2JG7

Crystal structure of Seabream Antiquitin and Elucidation of its substrate specificity

• PDB DOI: https://doi.org/10.2210/pdb2JG7/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Acanthopagrus schlegelii
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2007-02-09 Released: 2008-05-13 
• Deposition Author(s): Tang, W.K., Wong, K.B., Cha, S.S., Lee, H.S., Cheng, C.H.K., Fong, W.P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 0.228 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 

Starting Model: experimental

Literature

The Crystal Structure of Seabream Antiquitin Reveals the Structural Basis of its Substrate Specificity.

Tang, W.K., Wong, K.B., Lam, Y.M., Cha, S.S., Cheng, C.H.K., Fong, W.P.

(2008) FEBS Lett 582: 3090

• PubMed: 18694748 
• DOI: https://doi.org/10.1016/j.febslet.2008.07.059
• Primary Citation of Related Structures:  
  2JG7


• PubMed Abstract: 
  

  The crystal structure of seabream antiquitin in complex with the cofactor NAD(+) was solved at 2.8A resolution. The mouth of the substrate-binding pocket is guarded by two conserved residues, Glu120 and Arg300. To test the role of these two residues, we have prepared the two mutants E120A and R300A. Our model and kinetics data suggest that antiquitin's specificity towards the substrate alpha-aminoadipic semialdehyde is contributed mainly by Glu120 which interacts with the alpha-amino group of the substrate. On the other hand, Arg300 does not have any specific interaction with the alpha-carboxylate group of the substrate, but is important in maintaining the active site conformation.

---

Organizational Affiliation: 

Department of Biochemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China.

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

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 447.08 kDa 
• Atom Count: 31,475 
• Modelled Residue Count: 4,072 
• Deposited Residue Count: 4,080 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTIQUITIN	A, B, C, D, E, F, G, H	510	Acanthopagrus schlegelii	Mutation(s): 0  EC: 1.2.1.3
UniProt
Find proteins for Q4KTQ7 (Acanthopagrus schlegelii) Explore Q4KTQ7  Go to UniProtKB:  Q4KTQ7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 0.228 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.16	α = 90.5
b = 111.02	β = 98.1
c = 113.64	γ = 111.59

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-13 
Deposition Author(s): Tang, W.K., Wong, K.B., Cha, S.S., Lee, H.S., Cheng, C.H.K., Fong, W.P.

Revision History  

• Version 1.0: 2008-05-13
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description