Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 88020.58 
• Atom Count: 6217 
• Residue Count: 776 
• Unique protein chains: 1

1XQK

Effect of a Y265F Mutant on the Transamination Based Cycloserine Inactivation of Alanine Racemase

• DOI: 10.2210/pdb1XQK/pdb

• Classification: ISOMERASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2004-10-12 Released: 2005-01-18 
• Deposition Author(s): Fenn, T.D., Holyoak, T., Stamper, G.F., Ringe, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.240 
• R-Value Work: 0.191 

Literature

Effect of a Y265F Mutant on the Transamination-Based Cycloserine Inactivation of Alanine Racemase

Fenn, T.D., Holyoak, T., Stamper, G.F., Ringe, D.

(2005) Biochemistry 44: 5317-5327

• PubMed: 15807525 
• DOI: 10.1021/bi047842l
• Primary Citation of Related Structures:  
  1XQL


• PubMed Abstract: 
  

The requirement for d-alanine in the peptidoglycan layer of bacterial cell walls is fulfilled in part by alanine racemase (EC 5.1.1.1), a pyridoxal 5'-phosphate (PLP)-assisted enzyme. The enzyme utilizes two antiparallel bases focused at the C(alpha) position and oriented perpendicular to the PLP ring to facilitate the equilibration of alanine enantiomers. Understanding how this two-base system is utilized and controlled to yield reaction specificity is therefore a potential means for designing antibiotics. Cycloserine is a known alanine racemase suicide substrate, although its mechanism of inactivation is based on transaminase chemistry. Here we characterize the effects of a Y265F mutant (Tyr265 acts as the catalytic base in the l-isomer case) of Bacillus stearothermophilus alanine racemase on cycloserine inactivation. The Y265F mutant reduces racemization activity 1600-fold [Watanabe, A., Yoshimura, T., Mikami, B., and Esaki, N. (1999) J. Biochem. 126, 781-786] and only leads to formation of the isoxazole end product (the result of the transaminase pathway) in the case of d-cycloserine, in contrast to results obtained using the wild-type enzyme. l-Cycloserine, on the other hand, utilizes a number of alternative pathways in the absence of Y265, emphasizing the importance of Y265 in both the inactivation and racemization pathway. In combination with the kinetics of inactivation, these results suggest roles for each of the two catalytic bases in racemization and inactivation, as well as the importance of Y265 in "steering" the chemistry to favor one pathway over another.

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Organizational Affiliation: 

Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Alanine racemase	A, B	388	Geobacillus stearothermophilus	Mutation(s): 1  Gene Names: alr (dal) EC: 5.1.1.1
Find proteins for P10724 (Geobacillus stearothermophilus) Go to UniProtKB:  P10724

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PMH	A, B	(5-HYDROXY-4-{[(3-HYDROXYISOXAZOL-4-YL)AMINO]METHYL}-6-METHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE PMP-HYDROXYISOXAZOLE, PYRIDOXAMINE-5-PHOSPHATE-HYDROXYISOXAZOLE C11 H14 N3 O7 P PXWFNGNWQUPGPJ-UHFFFAOYSA-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: 1.95 Å
• R-Value Free: 0.240 
• R-Value Work: 0.191 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 84.965	α = 90.00
b = 85.627	β = 90.00
c = 97.963	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-10-12 
• Released Date: 2005-01-18 
• Deposition Author(s): Fenn, T.D., Holyoak, T., Stamper, G.F., Ringe, D.

Revision History 

• Version 1.0: 2005-01-18
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2018-01-31
  Type: Experimental preparation