Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 51.24 kDa 
• Atom Count: 4000 
• Modelled Residue Count: 455 
• Deposited Residue Count: 462 
• Unique protein chains: 1

7JRM

The structure of CBM51-2 and INT domains from Clostridium perfringens ZmpB

• PDB DOI: 10.2210/pdb7JRM/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Clostridium perfringens ATCC 13124
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-08-12 Released: 2021-02-03 
• Deposition Author(s): Pluvinage, B., Boraston, A.B.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR), Canadian Glycomics Network (GLYCONET)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.272 
• R-Value Work: 0.248 
• R-Value Observed: 0.249 

Literature

Architecturally complex O -glycopeptidases are customized for mucin recognition and hydrolysis.

Pluvinage, B., Ficko-Blean, E., Noach, I., Stuart, C., Thompson, N., McClure, H., Buenbrazo, N., Wakarchuk, W., Boraston, A.B.

(2021) Proc Natl Acad Sci U S A 118

• PubMed: 33658366 
• DOI: 10.1073/pnas.2019220118
• Primary Citation of Related Structures:  
  7JFS, 7JNB, 7JND, 7JNF, 7JRL, 7JRM, 7JS4


• PubMed Abstract: 
  

A challenge faced by peptidases is the recognition of highly diverse substrates. A feature of some peptidase families is the capacity to specifically use post-translationally added glycans present on their protein substrates as a recognition determinant. This is ultimately critical to enabling peptide bond hydrolysis. This class of enzyme is also frequently large and architecturally sophisticated. However, the molecular details underpinning glycan recognition by these O -glycopeptidases, the importance of these interactions, and the functional roles of their ancillary domains remain unclear. Here, using the Clostridium perfringens ZmpA, ZmpB, and ZmpC M60 peptidases as model proteins, we provide structural and functional insight into how these intricate proteins recognize glycans as part of catalytic and noncatalytic substrate recognition. Structural, kinetic, and mutagenic analyses support the key role of glycan recognition within the M60 domain catalytic site, though they point to ZmpA as an apparently inactive enzyme. Wider examination of the Zmp domain content reveals noncatalytic carbohydrate binding as a feature of these proteins. The complete three-dimensional structure of ZmpB provides rare insight into the overall molecular organization of a highly multimodular enzyme and reveals how the interplay of individual domain function may influence biological activity. O -glycopeptidases frequently occur in host-adapted microbes that inhabit or attack mucus layers. Therefore, we anticipate that these results will be fundamental to informing more detailed models of how the glycoproteins that are abundant in mucus are destroyed as part of pathogenic processes or liberated as energy sources during normal commensal lifestyles.

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Organizational Affiliation: 

Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada; [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
F5/8 type C domain protein	A	462	Clostridium perfringens ATCC 13124	Mutation(s): 0  Gene Names: CPF_1489
UniProt
Find proteins for A0A0H2YN38 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)) Explore A0A0H2YN38  Go to UniProtKB:  A0A0H2YN38

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.272 
• R-Value Work: 0.248 
• R-Value Observed: 0.249 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.05	α = 90
b = 49.16	β = 112.05
c = 78.5	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-08-12 
• Released Date: 2021-02-03 
Deposition Author(s): Pluvinage, B., Boraston, A.B.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--
Canadian Glycomics Network (GLYCONET)	Canada	--

Revision History  

• Version 1.0: 2021-02-03
  Type: Initial release
  
• Version 1.1: 2021-08-18
  Changes: Database references