8F1B

Structure of zinc-bound ZrgA deletion 124-184 from Vibrio cholerae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure and Function of the Zinc Binding Protein ZrgA from Vibrio cholerae.

Valencia, D.W.Melendez, A.B.Melendrez, I.A.Yukl, E.T.

(2022) Int J Mol Sci 24

  • DOI: https://doi.org/10.3390/ijms24010548
  • Primary Citation of Related Structures:  
    8EZW, 8F1B

  • PubMed Abstract: 

    ATP binding cassette (ABC) transporters are the primary means by which bacteria acquire trace elements from the environment. They rely on solute binding proteins (SBPs) to bind the relevant substrate and deliver it to the integral membrane permease for ATP-powered import into the cytoplasm. SBPs of cluster A-I are known to facilitate the transport of essential metals zinc, manganese, and iron, and many have been characterized to date. A group of ABC transporter operons dubbed zinc-regulated genes ( zrg ) have recently been shown to transport zinc with putative SBPs ( zrgA ) bearing no homology to the classical cluster A-I family, and a recent crystal structure of a representative protein from Pseudomonas aeruginosa shows no structural similarity to classical SBPs. Thus, the ZrgA proteins appear to represent a newly discovered family of zinc SBPs widespread among Gram-negative bacteria, including human pathogens. Here, we have determined the crystal structure of ZrgA from Vibrio cholerae and characterized its zinc binding in vitro and function in vivo. We also assessed the role of a histidine-rich sequence that appears to be a hallmark of ZrgA proteins that is particularly long in V. cholerae ZrgA. The results show that the zrgA gene is critical to the function of the operon, consistent with a function as an SBP in this system. Further, the His-rich region is not essential to the function of ZrgA, but it does provide additional zinc binding sites in vitro. The structure and zinc binding data for ZrgA reveal interesting differences between it and its homologue from P. aeruginosa , illustrating diversity within this little-studied protein family.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc-binding protein
A, B, C, D, E
A, B, C, D, E, F
160Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 0 
Gene Names: VC_2552
UniProt
Find proteins for Q9KP27 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KP27 
Go to UniProtKB:  Q9KP27
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KP27
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download Ideal Coordinates CCD File 
J [auth B]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth F]
G [auth A]
H [auth A]
I [auth A]
AA [auth F],
BA [auth F],
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth C],
P [auth C],
Q [auth C],
R [auth C],
S [auth D],
T [auth D],
U [auth D],
V [auth D],
W [auth E],
X [auth E],
Y [auth E],
Z [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.991α = 90
b = 66.914β = 99.92
c = 88.242γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM122819-01

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-18
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description