5Z7N

SmChiA sliding-intermediate with chitopentaose

  • Classification: HYDROLASE
  • Organism(s): Serratia marcescens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2018-01-30 Released: 2018-09-26 
  • Deposition Author(s): Nakamura, A., Iino, R.
  • Funding Organization(s): Grants-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science, and Technology

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report



Literature

Processive chitinase is Brownian monorail operated by fast catalysis after peeling rail from crystalline chitin.

Nakamura, A.Okazaki, K.I.Furuta, T.Sakurai, M.Iino, R.

(2018) Nat Commun 9: 3814-3814

  • DOI: 10.1038/s41467-018-06362-3
  • Primary Citation of Related Structures:  
    5Z7M, 5Z7O, 5Z7N, 5Z7P

  • PubMed Abstract: 
  • Processive chitinase is a linear molecular motor which moves on the surface of crystalline chitin driven by processive hydrolysis of single chitin chain. Here, we analyse the mechanism underlying unidirectional movement of Serratia marcescens chitina ...

    Processive chitinase is a linear molecular motor which moves on the surface of crystalline chitin driven by processive hydrolysis of single chitin chain. Here, we analyse the mechanism underlying unidirectional movement of Serratia marcescens chitinase A (SmChiA) using high-precision single-molecule imaging, X-ray crystallography, and all-atom molecular dynamics simulation. SmChiA shows fast unidirectional movement of ~50 nm s -1 with 1 nm forward and backward steps, consistent with the length of reaction product chitobiose. Analysis of the kinetic isotope effect reveals fast substrate-assisted catalysis with time constant of ~3 ms. Decrystallization of the single chitin chain from crystal surface is the rate-limiting step of movement with time constant of ~17 ms, achieved by binding free energy at the product-binding site of SmChiA. Our results demonstrate that SmChiA operates as a burnt-bridge Brownian ratchet wherein the Brownian motion along the single chitin chain is rectified forward by substrate-assisted catalysis.


    Organizational Affiliation

    Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Hayama, 240-0193, Japan. iino@ims.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chitinase AA546Serratia marcescensMutation(s): 0 
Gene Names: chiA
EC: 3.2.1.14
Find proteins for P07254 (Serratia marcescens)
Explore P07254 
Go to UniProtKB:  P07254
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose
B
5 N/A
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2 N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.173 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.11α = 90
b = 200.36β = 90
c = 59.51γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-01-30 
  • Released Date: 2018-09-26 
  • Deposition Author(s): Nakamura, A., Iino, R.

Funding OrganizationLocationGrant Number
Grants-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science, and TechnologyJapanJP15H06898
Grants-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science, and TechnologyJapanJP17K18429
Grants-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science, and TechnologyJapanJP17H05899

Revision History 

  • Version 1.0: 2018-09-26
    Type: Initial release
  • Version 1.1: 2018-10-03
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary