5XWF | pdb_00005xwf

Crystal structure of chitinase (RmChi1) from Rhizomucor miehei (SP3221/SAD)

• PDB DOI: https://doi.org/10.2210/pdb5XWF/pdb

• Classification: HYDROLASE
• Organism(s): Rhizomucor miehei
• Expression System: Enterobacteria phage L1
• Mutation(s): No 


• Deposited: 2017-06-29 Released: 2018-07-04 
• Deposition Author(s): Jiang, Z.Q., Hu, S.Q., Liu, Y.C., Qin, Z., Yan, Q.J., Yang, S.Q.
• Funding Organization(s): the National Science Fund for Distinguished Young Scholars

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 
  0.206 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

Crystal structure of a chitinase (RmChiA) from the thermophilic fungus Rhizomucor miehei with a real active site tunnel.

Jiang, Z.Q., Hu, S.Q., Ma, J., Liu, Y.C., Qiao, Z., Yan, Q.J., Gao, Y., Yang, S.Q.

(2021) Biochim Biophys Acta Proteins Proteom : 140709-140709

• PubMed: 34358705 
• DOI: https://doi.org/10.1016/j.bbapap.2021.140709
• Primary Citation Related Structures: 
  5XWF, 5YUQ, 7FBT


• PubMed Abstract: 
  

  A chitinase gene (RmChiA) encoding 445 amino acid (aa) residues from a fungus Rhizomucor miehei was cloned and overexpressed in Escherichia coli. Two kinds of RmChiA crystal forms, with space groups P3 ₂ 2 1 and P1, were obtained by sitting-drop vapor diffusion and the structures were determined by X-ray diffraction. The overall structure of RmChiA monomer, which is the first structure of bacterial-type chitinases from nonpathogenic fungi, adopts a canonical triosephosphate isomerase (TIM) barrel fold with two protruding chitinase insertion domains. RmChiA exhibited a unique NxDxE catalytical motif and a real active site tunnel structure, which are firstly found in GH family 18 chitinases. The motif had high structural homolog with the typical DxDxE motif in other GH family 18 chitinases. The tunnel is formed by two unusual long loops, containing 15 aa and 45 aa respectively, linked by a disulfide bond across the substrate-binding cleft. Mutation experiments found that opening the roof of tunnel structure increased the hydrolysis efficiency of RmChiA, but the thermostability of the mutants decreased. Moreover, the tunnel structure endowed RmChiA with the exo-chitinase character.

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Organizational Affiliation: 
• College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
College of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong 510640, China.
Bioresource Utilization Laboratory, College of Engineering, China Agricultural University, Beijing 100083, China.
School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.
College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 41.6 kDa 
• Atom Count: 2,957 
• Modeled Residue Count: 369 
• Deposited Residue Count: 378 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fungal chitinase from Rhizomucor miehei (SeMet-substituted proteins)	A	378	Rhizomucor miehei	Mutation(s): 0  EC: 3.2.1.14
UniProt
Find proteins for A0A3B6UEQ2 (Rhizomucor miehei) Explore A0A3B6UEQ2  Go to UniProtKB:  A0A3B6UEQ2

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free:  0.206 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.811	α = 90
b = 48.811	β = 90
c = 247.516	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-07-04 
Deposition Author(s): Jiang, Z.Q., Hu, S.Q., Liu, Y.C., Qin, Z., Yan, Q.J., Yang, S.Q.

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Funding Organization	Location	Grant Number
the National Science Fund for Distinguished Young Scholars	China	31325021

Revision History  

• Version 1.0: 2018-07-04
  Type: Initial release
  
• Version 1.1: 2021-08-18
  Changes: Database references
• Version 1.2: 2024-10-30
  Changes: Data collection, Structure summary