Crystal structure of Paracoccus denitrificans AztD

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Crystal structures of AztD provide mechanistic insights into direct zinc transfer between proteins.

Neupane, D.P.Fullam, S.H.Chacon, K.N.Yukl, E.T.

(2019) Commun Biol 2: 308-308

  • DOI: https://doi.org/10.1038/s42003-019-0542-z
  • Primary Citation of Related Structures:  
    6CK1, 6CMK, 6N01

  • PubMed Abstract: 

    Zinc acquisition from limited environments is critical for bacterial survival and pathogenesis. AztD has been identified as a periplasmic or cell surface zinc-binding protein in numerous bacterial species. In Paracoccus denitrificans , AztD can transfer zinc directly to AztC, the solute binding protein for a zinc-specific ATP-binding cassette transporter system, suggesting a role in zinc acquisition and homeostasis. Here, we present the first cry stal structures of AztD from P. denitrificans and tbe human pathogen Citrobacter koseri , revealing a beta-propeller fold and two high-affinity zinc-binding sites that are highly conserved among AztD homologs. These structures combined with transfer assays using WT and mutant proteins provide rare insight into the mechanism of direct zinc transfer from one protein to another. Given the importance of zinc import to bacterial pathogenesis, these insights may prove valuable to the development of zinc transfer inhibitors as antibiotics.

  • Organizational Affiliation

    1Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM 88003 USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A1B2F4 proteinA [auth B],
B [auth A],
408Paracoccus denitrificans PD1222Mutation(s): 0 
Gene Names: Pden_1598
Find proteins for A1B2F4 (Paracoccus denitrificans (strain Pd 1222))
Explore A1B2F4 
Go to UniProtKB:  A1B2F4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1B2F4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.51α = 90
b = 96.38β = 90
c = 175.52γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

  • Released Date: 2019-03-06 
  • Deposition Author(s): Yukl, E.T.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesSC2GM111170

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-06
    Type: Initial release
  • Version 1.1: 2019-09-18
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence