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PDBsum entry 2uyk
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protein ligands Protein-protein interface(s) links
Unknown function PDB id
2uyk

 

 

 

 

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Contents
Protein chains
127 a.a. *
Ligands
SER
Waters ×457
* Residue conservation analysis
PDB id:
2uyk
Name: Unknown function
Title: Crystal structure of e. Coli tdcf with bound serine
Structure: Protein tdcf. Chain: a, b, c. Synonym: tdcf. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Strain: mc4100. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
1.60Å     R-factor:   0.157     R-free:   0.199
Authors: J.D.Burman,C.E.M.Stevenson,R.G.Sawers,D.M.Lawson
Key ref: J.D.Burman et al. (2007). The crystal structure of Escherichia coli TdcF, a member of the highly conserved YjgF/YER057c/UK114 family. Bmc Struct Biol, 7, 30. PubMed id: 17506874
Date:
10-Apr-07     Release date:   29-May-07    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0AGL2  (TDCF_ECOLI) -  Putative reactive intermediate deaminase TdcF from Escherichia coli (strain K12)
Seq:
Struc: 		129 a.a.
127 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.3.5.4.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
Bmc Struct Biol 7:30 (2007)
PubMed id: 17506874  
 
 
The crystal structure of Escherichia coli TdcF, a member of the highly conserved YjgF/YER057c/UK114 family.
J.D.Burman, C.E.Stevenson, R.G.Sawers, D.M.Lawson.
 
  ABSTRACT  
 
BACKGROUND: The YjgF/YER057c/UK114 family of proteins is widespread in nature, but has as yet no clearly defined biological role. Members of the family exist as homotrimers and are characterised by intersubunit clefts that are delineated by well-conserved residues; these sites are likely to be of functional significance, yet catalytic activity has never been detected for any member of this family. The gene encoding the TdcF protein of E. coli, a YjgF/YER057c/UK114 family member, resides in an operon that strongly suggests a role in the metabolism of 2-ketobutyrate for this protein. RESULTS: We have determined the crystal structure of E. coli TdcF by molecular replacement to a maximum resolution of 1.6 A. Structures are also presented of TdcF complexed with a variety of ligands. CONCLUSION: The TdcF structure closely resembles those of all YjgF/YER057c/UK114 family members determined thus far. It has the trimeric quaternary structure and intersubunit cavities characteristic of this family of proteins. We show that TdcF is capable of binding several low molecular weight metabolites bearing a carboxylate group, although the interaction with 2-ketobutyrate appears to be the most well defined. These observations may be indicative of a role for TdcF in sensing this potentially toxic metabolite.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21383123 J.N.Andexer, S.G.Kendrew, M.Nur-e-Alam, O.Lazos, T.A.Foster, A.S.Zimmermann, T.D.Warneck, D.Suthar, N.J.Coates, F.E.Koehn, J.S.Skotnicki, G.T.Carter, M.A.Gregory, C.J.Martin, S.J.Moss, P.F.Leadlay, and B.Wilkinson (2011).
Biosynthesis of the immunosuppressants FK506, FK520, and rapamycin involves a previously undescribed family of enzymes acting on chorismate.
  Proc Natl Acad Sci U S A, 108, 4776-4781.  
  19899170 K.G.Thakur, T.Praveena, and B.Gopal (2010).
Mycobacterium tuberculosis Rv2704 is a member of the YjgF/YER057c/UK114 family.
  Proteins, 78, 773-778.
PDB code: 3i7t
20230003 K.J.Rangan, Y.Y.Yang, G.Charron, and H.C.Hang (2010).
Rapid visualization and large-scale profiling of bacterial lipoproteins with chemical reporters.
  J Am Chem Soc, 132, 10628-10629.  
20400551 K.S.Kim, J.G.Pelton, W.B.Inwood, U.Andersen, S.Kustu, and D.E.Wemmer (2010).
The Rut pathway for pyrimidine degradation: novel chemistry and toxicity problems.
  J Bacteriol, 192, 4089-4102.  
20382023 M.J.Koenigsknecht, and D.M.Downs (2010).
Thiamine biosynthesis can be used to dissect metabolic integration.
  Trends Microbiol, 18, 240-247.  
20647113 M.Y.Galperin, and E.V.Koonin (2010).
From complete genome sequence to 'complete' understanding?
  Trends Biotechnol, 28, 398-406.  
19175791 C.Alpert, J.Scheel, W.Engst, G.Loh, and M.Blaut (2009).
Adaptation of protein expression by Escherichia coli in the gastrointestinal tract of gnotobiotic mice.
  Environ Microbiol, 11, 751-761.  
18296521 M.R.Christopherson, G.E.Schmitz, and D.M.Downs (2008).
YjgF is required for isoleucine biosynthesis when Salmonella enterica is grown on pyruvate medium.
  J Bacteriol, 190, 3057-3062.  
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.  
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.

 

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