4EIB

Crystal Structure of Circular Permuted CBM21 (CP90) Gives Insight into the Altered Selectivity on Carbohydrate Binding.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.160 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of circular permuted RoCBM21 (CP90): dimerisation and proximity of binding sites

Stephen, P.Cheng, K.C.Lyu, P.C.

(2012) PLoS One 7: e50488-e50488

  • DOI: 10.1371/journal.pone.0050488
  • Primary Citation of Related Structures:  
    4EIB

  • PubMed Abstract: 
  • Glucoamylases, containing starch-binding domains (SBD), have a wide range of scientific and industrial applications. Random mutagenesis and DNA shuffling of the gene encoding a starch-binding domain have resulted in only minor improvements in the affinities of the corresponding protein to their ligands, whereas circular permutation of the RoCBM21 substantially improved its binding affinity and selectivity towards longer-chain carbohydrates ...

    Glucoamylases, containing starch-binding domains (SBD), have a wide range of scientific and industrial applications. Random mutagenesis and DNA shuffling of the gene encoding a starch-binding domain have resulted in only minor improvements in the affinities of the corresponding protein to their ligands, whereas circular permutation of the RoCBM21 substantially improved its binding affinity and selectivity towards longer-chain carbohydrates. For the study reported herein, we used a standard soluble ligand (amylose EX-I) to characterize the functional and structural aspects of circularly permuted RoCBM21 (CP90). Site-directed mutagenesis and the analysis of crystal structure reveal the dimerisation and an altered binding path, which may be responsible for improved affinity and altered selectivity of this newly created starch-binding domain. The functional and structural characterization of CP90 suggests that it has significant potential in industrial applications.


    Organizational Affiliation

    Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GlucoamylaseA, B109Rhizopus oryzaeMutation(s): 0 
Gene Names: amyACBM21
EC: 3.2.1.3
Find proteins for B7XC04 (Rhizopus oryzae)
Explore B7XC04 
Go to UniProtKB:  B7XC04
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], F [auth A], R [auth B], S [auth B], T [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
Q [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
BA [auth B] , CA [auth B] , DA [auth B] , EA [auth B] , FA [auth B] , GA [auth B] , M [auth A] , N [auth A] , 
BA [auth B],  CA [auth B],  DA [auth B],  EA [auth B],  FA [auth B],  GA [auth B],  M [auth A],  N [auth A],  O [auth A],  P [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
AA [auth B] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , L [auth A] , V [auth B] , 
AA [auth B],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  V [auth B],  W [auth B],  X [auth B],  Y [auth B],  Z [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
NH4
Query on NH4

Download Ideal Coordinates CCD File 
E [auth A], HA [auth B], IA [auth B], U [auth B]AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.160 
  • Space Group: P 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.945α = 90
b = 66.945β = 90
c = 44.356γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
ARP/wARPmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-12
    Type: Initial release
  • Version 1.1: 2013-07-24
    Changes: Database references
  • Version 1.2: 2017-08-23
    Changes: Refinement description, Source and taxonomy