1GD9

CRYSTALL STRUCTURE OF PYROCOCCUS PROTEIN-A1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

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This is version 1.4 of the entry. See complete history. 


Literature

Temperature dependence of the enzyme-substrate recognition mechanism.

Ura, H., Harata, K., Matsui, I., Kuramitsu, S.

(2001) J Biochem 129: 173-178

  • DOI: https://doi.org/10.1093/oxfordjournals.jbchem.a002829
  • Primary Citation of Related Structures:  
    1GD9, 1GDE

  • PubMed Abstract: 

    We determined the crystal structure of the liganded form of alpha-aminotransferase from a hyperthermophile, Pyrococcus horikoshii. This hyperthermophilic enzyme did not show domain movement upon binding of an acidic substrate, glutamate, except for a small movement of the alpha-helix from Glu16 to Ala25. The omega-carboxyl group of the acidic substrate was recognized by Tyr70* without its side-chain movement, but not by positively charged Arg or Lys. Compared with the homologous enzymes from Thermus thermophilus HB8 and Escherichia coli, it was suggested that the more thermophilic the enzyme is, the smaller the domain movement is. This rule seems to be applicable to many other enzymes already reported.

    • Organizational Affiliation: 

    Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ASPARTATE AMINOTRANSFERASE
A, B
389Pyrococcus horikoshiiMutation(s): 0 
EC: 2.6.1
UniProt
Find proteins for O59096 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O59096 
Go to UniProtKB:  O59096
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO59096
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.67α = 90
b = 122.28β = 90
c = 127.17γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
TRUNCATEdata reduction
AMoREphasing
X-PLORrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-09-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2019-10-16
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Derived calculations