6KGF

Crystal structure of CaDoc0917(R16D)-CaCohA2 complex at pH 8.2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Discovery and mechanism of a pH-dependent dual-binding-site switch in the interaction of a pair of protein modules.

Yao, X.Chen, C.Wang, Y.Dong, S.Liu, Y.J.Li, Y.Cui, Z.Gong, W.Perrett, S.Yao, L.Lamed, R.Bayer, E.A.Cui, Q.Feng, Y.

(2020) Sci Adv 6

  • DOI: https://doi.org/10.1126/sciadv.abd7182
  • Primary Citation of Related Structures:  
    6KG8, 6KG9, 6KGC, 6KGD, 6KGE, 6KGF

  • PubMed Abstract: 

    Many important proteins undergo pH-dependent conformational changes resulting in "on-off" switches for protein function, which are essential for regulation of life processes and have wide application potential. Here, we report a pair of cellulosomal assembly modules, comprising a cohesin and a dockerin from Clostridium acetobutylicum , which interact together following a unique pH-dependent switch between two functional sites rather than on-off states. The two cohesin-binding sites on the dockerin are switched from one to the other at pH 4.8 and 7.5 with a 180° rotation of the bound dockerin. Combined analysis by nuclear magnetic resonance spectroscopy, crystal structure determination, mutagenesis, and isothermal titration calorimetry elucidates the chemical and structural mechanism of the pH-dependent switching of the binding sites. The pH-dependent dual-binding-site switch not only represents an elegant example of biological regulation but also provides a new approach for developing pH-dependent protein devices and biomaterials beyond an on-off switch for biotechnological applications.


  • Organizational Affiliation

    CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probably cellulosomal scaffolding protein, secreted cellulose-binding and cohesin domainA [auth C],
C [auth A]
150Clostridium acetobutylicum ATCC 824Mutation(s): 0 
Gene Names: CA_C0910
UniProt
Find proteins for Q977Y4 (Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W))
Explore Q977Y4 
Go to UniProtKB:  Q977Y4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ977Y4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
And cellulose-binding endoglucanase family 9 CelL ortholog dockerin domainB [auth D],
D [auth B]
62Clostridium acetobutylicum ATCC 824Mutation(s): 1 
Gene Names: CA_C0917
UniProt
Find proteins for Q97KK2 (Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W))
Explore Q97KK2 
Go to UniProtKB:  Q97KK2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ97KK2
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.65α = 90
b = 75.97β = 90
c = 120.33γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
Cootmodel building
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31270784
National Natural Science Foundation of ChinaChina31670735

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-11-04
    Changes: Database references, Structure summary
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description