1CQ7

ASPARTATE AMINOTRANSFERASE (E.C. 2.6.1.1) COMPLEXED WITH C5-PYRIDOXAL-5P-PHOSPHATE

• PDB DOI: https://doi.org/10.2210/pdb1CQ7/pdb

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


• Deposited: 1999-08-06 Released: 2000-12-20 
• Deposition Author(s): Ishijima, J., Nakai, T., Kawaguchi, S., Hirotsu, K., Kuramitsu, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.251 
• R-Value Work: 0.215 

Literature

Free energy requirement for domain movement of an enzyme

Ishijima, J., Nakai, T., Kawaguchi, S., Hirotsu, K., Kuramitsu, S.

(2000) J Biol Chem 275: 18939-18945

• PubMed: 10858450 
• DOI: https://doi.org/10.1074/jbc.275.25.18939
• Primary Citation of Related Structures:  
  1C9C, 1CQ6, 1CQ7, 1CQ8


• PubMed Abstract: 
  

  Domain movement is sometimes essential for substrate recognition by an enzyme. X-ray crystallography of aminotransferase with a series of aliphatic substrates showed that the domain movement of aspartate aminotransferase was changed dramatically from an open to a closed form by the addition of only one CH(2) to the side chain of the C4 substrate CH(3)(CH(2))C((alpha))H(NH(3)(+))COO(-). These crystallographic results and reaction kinetics (Kawaguchi, S., Nobe, Y., Yasuoka, J., Wakamiya, T., Kusumoto, S., and Kuramitsu, S. (1997) J. Biochem. (Tokyo) 122, 55-63; Kawaguchi, S. and Kuramitsu, S. (1998) J. Biol. Chem. 273, 18353-18364) enabled us to estimate the free energy required for the domain movement.

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Organizational Affiliation: 

Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan. Osaka 558-8585, 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,PQS (software)

Macromolecule Content

• Total Structure Weight: 43.97 kDa 
• Atom Count: 3,201 
• Modelled Residue Count: 396 
• Deposited Residue Count: 396 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ASPARTATE AMINOTRANSFERASE	A	396	Escherichia coli	Mutation(s): 0  EC: 2.6.1.1
UniProt
Find proteins for P00509 (Escherichia coli (strain K12)) Explore P00509  Go to UniProtKB:  P00509

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PY5	B [auth A]	2-[O-PHOSPHONOPYRIDOXYL]-AMINO-PENTANOIC ACID C13 H21 N2 O7 P YYAMSLLSQINIQO-NSHDSACASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.251 
• R-Value Work: 0.215 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.58	α = 90
b = 85.59	β = 90
c = 78.92	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-12-20 
Deposition Author(s): Ishijima, J., Nakai, T., Kawaguchi, S., Hirotsu, K., Kuramitsu, S.

Revision History  

• Version 1.0: 2000-12-20
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations