1IU9

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


Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


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

  • DOI: https://doi.org/10.1016/s0014-5793(02)03264-7
  • Primary Citation of 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.


  • Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
aspartate racemase111Pyrococcus horikoshii OT3Mutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO58403
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.829α = 90
b = 45.328β = 90
c = 57.366γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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