PDBsum entry 1v2d

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Transferase PDB id
Protein chain
365 a.a. *
Waters ×171
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Crystal structure of t.Th hb8 glutamine aminotransferase
Structure: Glutamine aminotransferase. Chain: a. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 274. Gene: hb8. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
1.90Å     R-factor:   0.181     R-free:   0.218
Authors: M.Goto,Riken Structural Genomics/proteomics Initiative (Rsgi
Key ref:
M.Goto et al. (2004). Crystal structures of glutamine:phenylpyruvate aminotransferase from Thermus thermophilus HB8: induced fit and substrate recognition. J Biol Chem, 279, 16518-16525. PubMed id: 14761974 DOI: 10.1074/jbc.M311575200
15-Oct-03     Release date:   06-Jul-04    
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Protein chain
Pfam   ArchSchema ?
Q75WK2  (Q75WK2_THETH) -  Aminotransferase
381 a.a.
365 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     biosynthetic process   1 term 
  Biochemical function     catalytic activity     4 terms  


DOI no: 10.1074/jbc.M311575200 J Biol Chem 279:16518-16525 (2004)
PubMed id: 14761974  
Crystal structures of glutamine:phenylpyruvate aminotransferase from Thermus thermophilus HB8: induced fit and substrate recognition.
M.Goto, R.Omi, I.Miyahara, A.Hosono, H.Mizuguchi, H.Hayashi, H.Kagamiyama, K.Hirotsu.
The following three-dimensional structures of three forms of glutamine:phenylpyruvate aminotransferase from Thermus thermophilus HB8 have been determined and represent the first x-ray analysis of the enzyme: the unliganded pyridoxal 5'-phosphate form at 1.9 A resolution and two complexes with 3-phenylpropionate and alpha-keto-gamma-methylthiobutyrate at 2.35 and 2.6 A resolution, respectively. The enzyme shows high activity toward phenylalanine, tyrosine, tryptophan, kynurenine, methionine, and glutamine. The enzyme is a homodimer, and each subunit is divided into an N-terminal arm and small and large domains. Based on its folding, the enzyme belongs to fold type I, aminotransferase subclass Ib. The subclass I aminotransferases whose structures have so far been determined exhibit a large movement of the small domain region upon binding of a substrate. Similarly, the glutamine:phenylpyruvate aminotransferase undergoes a large movement in part of the small domain to close the active site. The active-site pocket has a shape and size suitable to enclose the side chain of an aromatic amino acid or that of methionine. The inner side of the pocket is mostly hydrophobic, but also has polar sites. The kynurenine complex generated by computer modeling fits the pocket of the enzyme and its hydrophilic groups interact with the polar sites of the pocket.
  Selected figure(s)  
Figure 5.
FIG. 5. Schematic diagram showing hydrogen bond and salt bridge interactions of the active-site residues. Putative interactions are shown by dotted lines if the acceptor and donor are less than 3.5 Å apart. Phe-112 and Val-193, which sandwich the pyridine ring of PLP, are omitted for clarity. A, the unliganded ttGlnAT in the closed form. B, the ttGlnAT complex with 3PP. The hydrogen bonds between Ser-13 and Asp-113 have been omitted for clarity.
Figure 6.
FIG. 6. Superimposition of the active site of the ttGlnAT·kynurenine complex model onto ttGlnAT·3PP. The residues that represent the ttGlnAT· kynurenine complex and ttGlnAT·3PP are shown in brown and deep blue, respectively. Kynurenine and 3PP are represented by thick lines in pale blue and brown. The oxygen and nitrogen atoms of kynurenine and 3PP are colored red and deep blue, respectively. The dotted lines (green) show the hydrogen bonding interactions of the amino and carbonyl groups of the 3-anthraniloyl moiety of kynurenine with Asp-113 and Tyr-57^*, respectively.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 16518-16525) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20482848 Q.Han, T.Cai, D.A.Tagle, and J.Li (2010).
Thermal stability, pH dependence and inhibition of four murine kynurenine aminotransferases.
  BMC Biochem, 11, 19.  
19826765 Q.Han, T.Cai, D.A.Tagle, and J.Li (2010).
Structure, expression, and function of kynurenine aminotransferases in human and rodent brains.
  Cell Mol Life Sci, 67, 353-368.
PDB code: 3hlm
19029248 Q.Han, H.Robinson, T.Cai, D.A.Tagle, and J.Li (2009).
Biochemical and structural properties of mouse kynurenine aminotransferase III.
  Mol Cell Biol, 29, 784-793.
PDB codes: 3e2f 3e2y 3e2z
19338303 Q.Han, H.Robinson, T.Cai, D.A.Tagle, and J.Li (2009).
Structural insight into the inhibition of human kynurenine aminotransferase I/glutamine transaminase K.
  J Med Chem, 52, 2786-2793.
PDB codes: 3fvs 3fvu 3fvx
18186649 Q.Han, Y.G.Gao, H.Robinson, and J.Li (2008).
Structural insight into the mechanism of substrate specificity of aedes kynurenine aminotransferase.
  Biochemistry, 47, 1622-1630.
PDB codes: 2r5c 2r5e
  16511030 H.Chon, H.Matsumura, S.Shimizu, N.Maeda, Y.Koga, K.Takano, and S.Kanaya (2005).
Overproduction and preliminary crystallographic study of a human kynurenine aminotransferase II homologue from Pyrococcus horikoshii OT3.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 319-322.  
16138312 H.Chon, H.Matsumura, Y.Koga, K.Takano, and S.Kanaya (2005).
Crystal structure of a human kynurenine aminotransferase II homologue from Pyrococcus horikoshii OT3 at 2.20 A resolution.
  Proteins, 61, 685-688.
PDB code: 1x0m
15889412 K.Hirotsu, M.Goto, A.Okamoto, and I.Miyahara (2005).
Dual substrate recognition of aminotransferases.
  Chem Rec, 5, 160-172.  
15853804 Q.Han, Y.G.Gao, H.Robinson, H.Ding, S.Wilson, and J.Li (2005).
Crystal structures of Aedes aegypti kynurenine aminotransferase.
  FEBS J, 272, 2198-2206.
PDB codes: 1yiy 1yiz
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.