8JIY | pdb_00008jiy

A carbohydrate binding domain of a putative chondroitinase

• PDB DOI: https://doi.org/10.2210/pdb8JIY/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Polaribacter haliotis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-05-29 Released: 2023-09-20 
• Deposition Author(s): Liu, G.C., Chang, Y.G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.228 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: in silico

Literature

Identification and structural characterization of a novel chondroitin sulfate-specific carbohydrate-binding module: The first member of a new family, CBM100.

Liu, G., Chang, Y., Mei, X., Chen, G., Zhang, Y., Jiang, X., Tao, W., Xue, C.

(2024) Int J Biol Macromol 255: 127959-127959

• PubMed: 37951443 
• DOI: https://doi.org/10.1016/j.ijbiomac.2023.127959
• Primary Citation Related Structures: 
  8JIY


• PubMed Abstract: 
  

  Chondroitin sulfate is a biologically and commercially important polysaccharide with a variety of applications. Carbohydrate-binding module (CBM) is an important class of carbohydrate-binding protein, which could be utilized as a promising tool for the applications of polysaccharides. In the present study, an unknown function domain was explored from a putative chondroitin sulfate lyase in PL29 family. Recombinant PhCBM100 demonstrated binding capacity to chondroitin sulfates with K _a values of 2.1 ± 0.2 × 10 ⁶  M ^-1 and 6.0 ± 0.1 × 10 ⁶  M ^-1 to chondroitin sulfate A and chondroitin sulfate C, respectively. The 1.55 Å resolution X-ray crystal structure of PhCBM100 exhibited a β-sandwich fold formed by two antiparallel β-sheets. A binding groove in PhCBM100 interacting with chondroitin sulfate was subsequently identified, and the potential of PhCBM100 for visualization of chondroitin sulfate was evaluated. PhCBM100 is the first characterized chondroitin sulfate-specific CBM. The novelty of PhCBM100 proposed a new CBM family of CBM100.

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Organizational Affiliation: 
• College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China.
College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, 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: 27.12 kDa 
• Atom Count: 1,976 
• Modeled Residue Count: 216 
• Deposited Residue Count: 241 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF4955 domain-containing protein	A	241	Polaribacter haliotis	Mutation(s): 0  Gene Names: H9I45_07735
UniProt
Find proteins for A0A7L8AJZ3 (Polaribacter haliotis) Explore A0A7L8AJZ3  Go to UniProtKB:  A0A7L8AJZ3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.228 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.313	α = 90
b = 56.634	β = 90
c = 69.456	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-09-20 
Deposition Author(s): Liu, G.C., Chang, Y.G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-09-20
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Database references