6CMK | pdb_00006cmk

Crystal structure of Citrobacter koseri AztD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 
    0.188 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.153 (Depositor), 0.154 (DCC) 
  • R-Value Observed: 
    0.154 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6CMK

This is version 1.3 of the entry. See complete history

Literature

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 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.

Macromolecule Content 

  • Total Structure Weight: 92.09 kDa 
  • Atom Count: 6,480 
  • Modeled Residue Count: 748 
  • Deposited Residue Count: 842 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AztD proteinA [auth B],
B [auth A]
421Citrobacter koseri ATCC BAA-895Mutation(s): 0 
Gene Names: CKO_00948
UniProt
Find proteins for A8AF35 (Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696))
Explore A8AF35 
Go to UniProtKB:  A8AF35
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8AF35
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MES

Query on MES



Download:Ideal Coordinates CCD File
C [auth B],
H [auth A]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
M [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
N [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
D [auth B],
E [auth B],
I [auth A],
J [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
F [auth B],
G [auth B],
K [auth A],
L [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free:  0.188 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.153 (Depositor), 0.154 (DCC) 
  • R-Value Observed: 0.154 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.23α = 90
b = 128.79β = 105.2
c = 56.85γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data

  • Released Date: 2019-03-13 
  • 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: 2019-03-13
    Type: Initial release
  • Version 1.1: 2019-09-25
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2024-10-23
    Changes: Data collection, Database references, Structure summary