5KVP | pdb_00005kvp

Solution structure of the catalytic domain of zoocin A

• PDB DOI: https://doi.org/10.2210/pdb5KVP/pdb
• BMRB: 30139

• Classification: HYDROLASE
• Organism(s): Streptococcus equi subsp. zooepidemicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-07-15 Released: 2016-10-26 
• Deposition Author(s): Timkovich, R., Xing, M., Simmonds, R.S.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Solution structure of the Cys74 to Ala74 mutant of the recombinant catalytic domain of Zoocin A.

Xing, M., Simmonds, R.S., Timkovich, R.

(2017) Proteins 85: 177-181

• PubMed: 27699884 
• DOI: https://doi.org/10.1002/prot.25178
• Primary Citation Related Structures: 
  5KVP


• PubMed Abstract: 
  

  Zoocin A is a Zn-metallopeptidase secreted by Streptococcus zooepidemicus strain 4881. Its catalytic domain is responsible for cleaving the D-alanyl-L-alanine peptide bond in streptococcal peptidoglycan. The solution NMR structure of the Cys74 to Ala74 mutant of the recombinant catalytic domain (rCAT C74A) has been determined. With a previous structure determination for the recombinant target recognition domain (rTRD), this completes the 3D structure of zoocin A. While the structure of rCAT C74A resembles those of the catalytic domains of lysostaphin and LytM, the substrate binding groove is wider and no tyrosine residue was observed in the active site. Proteins 2016; 85:177-181. © 2016 Wiley Periodicals, Inc.

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Organizational Affiliation: 
• Department of Chemistry, University of Alabama, Tuscaloosa, Alabama, 35487.
Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 16.92 kDa 
• Atom Count: 1,192 
• Modeled Residue Count: 159 
• Deposited Residue Count: 159 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zoocin A endopeptidase	A	159	Streptococcus equi subsp. zooepidemicus	Mutation(s): 1  Gene Names: zooA EC: 3.4.24.75
UniProt
Find proteins for O54308 (Streptococcus equi subsp. zooepidemicus) Explore O54308  Go to UniProtKB:  O54308

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
UNL	C [auth A]	Unknown ligand PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-26 
Deposition Author(s): Timkovich, R., Xing, M., Simmonds, R.S.

Revision History  

• Version 1.0: 2016-10-26
  Type: Initial release
  
• Version 1.1: 2016-12-28
  Changes: Database references
• Version 1.2: 2017-07-26
  Changes: Data collection, Database references, Structure summary
• Version 1.3: 2024-05-01
  Changes: Data collection, Database references