1IU9 | pdb_00001iu9

Crystal structure of the C-terminal domain of aspartate racemase from Pyrococcus horikoshii OT3

• PDB DOI: https://doi.org/10.2210/pdb1IU9/pdb

• Classification: ISOMERASE
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2002-02-28 Released: 2003-09-09 
• Deposition Author(s): Liu, L., Iwata, K., Yohda, M., Miki, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.267 (Depositor) 
• R-Value Work: 
  0.225 (Depositor) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Structural insight into gene duplication, gene fusion and domain swapping in the evolution of PLP-independent amino acid racemases

Liu, L., Iwata, K., Yohda, M., Miki, K.

(2002) FEBS Lett 528: 114-118

• PubMed: 12297289 
• DOI: https://doi.org/10.1016/s0014-5793(02)03264-7
• Primary Citation Related Structures: 
  1IU9


• PubMed Abstract: 
  

  The X-ray crystal structure has revealed two similar alpha/beta domains of aspartate racemase (AspR) from Pyrococcus horikoshii OT3, and identified a pseudo mirror-symmetric distribution of the residues around its active site [Liu et al. (2002) J. Mol. Biol. 319, 479-489]. Structural homology and functional similarity between the two domains suggested that this enzyme evolved from an ancestral domain by gene duplication and gene fusion. We have expressed solely the C-terminal domain of this AspR and determined its three-dimensional structure by X-ray crystallography. The high structural stability of this domain supports the existence of the ancestral domain. In comparison with other amino acid racemases (AARs), we suggest that gene duplication and gene fusion are conventional ways in the evolution of pyridoxal 5'-phosphate-independent AARs.

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Organizational Affiliation: 
• Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 12.22 kDa 
• Atom Count: 907 
• Modeled Residue Count: 111 
• Deposited Residue Count: 111 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
aspartate racemase	A	111	Pyrococcus horikoshii OT3	Mutation(s): 0  Gene Names: pPH0670E EC: 5.1.1.13
UniProt
Find proteins for O58403 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58403  Go to UniProtKB:  O58403

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.267 (Depositor) 
• R-Value Work:  0.225 (Depositor) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.829	α = 90
b = 45.328	β = 90
c = 57.366	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-09-09 
Deposition Author(s): Liu, L., Iwata, K., Yohda, M., Miki, K.

Revision History  

• Version 1.0: 2003-09-09
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description