PDBsum entry 1cl2

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Methionine biosynthesis PDB id
Protein chains
391 a.a. *
PPG ×2
Waters ×1290
* Residue conservation analysis
PDB id:
Name: Methionine biosynthesis
Title: Cystathionine beta-lyase (cbl) from escherichia coli in comp aminoethoxyvinylglycine
Structure: Cystathionine beta-lyase. Chain: a, b. Synonym: beta cystathionase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: metc. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
2.20Å     R-factor:   0.164    
Authors: T.Clausen,R.Huber,A.Messerschmidt
Key ref:
T.Clausen et al. (1997). Slow-binding inhibition of Escherichia coli cystathionine beta-lyase by L-aminoethoxyvinylglycine: a kinetic and X-ray study. Biochemistry, 36, 12633-12643. PubMed id: 9376370 DOI: 10.1021/bi970630m
04-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

 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)
+ pyruvate
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Bound ligand (Het Group name = PPG) matches with 55.56% similarity
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: 10.1021/bi970630m Biochemistry 36:12633-12643 (1997)
PubMed id: 9376370  
Slow-binding inhibition of Escherichia coli cystathionine beta-lyase by L-aminoethoxyvinylglycine: a kinetic and X-ray study.
T.Clausen, R.Huber, A.Messerschmidt, H.D.Pohlenz, B.Laber.
The pyridoxal 5'-phosphate (PLP)-dependent cystathionine beta-lyase (CBL) was previously found to be inhibited by the natural toxins rhizobitoxine and l-aminoethoxyvinylglycine (AVG). The present study characterizes the interaction of Escherichia coli CBL with AVG and methoxyvinylglycine (MVG) by a combination of kinetic methods and X-ray crystallography. Upon AVG treatment, time-dependent, slow-binding inhibition [Morrison, J. F. (1982) Trends Biochem. Sci. 7, 102-105] was observed due to the generation of a long-lived, slowly dissociating enzyme-inhibitor complex. Kinetic analysis revealed a one-step inhibition mechanism (CBL + AVG --> CBLAVG, Ki = 1.1 +/- 0.3 microM) with an association rate constant (k1) of 336 +/- 40 M-1 s-1. This value is several orders of magnitude lower than typical bimolecular rate constants of ES formation, suggesting that additional steps occur before formation of the first detectable CBLAVG complex. Loss of activity is paralleled by the conversion of the pyridoxaldimine 426 nm chromophore to a 341 nm-absorbing species. On the basis of the recently solved structure of native CBL [Clausen, T., et al. (1996) J. Mol. Biol. 262, 202-224], it was possible to elucidate the X-ray structure of the CBLAVG complex and to refine it to an R-factor of 16.4% at 2.2 A resolution. The refined structure reveals the geometry of the bound inhibitor and its interactions with residues in the active site of CBL. Both the X-ray structure and the absorbance spectrum of the CBLAVG complex are compatible with a ketimine as the reaction product. Thus, the inhibitor seems to bind in a similar way to CBL as the substrate, but after alpha-proton abstraction, the reaction proceeds in a CBL nontypical manner, i.e. protonation of PLP-C4', resulting in the "dead-end" ketimine PLP derivative. The CBLAVG structure furthermore suggests a binding mode for rhizobitoxine and explains the failure of MVG to inhibit CBL.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20306345 A.J.Cooper, B.F.Krasnikov, Z.V.Niatsetskaya, J.T.Pinto, P.S.Callery, M.T.Villar, A.Artigues, and S.A.Bruschi (2011).
Cysteine S-conjugate β-lyases: important roles in the metabolism of naturally occurring sulfur and selenium-containing compounds, xenobiotics and anticancer agents.
  Amino Acids, 41, 7.  
  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.  
19448746 P.H.Lodha, H.Shadnia, C.M.Woodhouse, J.S.Wright, and S.M.Aitken (2009).
Investigation of residues Lys112, Glu136, His138, Gly247, Tyr248, and Asp249 in the active site of yeast cystathionine beta-synthase.
  Biochem Cell Biol, 87, 531-540.  
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
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
12228256 G.Capitani, D.L.McCarthy, H.Gut, M.G.Grütter, and J.F.Kirsch (2002).
Apple 1-aminocyclopropane-1-carboxylate synthase in complex with the inhibitor L-aminoethoxyvinylglycine. Evidence for a ketimine intermediate.
  J Biol Chem, 277, 49735-49742.
PDB code: 1m7y
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
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.  
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.  
9914476 O.Ploux, O.Breyne, S.Carillon, and A.Marquet (1999).
Slow-binding and competitive inhibition of 8-amino-7-oxopelargonate synthase, a pyridoxal-5'-phosphate-dependent enzyme involved in biotin biosynthesis, by substrate and intermediate analogs. Kinetic and binding studies.
  Eur J Biochem, 259, 63-70.  
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.  
9636232 S.Ravanel, B.Gakière, D.Job, and R.Douce (1998).
The specific features of methionine biosynthesis and metabolism in plants.
  Proc Natl Acad Sci U S A, 95, 7805-7812.  
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
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.