P10724  Go to UniProtKB:  P10724

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DCS	C [auth A], D [auth B]	D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE C11 H16 N3 O7 P NNRZSZJOQKAGTO-SECBINFHSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.231 (Depositor) 
• R-Value Work:  0.194 (Depositor), 0.200 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.157	α = 90
b = 90.243	β = 90
c = 85.261	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-09-16 
Deposition Author(s): Fenn, T.D., Stamper, G.F., Morollo, A.A., Ringe, D.

Revision History  

• Version 1.0: 2003-09-16
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary