5YXC

Crystal structure of Zinc binding protein ZinT in complex with citrate from E. coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.763 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of E. coli ZinT with one zinc-binding mode and complexed with citrate

Chen, J.Wang, L.Shang, F.Dong, Y.Ha, N.C.Nam, K.H.Quan, C.Xu, Y.

(2018) Biochem. Biophys. Res. Commun. 500: 139-144

  • DOI: 10.1016/j.bbrc.2018.03.192

  • PubMed Abstract: 
  • The ZnuABC ATP-binding cassette transporter found in gram-negative bacteria has been implicated in ensuring adequate zinc import into Zn(II)-poor environments. ZinT is an essential component of ZnuABC and contributes to metal transport by transferrin ...

    The ZnuABC ATP-binding cassette transporter found in gram-negative bacteria has been implicated in ensuring adequate zinc import into Zn(II)-poor environments. ZinT is an essential component of ZnuABC and contributes to metal transport by transferring metals to ZnuA, which delivers them to ZnuB in periplasmic zinc recruitment. Although several structures of E. coli ZinT have been reported, its zinc-binding sites and oligomeric state have not been clearly identified. Here, we report the crystal structure of E. coli ZinT at 1.76 Å resolution. This structure contains one zinc ion in its calycin-like domain, and this ion is coordinated by three highly conserved histidine residues (His167, His176 and His178). Moreover, three oxygen atoms (O 1 , O 6 and O 7 ) from the citrate molecule interact with zinc, giving the zinc ion stable octahedral coordination. Our EcZinT structure shows the fewest zinc ions bound of all reported EcZinT structures. Crystallographic packing and size exclusion chromatography suggest that EcZinT prefers to form monomers in solution. Our results provide insights into the molecular function of ZinT.


    Organizational Affiliation

    School of Life Science and Biotechnology, Dalian University of Technology, No 2 Linggong Road, Dalian 116024, Liaoning, China.,Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea; Institute of Life Science and Natural Resources, Korea University, Seoul 02841, Republic of Korea. Electronic address: structure@postech.ac.kr.,Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China.,Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China; School of Life Science and Biotechnology, Dalian University of Technology, No 2 Linggong Road, Dalian 116024, Liaoning, China.,Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Gwanak-gu, Seoul 08826, Republic of Korea.,Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China. Electronic address: mikyeken@dlnu.edu.cn.,Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China. Electronic address: yongbinxu@dlnu.edu.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Metal-binding protein ZinT
A, B
216Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: zinT (yodA)
Find proteins for P76344 (Escherichia coli (strain K12))
Go to UniProtKB:  P76344
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CIT
Query on CIT

Download SDF File 
Download CCD File 
A, B
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.763 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.040α = 90.00
b = 65.866β = 91.35
c = 73.536γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31200556
National Natural Science Foundation of ChinaChina21272031
Program for Liaoning Excellent Talents in UniversityChinaLJQ2015030
Fundamental Research Funds for the Central UniversitiesChinaDC201502020203

Revision History 

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-12-12
    Type: Data collection, Database references