Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 

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This is version 1.3 of the entry. See complete history


Structure of Thermus thermophilus HB8 aspartate aminotransferase and its complex with maleate.

Nakai, T.Okada, K.Akutsu, S.Miyahara, I.Kawaguchi, S.Kato, R.Kuramitsu, S.Hirotsu, K.

(1999) Biochemistry 38: 2413-2424

  • DOI: https://doi.org/10.1021/bi9819881
  • Primary Citation of Related Structures:  
    1BJW, 1BKG

  • PubMed Abstract: 

    The three-dimensional structures of pyridoxal 5'-phosphate-type aspartate aminotransferase (AspAT) from Thermus thermophilus HB8 and pyridoxamine 5'-phosphate type one in complex with maleate have been determined by X-ray crystallography at 1.8 and 2.6 A resolution, respectively. The enzyme is a homodimer, and the polypeptide chain of the subunit is folded into one arm, one small domain, and one large domain. AspATs from many species were classified into aminotransferase subgroups Ia and Ib. The enzyme belongs to subgroup Ib, its sequence being less than 16% identical to the primary sequences of Escherichia coli, pig cytosolic, and chicken mitochondrial AspATs, which belong to subgroup Ia whose sequences are more than 40% identical and whose three-dimensional structures are quite similar with the active site residues almost completely conserved. The first X-ray analysis of AspAT subgroup Ib indicated that the overall and the active site structures are essentially conserved between the AspATs of subgroup Ia and the enzyme of subgroup Ib, but there are two distinct differences between them. (1) In AspAT subgroup Ia, substrate (or inhibitor) binding induces a large movement of the small domain as a whole to close the active site. However, in the enzyme of subgroup Ib, only the N-terminal region (Lys13-Val30) of the small domain approaches the active site to interact with the maleate. (2) In AspAT subgroup Ia, Arg292 recognizes the side chain carboxylate of the substrate; however, residue 292 of the enzyme in subgroup Ib is not Arg, and in place of Arg292, Lys109 forms a salt bridge with the side chain carboxylate. The thermostability of the enzyme is attained at least in part by the high content of Pro residues in the beta-turns and the marked increase in the number of salt bridges on the molecular surface compared with the mesophilic AspAT.

  • Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Osaka City University, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
385Thermus thermophilus HB8Mutation(s): 0 
Gene Names: aspCTTHA0046
EC: (PDB Primary Data), (UniProt)
Find proteins for Q56232 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q56232 
Go to UniProtKB:  Q56232
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ56232
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.25α = 90
b = 109.71β = 90
c = 197.3γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-07-22
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2023-08-02
    Changes: Database references, Derived calculations, Other, Refinement description