Y274F alanine racemase from E. coli inhibited by l-ala-p

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

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This is version 1.2 of the entry. See complete history


Mechanistic and Evolutionary Insights from the Reciprocal Promiscuity of Two Pyridoxal Phosphate-dependent Enzymes.

Soo, V.W.Yosaatmadja, Y.Squire, C.J.Patrick, W.M.

(2016) J Biol Chem 291: 19873-19887

  • DOI: https://doi.org/10.1074/jbc.M116.739557
  • Primary Citation of Related Structures:  
    4ITG, 4ITX, 4WR3, 4XBJ

  • PubMed Abstract: 

    Enzymes that utilize the cofactor pyridoxal 5'-phosphate play essential roles in amino acid metabolism in all organisms. The cofactor is used by proteins that adopt at least five different folds, which raises questions about the evolutionary processes that might explain the observed distribution of functions among folds. In this study, we show that a representative of fold type III, the Escherichia coli alanine racemase (ALR), is a promiscuous cystathionine β-lyase (CBL). Furthermore, E. coli CBL (fold type I) is a promiscuous alanine racemase. A single round of error-prone PCR and selection yielded variant ALR(Y274F), which catalyzes cystathionine β-elimination with a near-native Michaelis constant (Km = 3.3 mm) but a poor turnover number (kcat ≈10 h(-1)). In contrast, directed evolution also yielded CBL(P113S), which catalyzes l-alanine racemization with a poor Km (58 mm) but a high kcat (22 s(-1)). The structures of both variants were solved in the presence and absence of the l-alanine analogue, (R)-1-aminoethylphosphonic acid. As expected, the ALR active site was enlarged by the Y274F substitution, allowing better access for cystathionine. More surprisingly, the favorable kinetic parameters of CBL(P113S) appear to result from optimizing the pKa of Tyr-111, which acts as the catalytic acid during l-alanine racemization. Our data emphasize the short mutational routes between the functions of pyridoxal 5'-phosphate-dependent enzymes, regardless of whether or not they share the same fold. Thus, they confound the prevailing model of enzyme evolution, which predicts that overlapping patterns of promiscuity result from sharing a common multifunctional ancestor.

  • Organizational Affiliation

    From the Institute of Natural and Mathematical Sciences, Massey University, Auckland 0632.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alanine racemase, biosynthetic
A, B, C, D
359Escherichia coliMutation(s): 1 
Gene Names: alr
Find proteins for P0A6B4 (Escherichia coli (strain K12))
Explore P0A6B4 
Go to UniProtKB:  P0A6B4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6B4
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on IN5

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
K [auth C]
C10 H18 N2 O8 P2
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
J [auth B]
L [auth C]
F [auth A],
G [auth A],
H [auth A],
J [auth B],
L [auth C],
M [auth C],
N [auth C],
O [auth D]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.25 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.978α = 90
b = 147.978β = 90
c = 163.578γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-23
    Type: Initial release
  • Version 1.1: 2021-09-22
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-09-27
    Changes: Data collection, Refinement description