PDBsum entry 2gn1

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Lyase PDB id
Jmol PyMol
Protein chains
327 a.a. *
Waters ×274
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Crystal structure of dimeric biodegradative threonine deamin from salmonella typhimurium at 2.2a resolution (triclinic f one dimer of tdcb in the asymmetric unit)
Structure: Threonine dehydratase catabolic. Chain: a, b. Synonym: threonine deaminase. Engineered: yes
Source: Salmonella typhimurium. Organism_taxid: 602. Strain: ifo 12529. Gene: tdcb. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
2.20Å     R-factor:   0.212     R-free:   0.253
Authors: D.K.Simanshu,H.S.Savithri,M.R.N.Murthy
Key ref:
D.K.Simanshu et al. (2006). Crystal structures of Salmonella typhimurium biodegradative threonine deaminase and its complex with CMP provide structural insights into ligand-induced oligomerization and enzyme activation. J Biol Chem, 281, 39630-39641. PubMed id: 17046821 DOI: 10.1074/jbc.M605721200
09-Apr-06     Release date:   07-Nov-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P11954  (TDCB_SALTY) -  L-threonine dehydratase catabolic TdcB
329 a.a.
327 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 1: E.C.  - L-serine ammonia-lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-serine = pyruvate + NH3
= pyruvate
+ NH(3)
      Cofactor: Pyridoxal 5'-phosphate or iron-sulfur
Pyridoxal 5'-phosphate
or iron-sulfur
   Enzyme class 2: E.C.  - Threonine ammonia-lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Reaction: L-threonine = 2-oxobutanoate + NH3
= 2-oxobutanoate
+ NH(3)
      Cofactor: Pyridoxal 5'-phosphate or iron-sulfur
Pyridoxal 5'-phosphate
or iron-sulfur
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     5 terms  


DOI no: 10.1074/jbc.M605721200 J Biol Chem 281:39630-39641 (2006)
PubMed id: 17046821  
Crystal structures of Salmonella typhimurium biodegradative threonine deaminase and its complex with CMP provide structural insights into ligand-induced oligomerization and enzyme activation.
D.K.Simanshu, H.S.Savithri, M.R.Murthy.
Two different pyridoxal 5'-phosphate-containing l-threonine deaminases (EC, biosynthetic and biodegradative, which catalyze the deamination of l-threonine to alpha-ketobutyrate, are present in Escherichia coli and Salmonella typhimurium. Biodegradative threonine deaminase (TdcB) catalyzes the first reaction in the anaerobic breakdown of l-threonine to propionate. TdcB, unlike the biosynthetic threonine deaminase, is insensitive to l-isoleucine and is activated by AMP. In the present study, TdcB from S. typhimurium was cloned and overexpressed in E. coli. In the presence of AMP or CMP, the recombinant enzyme was converted to the tetrameric form accompanied by significant enzyme activation. To provide insights into ligand-mediated oligomerization and enzyme activation, crystal structures of S. typhimurium TdcB and its complex with CMP were determined. In the native structure, TdcB is in a dimeric form, whereas in the TdcB.CMP complex, it exists in a tetrameric form with 222 symmetry and appears as a dimer of dimers. Tetrameric TdcB binds to four molecules of CMP, two at each of the dimer interfaces. Comparison of the dimer structure in the ligand (CMP)-free and -bound forms suggests that the changes induced by ligand binding at the dimer interface are essential for tetramerization. The differences observed in the tertiary and quaternary structures of TdcB in the absence and presence of CMP appear to account for enzyme activation and increased binding affinity for l-threonine. Comparison of TdcB with related pyridoxal 5'-phosphate-dependent enzymes points to structural and mechanistic similarities.
  Selected figure(s)  
Figure 5.
FIGURE 5. PLP in the active site pocket of TdcB. a, stereo view of electron density corresponding to PLP bound to Lys^58 from a 2F[o] - F[c] map contoured at 1.5 . b, stereo diagram of the active site region showing hydrogen bonding network of PLP. Hydrogen bonds formed by PLP ( 3.5 Å) with protein atoms and water molecules are shown as broken lines. PLP bound to Lys^58 is shown as a ball and stick model.
Figure 6.
FIGURE 6. CMP in the inter-subunit interface in the tetrameric TdcB·CMP complex. a, stereo view of electron density corresponding to CMP from a 2F[o] - F[c] map contoured at 1.0 . b, stereo diagram of the CMP binding region showing bound CMP. Residues interacting with CMP from the two subunits of tetrameric TdcB are shown in dark gray, whereas the corresponding residues from the dimeric TdcB are shown in light gray. CMP is shown as a ball and stick model. Hydrogen bonds formed by CMP ( 3.5 Å) with protein atoms are shown as broken lines.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 39630-39641) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21436043 E.Gonzales-Vigil, C.M.Bianchetti, G.N.Phillips, and G.A.Howe (2011).
Adaptive evolution of threonine deaminase in plant defense against insect herbivores.
  Proc Natl Acad Sci U S A, 108, 5897-5902.
PDB code: 3iau
19640845 M.Goto, T.Yamauchi, N.Kamiya, I.Miyahara, T.Yoshimura, H.Mihara, T.Kurihara, K.Hirotsu, and N.Esaki (2009).
Crystal structure of a homolog of mammalian serine racemase from Schizosaccharomyces pombe.
  J Biol Chem, 284, 25944-25952.
PDB codes: 1wtc 2zr8
19193709 T.Murakami, T.Maeda, A.Yokota, and M.Wada (2009).
Gene cloning and expression of pyridoxal 5'-phosphate-dependent L-threo-3-hydroxyaspartate dehydratase from Pseudomonas sp. T62, and characterization of the recombinant enzyme.
  J Biochem, 145, 661-668.  
18931110 N.J.Zelyas, H.Cai, T.Kwong, and S.E.Jensen (2008).
Alanylclavam biosynthetic genes are clustered together with one group of clavulanic acid biosynthetic genes in Streptomyces clavuligerus.
  J Bacteriol, 190, 7957-7965.  
17954980 D.K.Simanshu, S.Chittori, H.S.Savithri, and M.R.Murthy (2007).
Structure and function of enzymes involved in the anaerobic degradation of L-threonine to propionate.
  J Biosci, 32, 1195-1206.  
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.