2ZC0

Crystal structure of an archaeal alanine:glyoxylate aminotransferase

• PDB DOI: https://doi.org/10.2210/pdb2ZC0/pdb

• Classification: TRANSFERASE
• Organism(s): Thermococcus litoralis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-10-31 Released: 2008-06-17 
• Deposition Author(s): Sakuraba, H., Yoneda, K., Tsuge, H., Ohshima, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.261 
• R-Value Work: 0.236 

Literature

Structure of an archaeal alanine:glyoxylate aminotransferase

Sakuraba, H., Yoneda, K., Takeuchi, K., Tsuge, H., Katunuma, N., Ohshima, T.

(2008) Acta Crystallogr D Biol Crystallogr 64: 696-699

• PubMed: 18560158 
• DOI: https://doi.org/10.1107/S0907444908006732
• Primary Citation of Related Structures:  
  2ZC0


• PubMed Abstract: 
  

  The crystal structure of a novel alanine:glyoxylate aminotransferase from the hyperthermophilic archaeon Thermococcus litoralis was determined at 2.3 A resolution. The asymmetric unit contains four homologous subunits and the functional tetramer is generated by noncrystallographic 222 symmetry. Although the main-chain coordinates of the monomer of the Thermococcus litoralis enzyme showed a high degree of similarity to those of aspartate aminotransferase from Thermus thermophilus HB8, the amino-acid residues involved in substrate binding in the aspartate aminotransferase are only partially conserved in the Thermococcus litoralis enzyme. This may account for the difference in the substrate specificities of the two enzymes.

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Organizational Affiliation: 

Department of Life System, Institute of Technology and Science, The University of Tokushima, 2-1 Minamijosanjima-cho, Tokushima 770-8506, Japan.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 182.44 kDa 
• Atom Count: 12,914 
• Modelled Residue Count: 1,620 
• Deposited Residue Count: 1,628 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alanine glyoxylate transaminase	A, B, C, D	407	Thermococcus litoralis	Mutation(s): 0  EC: 2.6.1.44
UniProt
Find proteins for Q9C4M4 (Thermococcus litoralis) Explore Q9C4M4  Go to UniProtKB:  Q9C4M4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PMP	F [auth A], I [auth B], L [auth C], O [auth D]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C8 H13 N2 O5 P ZMJGSOSNSPKHNH-UHFFFAOYSA-N
IMD	G [auth A], J [auth B], M [auth C], P [auth D]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN	E [auth A], H [auth B], K [auth C], N [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.261 
• R-Value Work: 0.236 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.694	α = 90
b = 112.519	β = 90
c = 207.287	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
CNS	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-17 
Deposition Author(s): Sakuraba, H., Yoneda, K., Tsuge, H., Ohshima, T.

Revision History  

• Version 1.0: 2008-06-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.2: 2012-04-11
  Changes: Database references
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations