8VAI | pdb_00008vai

Crystal structure of apo CtCADD from Chlamydia trachomatis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 
    0.219 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Assembly of a Heterobimetallic Fe/Mn Cofactor in the para -Aminobenzoate Synthase Chlamydia Protein Associating with Death Domains (CADD) Initiates Long-Range Radical Hole-Hopping.

Phan, H.N.Swartz, P.D.Gangopadhyay, M.Guo, Y.Smirnov, A.I.Makris, T.M.

(2024) Biochemistry 63: 3020-3029

  • DOI: https://doi.org/10.1021/acs.biochem.4c00326
  • Primary Citation Related Structures: 
    8VA9, 8VAB, 8VAG, 8VAI

  • PubMed Abstract: 

    Chlamydia protein associating with death domains ( Ct CADD) is involved in the biosynthesis of p -aminobenzoic acid (pABA) for integration into folate, a critical cofactor that is required for pathogenic survival. CADD activates dioxygen and utilizes its own tyrosine and lysine as synthons to furnish the carboxylate, carbon backbone, and amine group of pABA in a complex multistep mechanism. Unlike other members of the heme oxygenase-like dimetal oxidase (HDO) superfamily that typically house an Fe 2 cofactor, previous activity studies have shown that Ct CADD likely uses a heterobimetallic Fe/Mn center. The structure of the Fe 2+ /Mn 2+ cofactor and how the conserved HDO scaffold mediates metal selectivity have remained enigmatic. Adopting an in crystallo metalation approach, Ct CADD was solved in the apo, Fe 2+ 2 , Mn 2+ 2 , and catalytically active Fe 2+ /Mn 2+ forms to identify the probable site for Mn binding. The analysis of Ct CADD active-site variants further reinforces the importance of the secondary coordination sphere on cofactor preference for competent pABA formation. Rapid kinetic optical and electron paramagnetic resonance (EPR) studies show that the heterobimetallic cofactor selectively reacts with dioxygen and likely initiates pABA assembly through the formation of a transient tyrosine radical intermediate and a resultant heterobimetallic Mn 3+ /Fe 3+ cluster.


  • Organizational Affiliation
    • Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States.

Macromolecule Content 

  • Total Structure Weight: 55.63 kDa 
  • Atom Count: 3,753 
  • Modeled Residue Count: 428 
  • Deposited Residue Count: 480 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
4-aminobenzoate synthase
A, B
240Chlamydia trachomatis D/UW-3/CXMutation(s): 0 
Gene Names: CT_610
EC: 1.3.3
UniProt
Find proteins for O84616 (Chlamydia trachomatis serovar D (strain ATCC VR-885 / DSM 19411 / UW-3/Cx))
Explore O84616 
Go to UniProtKB:  O84616
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO84616
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
(Subject of Investigation/LOI)

Query on GOL



Download:Ideal Coordinates CCD File
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.528α = 90
b = 94.528β = 90
c = 120.673γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM135315

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release
  • Version 1.1: 2024-11-27
    Changes: Database references