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B6db families: 2.1.2.1

2.1.2.1
Activity 2.1.2.1
Description Glycine hydroxymethyltransferase.
Notes Very distinct family of PLP enzymes, diffused in the three kingdoms of life.
In eukarya, the mitochondrial isozymes are more similar to the cytosolic isozymes than they are to hydroxymethyltransferases from bacteria and archaea.
PDB 1BJ4;1DFO;1EJI;1EQB;1KKJ;1KKP;1KL2;
PLP Fold Type I
PLP-dependent Domain
Domain alignment
Domain hmm
Fold type I

Number of sequences
70
Sequences in seed alignment
ArchaeaGLYA_SULSO (Sulfolobus solfataricus); GLYA_ARCFU (Archaeoglobus fulgidus); GLYA_METTM (Methanobacterium thermoautotrophicum (strain Marburg / DSM 2133)); GLYA_PYRAB (Pyrococcus abyssi); GLYA_METTH (Methanobacterium thermoautotrophicum); GLYA_THEAC (Thermoplasma acidophilum); GLYA_METJA (Methanococcus jannaschii); GLYA_AERPE (Aeropyrum pernix);
BacteriaGLA1_MYCTU (Mycobacterium tuberculosis); GLYA_CHLTR (Chlamydia trachomatis); GLYA_AQUAE (Aquifex aeolicus); GLYA_CHLPN (Chlamydia pneumoniae); GLYA_BRAJA (Bradyrhizobium japonicum); GLYA_BUCAI (Buchnera aphidicola (subsp. Acyrthosiphon pisum)); GLYA_LACLA (Lactococcus lactis (subsp. lactis)); GLA2_MYCTU (Mycobacterium tuberculosis); GLYA_ACTAC (Actinobacillus actinomycetemcomitans); GLYA_MYCGE (Mycoplasma genitalium); GLYA_RICPR (Rickettsia prowazekii); GLYA_MYCPN (Mycoplasma pneumoniae); GLYA_SALTY (Salmonella typhimurium); GLYA_HELPY (Helicobacter pylori); GLYA_BORBU (Borrelia burgdorferi); GLYA_METEX (Methylobacterium extorquens); GLYA_CAMJE (Campylobacter jejuni); GLYA_HELPJ (Helicobacter pylori J99); GLYA_NEIMB (Neisseria meningitidis (serogroup B)); BAM33975 (Aphanothece halophytica); GLYA_BACSU (Bacillus subtilis); GLYA_ECOLI (Escherichia coli); AGO28160 (Shewanella algae); GLYA_TREPA (Treponema pallidum); GLYA_CORGL (Corynebacterium glutamicum); GLYA_SYNY3 (Synechocystis sp. (strain PCC 6803)); GLYA_NEIGO (Neisseria gonorrhoeae); AGD98699 (Pseudomonas plecoglossicida); S30382 (Bacillus stearothermophilus); GLYA_THEMA (Thermotoga maritima); GLYA_STRCO (Streptomyces coelicolor); GLYA_HAEIN (Haemophilus influenzae); GLYA_HYPME (Hyphomicrobium methylovorum); GLYA_PASMU (Pasteurella multocida); GLYA_ACIRA (Acinetobacter radioresistens);
FungiGLYC_SCHPO (Schizosaccharomyces pombe); GLYC_CANAL (Candida albicans); GLYM_YEAST (Saccharomyces cerevisiae); GLYC_NEUCR (Neurospora crassa); GLYC_ENCCU (Encephalitozoon cuniculi); GLYD_SCHPO (Schizosaccharomyces pombe); GLYC_YEAST (Saccharomyces cerevisiae); GLYM_CANAL (Candida albicans);
MetazoaGLYC_SHEEP (Ovis aries); GLYC_RABIT (Oryctolagus cuniculus); GLYC_HUMAN (Homo sapiens); GLYM_HUMAN (Homo sapiens); GLYM_RABIT (Oryctolagus cuniculus); GLYC_MOUSE (Mus musculus); GLYC_CAEEL (Caenorhabditis elegans);
Other_EukaryaAAO37746 (Leishmania donovani); AAF07198 (Plasmodium falciparum); XP_642026 (Dictyostelium discoideum); XP_001749016 (Monosiga brevicollis); EDL44165 (Plasmodium vivax); XP_001322593 (Trichomonas vaginalis);
ViridiplantaeGLYM_SOLTU (Solanum tuberosum); NP_195506 (Arabidopsis thaliana); AFK83587 (Glycine max); GLYM_PEA (Pisum sativum); GLYN_FLAPR (Flaveria pringlei); GLYM_FLAPR (Flaveria pringlei);

DISPLAY: Fasta format, alignment, hmm, hmm_local


Reference sequence GLYA_ECOLI
Domain interval 8-386
Catalytic site 229 K
 
References
 Jiang W, Xia B, Liu Z. (2013) A serine hydroxymethyltransferase from marine bacterium Shewanella algae: Isolation, purification, characterization and l-serine production. Microbiol Res 168 477-84.

 Wei Jiang, Bingzhao Xia, Junjie Huang and Ziduo Liu (2013) Characterization of a serine hydroxymethyltransferase for l-serine enzymatic production from Pseudomonas plecoglossicida World Journal of Microbiology and Biotechnology 29 2067-2076.

 Liu S, Kandoth PK, Warren SD, Yeckel G, Heinz R, Alden J, Yang C, Jamai A, El-Mellouki T, Juvale PS, Hill J, Baum TJ, Cianzio S, Whitham SA, Korkin D, Mitchum MG, Meksem K. (2012) A soybean cyst nematode resistance gene points to a new mechanism of plant resistance to pathogens. Nature 492 256-60.

 Waditee-Sirisattha R1, Sittipol D, Tanaka Y, Takabe T. (2012) Overexpression of serine hydroxymethyltransferase from halotolerant cyanobacterium in Escherichia coli results in increased accumulation of choline precursors and enhanced salinity tolerance. FEMS Microbiol Lett. 333 46-53.

 Shen P, Chao H, Jiang C, Long Z, Wang C, Wu B. (2010) Enhancing production of L-serine by increasing the glyA gene expression in Methylobacterium sp. MB200. Appl Biochem Biotechnol. 160 740-50.

 Sopitthummakhun K, Maenpuen S, Yuthavong Y, Leartsakulpanich U, Chaiyen P. (2009) Serine hydroxymethyltransferase from Plasmodium vivax is different in substrate specificity from its homologues. FEBS J. 276 4023-36.

 Vatsyayan, R.; Roy, U. (2007) Molecular cloning and biochemical characterization of Leishmania donovani serine hydroxymethyltransferase Protein Expr Purif. 52 433-40.

 Mukherjee M, Sievers SA, Brown MT, Johnson PJ. (2006) Identification and biochemical characterization of serine hydroxymethyl transferase in the hydrogenosome of Trichomonas vaginalis Eukaryot Cell 5 2072-8.

 Angelaccio S, Chiaraluce R, Consalvi V, Buchenau B, Giangiacomo L, Bossa F, Contestabile R. (2003) Catalytic and thermodynamic properties of tetrahydromethanopterin-dependent serine hydroxymethyltransferase from Methanococcus jannaschii J Biol Chem 278 41789-97.

 Chaturvedi S, Bhakuni V. (2003) Unusual structural, functional, and stability properties of serine hydroxymethyltransferase from Mycobacterium tuberculosis J Biol Chem 278 40793-805.

 Trivedi, V.; Gupta, A.; Jala, V. R.; Saravanan, P.; Rao, G. S.; Rao, N. A.; Savithri, H. S.; Subramanya, H. S. (2002) Crystal structure of binary and ternary complexes of serine hydroxymethyltransferase from Bacillus stearothermophilus: insights into the catalytic mechanism J Biol Chem 277 17161-9.

 Scarsdale, J. N.; Radaev, S.; Kazanina, G.; Schirch, V.; Wright, H. T. (2000) Crystal structure at 2.4 A resolution of E. coli serine hydroxymethyltransferase in complex with glycine substrate and 5-formyl tetrahydrofolate J Mol Biol 296 155-68.

 Szebenyi, D. M.; Liu, X.; Kriksunov, I. A.; Stover, P. J.; Thiel, D. J. (2000) Structure of a murine cytoplasmic serine hydroxymethyltransferase quinonoid ternary complex: evidence for asymmetric obligate dimers Biochemistry 39 13313-23.

 Scarsdale, J. N.; Kazanina, G.; Radaev, S.; Schirch, V.; Wright, H. T. (1999) Crystal structure of rabbit cytosolic serine hydroxymethyltransferase at 2.8 A resolution: mechanistic implications Biochemistry 38 8347-58.

 Delle Fratte, S.; White, R. H.; Maras, B.; Bossa, F.; Schirch, V. (1997) Purification and properties of serine hydroxymethyltransferase from Sulfolobus solfataricus J Bacteriol 179 7456-61.

 Jagath-Reddy, J.; Ganesan, K.; Savithri, H. S.; Datta, A.; Rao, N. A. (1995) cDNA cloning, overexpression in Escherichia coli, purification and characterization of sheep liver cytosolic serine hydroxymethyltransferase Eur J Biochem 230 533-7.

 Kruschwitz, H.; Ren, S.; Di Salvo, M.; Schirch, V. (1995) Expression, purification, and characterization of human cytosolic serine hydroxymethyltransferase Protein Expr Purif 6 411-6.

Articles on 2.1.2.1
last changed 2008/01/24 13:23

B6db families