1GDE

CRYSTAL STRUCTURE OF PYROCOCCUS PROTEIN A-1 E-FORM

• PDB DOI: https://doi.org/10.2210/pdb1GDE/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-09-23 Released: 2001-09-23 
• Deposition Author(s): Ura, H., Harata, K., Matsui, I., Kuramitsu, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.230 
• R-Value Work: 0.198 
• R-Value Observed: 0.206 

Literature

Temperature dependence of the enzyme-substrate recognition mechanism.

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

(2001) J Biochem 129: 173-178

• PubMed: 11134972 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 88.71 kDa 
• Atom Count: 6,544 
• Modelled Residue Count: 776 
• Deposited Residue Count: 778 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ASPARTATE AMINOTRANSFERASE	A, B	389	Pyrococcus horikoshii	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	E [auth A], F [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
GLU	C [auth A], D [auth A]	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.230 
• R-Value Work: 0.198 
• R-Value Observed: 0.206 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.33	α = 90
b = 121.9	β = 90
c = 127	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
TRUNCATE	data reduction
X-PLOR	model building
X-PLOR	refinement
CCP4	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-09-23 
Deposition Author(s): Ura, H., Harata, K., Matsui, I., Kuramitsu, S.

Revision History  

• Version 1.0: 2001-09-23
  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