EzCatDB D00271

Time-dependent inhibition of Bacillus stearothermophilus alanine racemase by (1-aminoethyl)phosphonate isomers by isomerization to noncovalent slowly dissociating enzyme-(1-aminoethyl)phosphonate complexes.

[4]

PubMed ID

3118951

Journal

Biochemistry

Year

1987

Volume

Pages

5878-84

Authors

Mobashery S, Johnston M

Title

Inactivation of alanine racemase by beta-chloro-L-alanine released enzymatically from amino acid and peptide C10-esters of deacetylcephalothin.

[5]

PubMed ID

3680197

Journal

J Biol Chem

Year

1987

Volume

262

Pages

15323-6

Authors

Neidhart DJ, Distefano MD, Tanizawa K, Soda K, Walsh CT, Petsko GA

Title

X-ray crystallographic studies of the alanine-specific racemase from Bacillus stearothermophilus. Overproduction, crystallization, and preliminary characterization.

[6]

PubMed ID

3167024

Journal

Biochemistry

Year

1988

Volume

Pages

4966-70

Authors

Copie V, Faraci WS, Walsh CT, Griffin RG

Title

Inhibition of alanine racemase by alanine phosphonate: detection of an imine linkage to pyridoxal 5'-phosphate in the enzyme-inhibitor complex by solid-state 15N nuclear magnetic resonance.

[7]

PubMed ID

2690935

Journal

Biochemistry

Year

1989

Volume

Pages

8167-74

Authors

Galakatos NG, Walsh CT

Title

Mutations at the interdomain hinge region of the DadB alanine racemase: effects of length and conformational constraint of the linker sequence on catalytic efficiency.

[8]

Comments

X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS), AND REVISIONS.

Medline ID

97178818

PubMed ID

9063881

Journal

Biochemistry

Year

1997

Volume

Pages

1329-42

Authors

Shaw JP, Petsko GA, Ringe D

Title

Determination of the structure of alanine racemase from Bacillus stearothermophilus at 1.9-A resolution.

Related PDB

1sft

Related UniProtKB

P10724

[9]

Comments

X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).

Medline ID

98337786

PubMed ID

9671513

Journal

Biochemistry

Year

1998

Volume

Pages

10438-45

Authors

Stamper GF, Morollo AA, Ringe D, Stamper CG

Title

Reaction of alanine racemase with 1-aminoethylphosphonic acid forms a stable external aldimine.

Related PDB

1bd0

Related UniProtKB

P10724

[10]

Comments

X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).

Medline ID

99178834

PubMed ID

10079072

Journal

Biochemistry

Year

1999

Volume

Pages

3293-301

Authors

Morollo AA, Petsko GA, Ringe D

Title

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

Related PDB

2sfp

Related UniProtKB

P10724

[11]

Comments

MUTAGENESIS OF ARG-219.

Medline ID

99212226

PubMed ID

10194319

Journal

Biochemistry

Year

1999

Volume

Pages

4058-65

Authors

Sun S, Toney MD

Title

Evidence for a two-base mechanism involving tyrosine-265 from arginine-219 mutants of alanine racemase.

Related UniProtKB

P10724

[12]

PubMed ID

10348897

Journal

J Biochem (Tokyo)

Year

1999

Volume

125

Pages

987-90

Authors

Watanabe A, Kurokawa Y, Yoshimura T, Esaki N

Title

Role of tyrosine 265 of alanine racemase from Bacillus stearothermophilus.

[13]

Comments

ACTIVE SITES, AND MUTAGENESIS.

Medline ID

99434146

PubMed ID

10502689

Journal

J Biochem (Tokyo)

Year

1999

Volume

126

Pages

781-6

Authors

Watanabe A, Yoshimura T, Mikami B, Esaki N

Title

Tyrosine 265 of alanine racemase serves as a base abstracting alpha-hydrogen from L-alanine: the counterpart residue to lysine 39 specific to D-alanine.

Related UniProtKB

P10724

[14]

PubMed ID

9933615

Journal

J Biol Chem

Year

1999

Volume

274

Pages

4189-94

Authors

Watanabe A, Kurokawa Y, Yoshimura T, Kurihara T, Soda K, Esaki N, Watababe A

Title

Role of lysine 39 of alanine racemase from Bacillus stearothermophilus that binds pyridoxal 5'-phosphate. Chemical rescue studies of Lys39 --> Ala mutant.

[15]

PubMed ID

11064190

Journal

FEMS Microbiol Lett

Year

2000

Volume

192

Pages

169-73

Authors

Okubo Y, Yokoigawa K, Esaki N, Soda K, Misono H

Title

High catalytic activity of alanine racemase from psychrophilic Bacillus psychrosaccharolyticus at high temperatures in the presence of pyridoxal 5'-phosphate.

[16]

PubMed ID

10673430

Journal

Structure Fold Des

Year

2000

Volume

Pages

R1-6

Authors

Schneider G, Kack H, Lindqvist Y

Title

The manifold of vitamin B6 dependent enzymes.

[17]

PubMed ID

11456969

Journal

J Am Chem Soc

Year

2001

Volume

123

Pages

2830-4

Authors

Ondrechen MJ, Briggs JM, McCammon JA

Title

A model for enzyme-substrate interaction in alanine racemase.

[18]

Comments

X-ray crystallography

PubMed ID

11886871

Journal

J Biol Chem

Year

2002

Volume

277

Pages

19166-72

Authors

Watanabe A, Yoshimura T, Mikami B, Hayashi H, Kagamiyama H, Esaki N

Title

Reaction mechanism of alanine racemase from Bacillus stearothermophilus: x-ray crystallographic studies of the enzyme bound with N-(5'-phosphopyridoxyl)alanine.

Related PDB

1l6f,1l6g

[19]

Comments

X-ray crystallography

PubMed ID

12741835

Journal

Biochemistry

Year

2003

Volume

Pages

5775-83

Authors

Fenn TD, Stamper GF, Morollo AA, Ringe D

Title

A side reaction of alanine racemase: transamination of cycloserine.

Related PDB

1epv,1niu

[20]

PubMed ID

14674749

Journal

Biochemistry

Year

2003

Volume

Pages

14752-61

Authors

LeMagueres P, Im H, Dvorak A, Strych U, Benedik M, Krause KL

Title

Crystal structure at 1.45 A resolution of alanine racemase from a pathogenic bacterium, Pseudomonas aeruginosa, contains both internal and external aldimine forms.

Related PDB

1rcq

[21]

PubMed ID

12718553

Journal

Biochemistry

Year

2003

Volume

Pages

5099-107

Authors

Spies MA, Toney MD

Title

Multiple hydrogen kinetic isotope effects for enzymes catalyzing exchange with solvent: application to alanine racemase.

[22]

PubMed ID

12686135

Journal

Biochim Biophys Acta

Year

2003

Volume

1647

Pages

214-9

Authors

Paiardini A, Contestabile R, D'Aguanno S, Pascarella S, Bossa F

Title

Threonine aldolase and alanine racemase: novel examples of convergent evolution in the superfamily of vitamin B6-dependent enzymes.

[23]

PubMed ID

14517907

Journal

Biopolymers

Year

2003

Volume

Pages

186-200

Authors

Mustata GI, Soares TA, Briggs JM

Title

Molecular dynamics studies of alanine racemase: a structural model for drug design.

[24]

PubMed ID

12725937

Journal

FEMS Microbiol Lett

Year

2003

Volume

221

Pages

263-7

Authors

Yokoigawa K, Okubo Y, Soda K

Title

Subunit interaction of monomeric alanine racemases from four Shigella species in catalytic reaction.

[25]

PubMed ID

15302886

Journal

J Biol Chem

Year

2004

Volume

279

Pages

46153-61

Authors

Noda M, Matoba Y, Kumagai T, Sugiyama M

Title

Structural evidence that alanine racemase from a D-cycloserine-producing microorganism exhibits resistance to its own product.

Related PDB

1vfh,1vfs,1vft

[26]

PubMed ID

15115851

Journal

Protein Eng Des Sel

Year

2004

Volume

Pages

223-34

Authors

Mustata G, Briggs JM

Title

Cluster analysis of water molecules in alanine racemase and their putative structural role.

[27]

PubMed ID

15581583

Journal

Arch Biochem Biophys

Year

2005

Volume

433

Pages

279-87

Authors

Toney MD

Title

Reaction specificity in pyridoxal phosphate enzymes.

[28]

Comments

X-ray crystallography

PubMed ID

15807525

Journal

Biochemistry

Year

2005

Volume

Pages

5317-27

Authors

Fenn TD, Holyoak T, Stamper GF, Ringe D

Title

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

Related PDB

1xqk,1xql

[29]

PubMed ID

15683232

Journal

Biochemistry

Year

2005

Volume

Pages

1471-81

Authors

LeMagueres P, Im H, Ebalunode J, Strych U, Benedik MJ, Briggs JM, Kohn H, Krause KL

Title

The 1.9 A crystal structure of alanine racemase from Mycobacterium tuberculosis contains a conserved entryway into the active site.

Related PDB

1xfc

comments

This enzyme belongs to the type-III PLP-dependent enzyme superfamily.
This enzyme catalyzes racemization, which is composed of the following reactions (see [8], [11], [14], [18], [21] & [27]):
(A) Formation of an external aldimine (with amine group of L-Ala, PLP-L-Ala; I00049):
(B) Isomerization (change in the position of double-bond), forming a quinonoid intermediate (PLP-Ala; I00032).
(C) Isomerization (change in the position of double-bond), forming an external aldimine (PLP-D-Ala; I00029).
(D) Formation of internal aldimine, leading to the release of the product from PLP.
These reactions proceed in the following way:
(A) Formation of external aldimine (PLP-L-Ala; I00049) (see [8], [11], [14], [18], [21] & [27]);
(A1) The interaction of Arg219 through His166 with Tyr265' (from the adjacent chain) keeps the sidechain of Tyr265' unprotonated. (Arg219/His166 act as modulators.) In addition, Asp313' may modulate the activity of Lys39.
(A2) Tyr265' acts as a general base to deprotonate and activate the protonated amine group of substrate, L-Ala.
(A3) The deprotonated amine group of L-Ala makes a nucleophilic attack on the C4' atom of PLP, which forms an internal aldimine with Lys39, forming a transient geminal diamine intermediate.
(A4) Proton transfer from the amine group of L-Ala to epsilon-nitrogen atom of Lys39 must occur (probably through alpha-carboxyl group, or C4' atom of PLP).
(A5) The lone pair of the amine group of L-Ala makes the second nucleophilic attack on the C4' atom, leading to the formation of the external aldimine with L-Ala and the release of Lys39 (unprotonated).
(B) Isomerization (change in the position of double-bond), forming a quinonoid intermediate (PLP-Ala; I00032) (see [8], [11], [14], [18], [21] & [27]);
(B1) Protonated Tyr265' must be deprotonated, whereas unprotonated Lys39 must be protonated. Here, alpha-carboxyl group of L-Ala=PLP might acts as a base-acid, which deprotonates the sidechain of Tyr265' and protonates that of Lys39 (see [18]). Here, Arg219/His166 may modulate the activity of Tyr265'.
(B2) Tyr265' acts as a general base to deprotonate the alpha-proton of the L-amino acid substrate, forming a quinonoid intermediate (or carbanion intermediate).
(B3) Arg219 interacts with the N1 atom of PLP, modulating and decreasing (or destabilizing) the activity of the PLP cofactor as an electron sink, which destabilizes quinonoid intermediate and facilitates the next step of reprotonation of alpha-carbon (see [8]).
(C) Isomerization (change in the position of double-bond), forming an external aldimine (PLP-D-Ala; I00029): (Inverse reaction of (B))
(C1) Arg219 interacts with the N1 atom of PLP, modulating and decreasing (or destabilizing) the activity of the PLP cofactor as an electron sink, which destabilizes quinonoid intermediate and facilitates the this step. In addition, Asp313' may modulate the activity of Lys39.
(C2) Lys39 acts as a general acid to protonate the alpha-carbon of the L-amino acid substrate from the opposite side of Tyr265' (from re face of PLP). This reaction leads to the formation of the external aldimine of D-Ala with PLP.
(D) Formation of internal aldimine, leading to the elimination of the product from PLP: (Inverse reaction of (A));
(D1) Asp313' may modulate the activity of Lys39.
(D2) The deprotonated amine group of Lys39 makes a nucleophilic attack on the C4' carbon of the PLP of the external aldimine, forming a transient geminal diamine intermediate.
(D2) Proton transfer from the epsilon-nitrogen atom of Lys39 to the amine group of D-Ala must occur (probably through alpha-carboxyl group, or C4' atom of PLP).
(D3) The lone pair of the amine nitrogen of Lys39 can attack on the C4' atom to form a double-bond, and to release the amine of the product, D-Ala.
(D4) The interaction of Arg219 through His166 with Tyr265' (from the adjacent chain) assists Tyr265' in acting as a general acid to protonate the amine group of the product. (Arg219/His166 act as modulators.)

created

updated

2005-04-18

2015-07-23

Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )