8T7J | pdb_00008t7j

Oxygen- and PLP-dependent Cap15 holoenzyme bound with phosphate anion

• PDB DOI: https://doi.org/10.2210/pdb8T7J/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Streptomyces sp. SANK 62799
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-06-20 Released: 2023-08-23 
• Deposition Author(s): Daniel-Ivad, P., Ryan, K.S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.268 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Structure of the Oxygen, Pyridoxal Phosphate-Dependent Capuramycin Biosynthetic Protein Cap15.

Daniel-Ivad, P.G., Van Lanen, S., Ryan, K.S.

(2023) Biochemistry 62: 2611-2621

• PubMed: 37556254 
• DOI: https://doi.org/10.1021/acs.biochem.3c00216
• Primary Citation Related Structures: 
  8T7J


• PubMed Abstract: 
  

  Pyridoxal phosphate-dependent enzymes able to use oxygen as a co-substrate have emerged in multiple protein families. Here, we use crystallography to solve the 2.40 Å resolution crystal structure of Cap15, a nucleoside biosynthetic enzyme that catalyzes the oxidative decarboxylation of glycyl uridine. Our structural study captures the internal aldimine, pinpointing the active site lysine as K230 and showing the site of phosphate binding. Our docking studies reveal how Cap15 is able to catalyze a stereoselective deprotonation reaction, and bioinformatic analysis reveals active site residues that distinguish Cap15 from the structurally related d-glucosaminate-6-phosphate ammonia lyase and l-seryl-tRNA(Sec) selenium transferase (SelA). Our work provides the structural basis for further mechanistic investigation of a unique biosynthetic enzyme and provides a blueprint for understanding how oxygen reactivity emerged in the SelA-like protein family.

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Organizational Affiliation: 
• Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada.
Pharmaceutical Sciences Department, University of Kentucky, Lexington, Kentucky 40506, United States.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 169.64 kDa 
• Atom Count: 10,019 
• Modeled Residue Count: 1,438 
• Deposited Residue Count: 1,596 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative selenocysteine synthase	A, B, C, D	399	Streptomyces sp. SANK 62799	Mutation(s): 0  EC: 1
UniProt
Find proteins for E1CG36 (Streptomyces sp) Explore E1CG36  Go to UniProtKB:  E1CG36

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4 (Subject of Investigation/LOI)	F [auth A], G [auth B], I [auth C], J [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	E [auth A], H [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B, C, D	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.268 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.59	α = 90
b = 220.986	β = 90
c = 96.735	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Blu-Ice	data collection
XDS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-23 
Deposition Author(s): Daniel-Ivad, P., Ryan, K.S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-08-23
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Database references
• Version 1.2: 2023-11-15
  Changes: Data collection