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B6db families: 5.1.1.1.a

5.1.1.1 a
Activity 5.1.1.1
Description Alanine racemase (family a)
Notes A family that includes mostly bacterial enzymes; exceptions are represented by two sequences from S. pombe and one from a prawn.

The Salmonella enzyme (ALR1) has a monomeric structure.

The enzymes from enterococci (VanT-type) have an additional, N-terminal domain that is membrane-bound and assigned to the acyl-transferase family 3 (PF01757) by Pfam. This additional domain should be removed from the sequences in quesion.

Additional_domain AAD22403.1 300-700

PDB 1SFT;1RCQ;4FS9;4LUS;6A2F;
PLP Fold Type III
PLP-dependent Domain
Domain alignment
Domain hmm
Fold type III

Number of sequences
49
Sequences in seed alignment
BacteriaAF430807_9 (Enterococcus faecalis); ALR1_PSEAE (Pseudomonas aeruginosa); AGL73884 (Aeromonas hydrophila); ALR_HELPY (Helicobacter pylori); ALR2_SALTY (Salmonella typhimurium); ALR_STRCO (Streptomyces coelicolor); ALR_LISMO (Listeria monocytogenes); BAC56127 (Bifidobacterium bifidum); NP_230026 (Vibrio cholerae O1 biovar El Tor str. N16961); Q8YU96 (Nostoc sp. PCC 7120); ALR2_KLEAE (Klebsiella aerogenes); APD32491 (Streptococcus iniae); ALR_TREPA (Treponema pallidum); ZP_00061927 (Clostridium thermocellum ); ALR_MYCAV (Mycobacterium avium); ALR_LACPL (Lactobacillus plantarum); WP_021418922 (Enterococcus faecalis); ALR_HAEIN (Haemophilus influenzae); BAH23434 (Pseudomonas taetrolens); ALR_MYCSM (Mycobacterium smegmatis); ALR_BACST (Bacillus stearothermophilus); ALR_AQUAE (Aquifex aeolicus); VATG_ENTFA (Enterococcus faecalis); AAK53980 (Enterococcus casseliflavus); ALR_BACPS (Bacillus psychrosaccharolyticus); ABG82585 (Clostridium perfringens ATCC 13124); AAD22403 (Enterococcus gallinarum); ALR_STRPN (Streptococcus pneumoniae); ADC50009 (Bacillus pseudofirmus OF4); AAM25327 (Thermoanaerobacter tengcongensis MB4); ALR_MYCTU (Mycobacterium tuberculosis); ALR_SYNY3 (Synechocystis sp. (strain PCC 6803)); WP_003437830 (Clostridioides difficile 630); WP_027312670 (Balneatrix alpica); ALR2_BACSU (Bacillus subtilis); ALR2_PSEAE (Pseudomonas aeruginosa); AAF23014 (Aquifex pyrophilus); ALR2_ECOLI (Escherichia coli); ALR_LACRE (Lactobacillus reuteri); EDT66487 (Bacillus anthracis); ALR1_CLOAB (Clostridium acetobutylicum); AAN70834 (Pseudomonas putida KT2440); ALR1_ECOLI (Escherichia coli); BAE19803 (Pseudomonas fluorescens);
FungiALR1_SCHPO (Schizosaccharomyces pombe); ALR2_SCHPO (Schizosaccharomyces pombe); KGQ06030 (Beauveria bassiana D1-5);
MetazoaBAH22617 (Marsupenaeus japonicus); XP_018014831 (Hyalella azteca);

DISPLAY: Fasta format, alignment, hmm, hmm_local


Reference sequence ALR_BACST
Domain interval 7-230
Catalytic site 39 K
 
References
 Israr M, Lv G, Xu S, Li Y, Ding S, Zhao B, Ju J (2019) Biochemical characterization and mutational analysis of alanine racemase from Clostridium perfringens J Biosci Bioeng 128 149-155.

 Muhammad M, Li Y, Gong S, Shi Y, Ju J, Zhao B, Liu D (2019) Purification, Characterization and Inhibition of Alanine Racemase from a Pathogenic Strain of Streptococcus iniae Pol J Microbiol 68 331-341.

 Dong H, Hu T, He G, Lu D, Qi J, Dou Y, Long W, He X, Ju J, Su D (2018) Structural features and kinetic characterization of alanine racemase from Bacillus pseudofirmus OF4 Biochem Biophys Res Commun 497 139-145.

 Tassoni R, van der Aart LT, Ubbink M, van Wezel GP, Pannu NS (2017) Structural and functional characterization of the alanine racemase from Streptomyces coelicolor A3(2) Biochem Biophys Res Commun 483 122-128.

 Liu D., Liu X., Zhang L., Jiao H., Ju J., Zhao B. (2015) Biochemical characteristics of an alanine racemase from Aeromonas hydrophila HBNUAh01 Microbiology 84 202–209.

 Meziane-Cherif D, Stogios PJ, Evdokimova E, Egorova O, Savchenko A, Courvalin P (2015) Structural and Functional Adaptation of Vancomycin Resistance VanT Serine Racemases mBio 6 e00806.

 Asojo OA, Nelson SK, Mootien S, Lee Y, Rezende WC, Hyman DA, Matsumoto MM, Reiling S, Kelleher A, Ledizet M, Koski RA, Anthony KG. (2014) Structural and biochemical analyses of alanine racemase from the multidrug-resistant Clostridium difficile strain 630 Acta Crystallogr D Biol Crystallogr. 70 1922-33.

 Espaillat A, Carrasco-López C, Bernardo-García N, Pietrosemoli N, Otero LH, Álvarez L, de Pedro MA, Pazos F, Davis BM, Waldor MK, Hermoso JA, Cava F. (2014) Structural basis for the broad specificity of a new family of amino-acid racemases. Acta Crystallographica. Section D, Biological Crystallography. 70 79-90.

 Radkov AD, Moe LA (2013) Amino acid racemization in Pseudomonas putida KT2440 J Bacteriol 195 5016-24.

 Xue Z, Hu Y, Xu S, Ohnishi K, Ma Y, Ju J, Zhao B. (2013) Characterization and preliminary mutation analysis of a thermostable alanine racemase from Thermoanaerobacter tengcongensis MB4 Extremophiles 17 611-21.

 Liu JL, Liu XQ, Shi YW. (2012) Expression, purification, and characterization of alanine racemase from Pseudomonas putida YZ-26. World J Microbiol Biotechnol. 28 267-74.

 Couñago RM, Davlieva M, Strych U, Hill RE, Krause KL. (2009) Biochemical and structural characterization of alanine racemase from Bacillus anthracis (Ames). BMC Struct Biol. 8 e71963.

 Yoshikawa N, Okada S, Abe H. (2009) Molecular Characterization of Alanine Racemase in the Kuruma Prawn Marsupenaeus japonicus J Biochem 145 249-58.

 Ju, J.; Yokoigawa, K.; Misono, H.; Ohnishi, K. (2005) Cloning of alanine racemase genes from Pseudomonas fluorescens strains and oligomerization states of gene products expressed in Escherichia coli J Biosci Bioeng 100 409-417.

 Strych, U.; Penland, R. L.; Jimenez, M.; Krause, K. L.; Benedik, M. J. (2001) Characterization of the alanine racemases from two mycobacteria FEMS Microbiol Lett 196 93-8.

 Uo, T.; Yoshimura, T.; Tanaka, N.; Takegawa, K.; Esaki, N. (2001) Functional characterization of alanine racemase from Schizosaccharomyces pombe: a eucaryotic counterpart to bacterial alanine racemase J Bacteriol 183 2226-33.

 Arias, C. A.; Weisner, J.; Blackburn, J. M.; Reynolds, P. E. (2000) Serine and alanine racemase activities of VanT: a protein necessary for vancomycin resistance in Enterococcus gallinarum BM4174 Microbiology 146 1727-34.

 Kim, S.S; Yu, Y.G. (2000) Molecular cloning of an eExtremely thermostable alanine racemase from Aquifex pyrophilus and enzymatic characterization of the expressed protein J Biochem Mol Biol 33 82-8.

 Strych, U.; Huang, H. C.; Krause, K. L.; Benedik, M. J. (2000) Characterization of the alanine racemases from Pseudomonas aeruginosa PAO1 Curr Microbiol 41 290-4.

 Okubo, Y.; Yokoigawa, K.; Esaki, N.; Soda, K.; Kawai, H. (1999) Characterization of psychrophilic alanine racemase from Bacillus psychrosaccharolyticus Biochem Biophys Res Commun 256 333-40.

 Shaw, J.P.; Petsko, G.A.; Ringe, D. (1997) Determination of the structure of alanine racemase from Bacillus stearothermophilus at 1.9-A resolution. Biochemistry 36 1329-1342.

 Neidhart, D. J.; Distefano, M. D.; Tanizawa, K.; Soda, K.; Walsh, C. T.; Petsko, G. A. (1987) X-ray crystallographic studies of the alanine-specific racemase from Bacillus stearothermophilus. Overproduction, crystallization, and preliminary characterization J Biol Chem 262 15323-6.

 Inagaki, K.; Tanizawa, K.; Badet, B.; Walsh, C. T.; Tanaka, H.; Soda, K. (1986) Thermostable alanine racemase from Bacillus stearothermophilus: molecular cloning of the gene, enzyme purification, and characterization Biochemistry 25 3268-74.

Articles on 5.1.1.1.a
last changed 2019/12/30 12:43

B6db families