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PDBsum entry 1iug

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1iug
Jmol
Contents
Protein chains
348 a.a. *
Ligands
PO4 ×2
Waters ×192
* Residue conservation analysis
PDB id:
1iug
Name: Transferase
Title: The crystal structure of aspartate aminotransferase which belongs to subgroup iv from thermus thermophilus
Structure: Putative aspartate aminotransferase. Chain: a, b. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 274. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
2.20Å     R-factor:   0.199     R-free:   0.236
Authors: Y.Katsura,M.Shirouzu,H.Yamaguchi,R.Ishitani,O.Nureki, S.Kuramitsu,H.Hayashi,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
Y.Katsura et al. (2004). Crystal structure of a putative aspartate aminotransferase belonging to subgroup IV. Proteins, 55, 487-492. PubMed id: 15103612 DOI: 10.1002/prot.20020
Date:
04-Mar-02     Release date:   25-Nov-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P83786  (P83786_THETH) -  Aspartate aminotransferase
Seq:
Struc:
352 a.a.
348 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.6.1.1  - Aspartate transaminase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate
L-aspartate
+ 2-oxoglutarate
= oxaloacetate
+ L-glutamate
      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!
  Biological process     metabolic process   1 term 
  Biochemical function     catalytic activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1002/prot.20020 Proteins 55:487-492 (2004)
PubMed id: 15103612  
 
 
Crystal structure of a putative aspartate aminotransferase belonging to subgroup IV.
Y.Katsura, M.Shirouzu, H.Yamaguchi, R.Ishitani, O.Nureki, S.Kuramitsu, H.Hayashi, S.Yokoyama.
 
  ABSTRACT  
 
Protein TT0402 from Thermus thermophilus HB8 exhibits about 30-35% sequence identity with proteins belonging to subgroup IV in the aminotransferase family of the fold-type I pyridoxal 5'-phosphate (PLP)-dependent enzymes. In this study, we determined the crystal structure of TT0402 at 2.3 A resolution (R(factor) = 19.9%, R(free) = 23.6%). The overall structure of TT0402 exhibits the fold conserved in aminotransferases, and is most similar to that of the Escherichia coli phosphoserine aminotransferase, which belongs to subgroup IV but shares as little as 13% sequence identity with TT0402. Kinetic assays confirmed that TT0402 has higher transamination activities with the amino group donor, L-glutamate, and somewhat lower activities with L-aspartate. These results indicate that TT0402 is a subgroup IV aminotransferase for the synthesis/degradation of either L-aspartate or a similar compound.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Crystal structures of TT0402. (A) Overall structure of TT0402. Helices are colored green, and sheets are yellow. The figure was drawn with the program RIBBONS.[21] (B) The 2F[o]-F[c] Electron density map at the active site. The two subunits are colored green and yellow, respectively. PLP is located at the center. The figure was prepared with the program SPOCK.
Figure 4.
Figure 4. Substrate recognition. (A) Kinetic parameters of the half-reaction of TT0402. The reactions were performed in 50 mM HEPES, 100 mM KCl, pH8.0, and at 25°C. The kcat/Km values are calculated with amino acids (Asp, Ala, Ser, Met, Tyr, Phe, Trp, His, Arg, Lys, Val, Ile, Thr, Leu, Gly, Asn, Gln, Glu, and phospho-L-serine) as amino donors. (B) Superposition of the TT0402 and E. coli AspAT substrate recognition sites. The E. coli AspAT belongs to subgroup I, which is colored green. This figure was prepared with the program SPOCK. (C) Superposition of the TT0402 and T. thermophilus HB8 substrate recognition sites. The T. thermophilus subgroup I AspAT is colored yellow. This figure was prepared with the program SPOCK.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2004, 55, 487-492) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20852637 I.Ramazzina, R.Costa, L.Cendron, R.Berni, A.Peracchi, G.Zanotti, and R.Percudani (2010).
An aminotransferase branch point connects purine catabolism to amino acid recycling.
  Nat Chem Biol, 6, 801-806.  
17989071 Y.Yoshikane, N.Yokochi, M.Yamasaki, K.Mizutani, K.Ohnishi, B.Mikami, H.Hayashi, and T.Yagi (2008).
Crystal structure of pyridoxamine-pyruvate aminotransferase from Mesorhizobium loti MAFF303099.
  J Biol Chem, 283, 1120-1127.
PDB codes: 2z9u 2z9v 2z9w 2z9x
17071763 S.Helgadóttir, G.Rosas-Sandoval, D.Söll, and D.E.Graham (2007).
Biosynthesis of phosphoserine in the Methanococcales.
  J Bacteriol, 189, 575-582.  
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 codes are shown on the right.