PDBsum entry 1cl1

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Methionine biosynthesis PDB id
Protein chains
391 a.a. *
BCT ×2
Waters ×1875
* Residue conservation analysis
PDB id:
Name: Methionine biosynthesis
Title: Cystathionine beta-lyase (cbl) from escherichia coli
Structure: Cystathionine beta-lyase. Chain: a, b. Synonym: beta cystathionase. Engineered: yes. Other_details: plp bound as cofactor to lys 210
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: metc. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
1.83Å     R-factor:   0.151     R-free:   0.221
Authors: T.Clausen,R.Huber,A.Messerschmidt
Key ref:
T.Clausen et al. (1996). Crystal structure of the pyridoxal-5'-phosphate dependent cystathionine beta-lyase from Escherichia coli at 1.83 A. J Mol Biol, 262, 202-224. PubMed id: 8831789 DOI: 10.1006/jmbi.1996.0508
02-Sep-97     Release date:   09-Sep-98    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P06721  (METC_ECOLI) -  Cystathionine beta-lyase MetC
395 a.a.
391 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Cystathionine beta-lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-cystathionine + H2O = L-homocysteine + NH3 + pyruvate
+ H(2)O
= L-homocysteine
+ NH(3)
Bound ligand (Het Group name = BCT)
matches with 42.86% similarity
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     cellular amino acid metabolic process   3 terms 
  Biochemical function     catalytic activity     5 terms  


DOI no: 10.1006/jmbi.1996.0508 J Mol Biol 262:202-224 (1996)
PubMed id: 8831789  
Crystal structure of the pyridoxal-5'-phosphate dependent cystathionine beta-lyase from Escherichia coli at 1.83 A.
T.Clausen, R.Huber, B.Laber, H.D.Pohlenz, A.Messerschmidt.
Cystathionine beta-lyase (CBL) is a member of the gamma-family of PLP-dependent enzymes, that cleaves C beta-S bonds of a broad variety of substrates. The crystal structure of CBL from E. coli has been solved using MIR phases in combination with density modification. The structure has been refined to an R-factor of 15.2% at 1.83 A resolution using synchroton radiation diffraction data. The asymmetric unit of the crystal cell (space group C222(1)) contains two monomers related by 2-fold symmetry. A homotetramer with 222 symmetry is built up by crystallographic and non-crystallographic symmetry. Each monomer of CBL can be described in terms of three spatially and functionally different domains. The N-terminal domain (residues 1 to 60) consists of three alpha-helices and one beta-strand. It contributes to tetramer formation and is part of the active site of the adjacent subunit. The second domain (residues 61 to 256) harbors PLP and has an alpha/beta-structure with a seven-stranded beta-sheet as the central part. The remaining C-terminal domain (residues 257 to 395), connected by a long alpha-helix to the PLP-binding domain, consists of four helices packed on the solvent-accessible side of an antiparallel four-stranded beta-sheet. The fold of the C-terminal and the PLP-binding domain and the location of the active site are similar to aminotransferases. Most of the residues in the active site are strongly conserved among the enzymes of the transsulfuration pathway. Additionally, CBL is homologous to the mal gamma gene product indicating an evolutionary relationship between alpha and gamma-family of PLP-dependent enzymes. The structure of the beta, beta, beta-trifluoroalanine inactivated CBL has been refined at 2.3 A resolution to an R-factor of 16.2%. It suggests that Lys210, the PLP-binding residue, mediates the proton transfer between C alpha and S gamma.
  Selected figure(s)  
Figure 11.
Figure 11. Proposed reaction mechanism (A)--(F) for inactivation of CBL by F3Ala. Lys210 is the nucleophile at the active site that reacts via Michael addition with the so-called activated Michael acceptor (C). Subsequent elimination of HF from C b results in the inactivation end product (F) which was observed in the crystal structure of the CBL--F3Ala complex. Abbreviation used: Pyr-C = NH + , enzyme-bound PLP.
Figure 13.
Figure 13. Proposed reaction mechanism for CBL. The colors used are: apoprotein, red; cofactor, black; substrate, blue. (a) Residues involved in substrate binding. (b) Residues essential for catalysis. (c) Mechanism of C b -S bond cleavage (Pyr-C = NH + , PLP derivative).
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 262, 202-224) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21439022 E.Passera, B.Campanini, F.Rossi, V.Casazza, M.Rizzi, R.Pellicciari, and A.Mozzarelli (2011).
Human kynurenine aminotransferase II - reactivity with substrates and inhibitors.
  FEBS J, 278, 1882-1900.  
  20014435 P.H.Lodha, A.F.Jaworski, and S.M.Aitken (2010).
Characterization of site-directed mutants of residues R58, R59, D116, W340 and R372 in the active site of E. coli cystathionine beta-lyase.
  Protein Sci, 19, 383-391.  
19370061 A.Farsi, P.H.Lodha, J.E.Skanes, H.Los, N.Kalidindi, and S.M.Aitken (2009).
Interconversion of a pair of active-site residues in Escherichia coli cystathionine gamma-synthase, E. coli cystathionine beta-lyase, and Saccharomyces cerevisiae cystathionine gamma-lyase and development of tools for the investigation of their mechanisms and reaction specificity.
  Biochem Cell Biol, 87, 445-457.  
18219122 A.Nikulin, S.Revtovich, E.Morozova, N.Nevskaya, S.Nikonov, M.Garber, and T.Demidkina (2008).
High-resolution structure of methionine gamma-lyase from Citrobacter freundii.
  Acta Crystallogr D Biol Crystallogr, 64, 211-218.
PDB code: 2rfv
18603802 D.Kudou, S.Misaki, M.Yamashita, T.Tamura, N.Esaki, and K.Inagaki (2008).
The role of cysteine 116 in the active site of the antitumor enzyme L-methionine gamma-lyase from Pseudomonas putida.
  Biosci Biotechnol Biochem, 72, 1722-1730.  
18950711 F.Rossi, R.Schwarcz, and M.Rizzi (2008).
Curiosity to kill the KAT (kynurenine aminotransferase): structural insights into brain kynurenic acid synthesis.
  Curr Opin Struct Biol, 18, 748-755.  
18056996 F.Rossi, S.Garavaglia, V.Montalbano, M.A.Walsh, and M.Rizzi (2008).
Crystal Structure of Human Kynurenine Aminotransferase II, a Drug Target for the Treatment of Schizophrenia.
  J Biol Chem, 283, 3559-3566.
PDB code: 2vgz
18093968 O.M.Ganichkin, X.M.Xu, B.A.Carlson, H.Mix, D.L.Hatfield, V.N.Gladyshev, and M.C.Wahl (2008).
Structure and catalytic mechanism of eukaryotic selenocysteine synthase.
  J Biol Chem, 283, 5849-5865.
PDB codes: 3bc8 3bca 3bcb
  18678949 P.T.Ngo, J.K.Kim, H.Kim, J.Jung, Y.J.Ahn, J.G.Kim, B.M.Lee, H.W.Kang, and L.W.Kang (2008).
Expression, crystallization and preliminary X-ray crystallographic analysis of XometC, a cystathionine gamma-lyase-like protein from Xanthomonas oryzae pv. oryzae.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 750-753.  
17223627 V.Ali, and T.Nozaki (2007).
Current therapeutics, their problems, and sulfur-containing-amino-acid metabolism as a novel target against infections by "amitochondriate" protozoan parasites.
  Clin Microbiol Rev, 20, 164-187.  
16557306 D.Alexeev, R.L.Baxter, D.J.Campopiano, O.Kerbarh, L.Sawyer, N.Tomczyk, R.Watt, and S.P.Webster (2006).
Suicide inhibition of alpha-oxamine synthases: structures of the covalent adducts of 8-amino-7-oxononanoate synthase with trifluoroalanine.
  Org Biomol Chem, 4, 1209-1212.
PDB code: 2g6w
16820483 M.C.Martínez-Cuesta, C.Peláez, J.Eagles, M.J.Gasson, T.Requena, and S.B.Hanniffy (2006).
YtjE from Lactococcus lactis IL1403 Is a C-S lyase with alpha, gamma-elimination activity toward methionine.
  Appl Environ Microbiol, 72, 4878-4884.  
  16511092 D.V.Mamaeva, E.A.Morozova, A.D.Nikulin, S.V.Revtovich, S.V.Nikonov, M.B.Garber, and T.V.Demidkina (2005).
Structure of Citrobacter freundii L-methionine gamma-lyase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 546-549.
PDB code: 1y4i
16307301 M.Wirtz, and M.Droux (2005).
Synthesis of the sulfur amino acids: cysteine and methionine.
  Photosynth Res, 86, 345-362.  
16000837 N.Awano, M.Wada, H.Mori, S.Nakamori, and H.Takagi (2005).
Identification and functional analysis of Escherichia coli cysteine desulfhydrases.
  Appl Environ Microbiol, 71, 4149-4152.  
15498941 A.Paiardini, F.Bossa, and S.Pascarella (2004).
Evolutionarily conserved regions and hydrophobic contacts at the superfamily level: The case of the fold-type I, pyridoxal-5'-phosphate-dependent enzymes.
  Protein Sci, 13, 2992-3005.  
15044494 C.R.Sweet, A.A.Ribeiro, and C.R.Raetz (2004).
Oxidation and transamination of the 3"-position of UDP-N-acetylglucosamine by enzymes from Acidithiobacillus ferrooxidans. Role in the formation of lipid a molecules with four amide-linked acyl chains.
  J Biol Chem, 279, 25400-25410.  
15155634 L.J.Ejim, V.M.D'Costa, N.H.Elowe, J.C.Loredo-Osti, D.Malo, and G.D.Wright (2004).
Cystathionine beta-lyase is important for virulence of Salmonella enterica serovar Typhimurium.
  Infect Immun, 72, 3310-3314.  
12715888 A.Messerschmidt, M.Worbs, C.Steegborn, M.C.Wahl, R.Huber, B.Laber, and T.Clausen (2003).
Determinants of enzymatic specificity in the Cys-Met-metabolism PLP-dependent enzymes family: crystal structure of cystathionine gamma-lyase from yeast and intrafamiliar structure comparison.
  Biol Chem, 384, 373-386.
PDB code: 1n8p
12882962 T.Ose, A.Fujino, M.Yao, N.Watanabe, M.Honma, and I.Tanaka (2003).
Reaction intermediate structures of 1-aminocyclopropane-1-carboxylate deaminase: insight into PLP-dependent cyclopropane ring-opening reaction.
  J Biol Chem, 278, 41069-41076.
PDB codes: 1j0c 1j0d 1j0e
12191993 J.Zhang, and G.C.Ferreira (2002).
Transient state kinetic investigation of 5-aminolevulinate synthase reaction mechanism.
  J Biol Chem, 277, 44660-44669.  
11756443 M.Garrido-Franco, S.Ehlert, A.Messerschmidt, S.Marinkovic', R.Huber, B.Laber, G.P.Bourenkov, and T.Clausen (2002).
Structure and function of threonine synthase from yeast.
  J Biol Chem, 277, 12396-12405.
PDB code: 1kl7
11933244 K.Soda, T.Yoshimura, and N.Esaki (2001).
Stereospecificity for the hydrogen transfer of pyridoxal enzyme reactions.
  Chem Rec, 1, 373-384.  
11483578 L.A.Nahum, and M.Riley (2001).
Divergence of function in sequence-related groups of Escherichia coli proteins.
  Genome Res, 11, 1375-1381.  
11737206 R.Contestabile, A.Paiardini, S.Pascarella, M.L.di Salvo, S.D'Aguanno, and F.Bossa (2001).
l-Threonine aldolase, serine hydroxymethyltransferase and fungal alanine racemase. A subgroup of strictly related enzymes specialized for different functions.
  Eur J Biochem, 268, 6508-6525.  
10673430 G.Schneider, H.Käck, and Y.Lindqvist (2000).
The manifold of vitamin B6 dependent enzymes.
  Structure, 8, R1-R6.  
10880431 H.I.Krupka, R.Huber, S.C.Holt, and T.Clausen (2000).
Crystal structure of cystalysin from Treponema denticola: a pyridoxal 5'-phosphate-dependent protein acting as a haemolytic enzyme.
  EMBO J, 19, 3168-3178.
PDB codes: 1c7n 1c7o
11193400 H.Inoue, K.Inagaki, N.Adachi, T.Tamura, N.Esaki, K.Soda, and H.Tanaka (2000).
Role of tyrosine 114 of L-methionine gamma-lyase from Pseudomonas putida.
  Biosci Biotechnol Biochem, 64, 2336-2343.  
10618201 M.Fernández, W.van Doesburg, G.A.Rutten, J.D.Marugg, A.C.Alting, R.van Kranenburg, and O.P.Kuipers (2000).
Molecular and functional analyses of the metC gene of Lactococcus lactis, encoding cystathionine beta-lyase.
  Appl Environ Microbiol, 66, 42-48.  
  10620674 N.Dobric, G.K.Limsowtin, A.J.Hillier, N.P.Dudman, and B.E.Davidson (2000).
Identification and characterization of a cystathionine beta/gamma-lyase from Lactococcus lactis ssp. cremoris MG1363.
  FEMS Microbiol Lett, 182, 249-254.  
10698925 T.Clausen, A.Schlegel, R.Peist, E.Schneider, C.Steegborn, Y.S.Chang, A.Haase, G.P.Bourenkov, H.D.Bartunik, and W.Boos (2000).
X-ray structure of MalY from Escherichia coli: a pyridoxal 5'-phosphate-dependent enzyme acting as a modulator in mal gene expression.
  EMBO J, 19, 831-842.
PDB code: 1d2f
10684605 T.Fujii, M.Maeda, H.Mihara, T.Kurihara, N.Esaki, and Y.Hata (2000).
Structure of a NifS homologue: X-ray structure analysis of CsdB, an Escherichia coli counterpart of mammalian selenocysteine lyase.
  Biochemistry, 39, 1263-1273.
PDB code: 1c0n
11092940 V.Sridhar, M.Xu, Q.Han, X.Sun, Y.Tan, R.M.Hoffman, and G.S.Prasad (2000).
Crystallization and preliminary crystallographic characterization of recombinant L-methionine-alpha-deamino-gamma-mercaptomethane lyase (methioninase).
  Acta Crystallogr D Biol Crystallogr, 56, 1665-1667.  
10378276 A.D.Kern, M.A.Oliveira, P.Coffino, and M.L.Hackert (1999).
Structure of mammalian ornithine decarboxylase at 1.6 A resolution: stereochemical implications of PLP-dependent amino acid decarboxylases.
  Structure, 7, 567-581.
PDB code: 7odc
10584065 A.Poupon, F.Jebai, G.Labesse, F.Gros, J.Thibault, J.P.Mornon, and M.Krieger (1999).
Structure modelling and site-directed mutagenesis of the rat aromatic L-amino acid pyridoxal 5'-phosphate-dependent decarboxylase: a functional study.
  Proteins, 37, 191-203.  
10212249 C.Steegborn, T.Clausen, P.Sondermann, U.Jacob, M.Worbs, S.Marinkovic, R.Huber, and M.C.Wahl (1999).
Kinetics and inhibition of recombinant human cystathionine gamma-lyase. Toward the rational control of transsulfuration.
  J Biol Chem, 274, 12675-12684.  
10212273 H.Ogawa, F.Takusagawa, K.Wakaki, H.Kishi, M.R.Eskandarian, M.Kobayashi, T.Date, N.H.Huh, and H.C.Pitot (1999).
Rat liver serine dehydratase. Bacterial expression and two folding domains as revealed by limited proteolysis.
  J Biol Chem, 274, 12855-12860.  
10509022 J.Brzywczy, and A.Paszewski (1999).
Cloning and characterization of the Kluyveromyces lactis homocysteine synthase gene.
  Yeast, 15, 1403-1409.  
10382666 P.K.Mehta, P.Argos, A.D.Barbour, and P.Christen (1999).
Recognizing very distant sequence relationships among proteins by family profile analysis.
  Proteins, 35, 387-400.  
10595588 T.Clausen, M.C.Wahl, A.Messerschmidt, R.Huber, J.C.Fuhrmann, B.Laber, W.Streber, and C.Steegborn (1999).
Cloning, purification and characterisation of cystathionine gamma-synthase from Nicotiana tabacum.
  Biol Chem, 380, 1237-1242.  
9488680 A.E.McKie, T.Edlind, J.Walker, J.C.Mottram, and G.H.Coombs (1998).
The primitive protozoon Trichomonas vaginalis contains two methionine gamma-lyase genes that encode members of the gamma-family of pyridoxal 5'-phosphate-dependent enzymes.
  J Biol Chem, 273, 5549-5556.  
9914259 J.N.Jansonius (1998).
Structure, evolution and action of vitamin B6-dependent enzymes.
  Curr Opin Struct Biol, 8, 759-769.  
9772188 K.H.Jhee, P.McPhie, H.S.Ro, and E.W.Miles (1998).
Tryptophan synthase mutations that alter cofactor chemistry lead to mechanism-based inactivation.
  Biochemistry, 37, 14591-14604.  
  9605314 K.Qu, D.L.Martin, and C.E.Lawrence (1998).
Motifs and structural fold of the cofactor binding site of human glutamate decarboxylase.
  Protein Sci, 7, 1092-1105.  
9753690 S.B.Renwick, K.Snell, and U.Baumann (1998).
The crystal structure of human cytosolic serine hydroxymethyltransferase: a target for cancer chemotherapy.
  Structure, 6, 1105-1116.
PDB code: 1bj4
  10082378 S.Ishii, H.Hayashi, A.Okamoto, and H.Kagamiyama (1998).
Aromatic L-amino acid decarboxylase: conformational change in the flexible region around Arg334 is required during the transaldimination process.
  Protein Sci, 7, 1802-1810.  
9843488 T.Clausen, R.Huber, L.Prade, M.C.Wahl, and A.Messerschmidt (1998).
Crystal structure of Escherichia coli cystathionine gamma-synthase at 1.5 A resolution.
  EMBO J, 17, 6827-6838.
PDB code: 1cs1
  9529892 W.Boos, and H.Shuman (1998).
Maltose/maltodextrin system of Escherichia coli: transport, metabolism, and regulation.
  Microbiol Mol Biol Rev, 62, 204-229.  
  9165087 L.Prade, P.Hof, and B.Bieseler (1997).
Dimer interface of glutathione S-transferase from Arabidopsis thaliana: influence of the G-site architecture on the dimer interface and implications for classification.
  Biol Chem, 378, 317-320.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.